Oikopleura

Oikopleura dioica (NCBI:txid34765) is a tunicate larvacean (synonym: urochordate appendicularian) plankton discovered by Hermann Fol). It belongs to the same "chordate" phylum as us. As the name indicates, it is the only dioecious species of Oikopleura (that is: male and female organisms are distinct). Its reproduction is semelparous: the animals die afer releasing its gametes. Each animal secretes a mucus "house" that is used for feeding (and perhaps defending). The main house proteins are called oikosins and half or them are unique to Oikopleura and related animals ("Appendicularia"). The japanese name of O. dioica is ワカレオタマボヤ. Review for non-specialists: Glover, 2020. Article in Scientific American: Alice Alldredge, 1976.

Some links:

Oikopleura Histone Database: http://apps.cbu.uib.no/oikohistonedb
Genoscope's genome browser: http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/
OikoBase: http://oikoarrays.biology.uiowa.edu/Oiko/ (Danks et al., 2013)
Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872 (ark:/13960/t7fr0vj77).
A day in the life of an Oikopleura lab.
OSAKA2016 genome (Wang and coll., 2020) on aniseed (Dardaillon and coll., 2020): https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica
OKI2018_I69 genome Bliznina and coll., 2021 on ZENBU: https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=0tPT7vwSO1Vm5QV9iKqfAC and in GenBank CAJRAX010000001-CAJRAX010000013.

Parasites: Oodinium pouchetii, microsporidia (on O. gracilis (Savelieva 2019)), bacteria (Flood, 1991), and others.

Phylogeny

Huxley (1851) identified appendicularians as tunicates.
18S rDNA phylogenies of Wada and Satoh, 1994, Wada 1998 and Swalla and coll., 2000 place larvaceans sister to all tunicates.
Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this clade is sister of Stolidobranchia (that is, not basal in Tunicates). Stolidobranchia. Nevertheless, it might be an artefact of AT-richness or long-branch attraction (Tsagkogeorga et al, 2009).
Studies based on 146 genes in 28 species (Delsuc et al., 2006), on 798 genes in 28 species (Kocot and coll., 2018), 258 orthologous proteins from 63 species (Delsuc et al., 2018), and 210 single-copy orthogroups from 37 tunicates + 10 outgroups DeBiasse and coll., 2020 show that appendicularians are sister to all other tunicates.
Study of 117 phenotypic characters in 49 tunicate species also support basal position of appendicularians (Braun, Leubner and Stach, 2019.
Molecular clock analysis of 177 single-copy orthologs also places appendicularians sister to all tunicates (Plessy, Mansfield and coll., 2024).
O. dioica is actually mutliple species. “The difference between coding sequences was considerably higher in comparisons between strains of different oceans than within the Bergen gene pool. We ignore whether and how Oikopleura dioica is subdivided into multiple species” (Denoeud et al., 2010). Masunaga and coll. (2022) demonstrated the existence of at least 3 species using molecular markers, and found that egg diameter distinguishes the “okinawan” one from the others. Gene order is scrambled between the 3 species (Plessy, Mansfield and coll., 2024).
Giant Oikopleurid species, such as exist in deeper waters. Bathochordaeus charon's 18S RNA is 97% identical to the one of O. dioica (Sherlock and coll, 2016).
CO1 DNA of B. mcnutti and B. strygius are ~12% different (Sherlock and coll., 2017).
There are two subgenus of Oikopleura: Vexillaria and Coecaria. Vexillaria, to which dioica and rufescens belong, have oral glands and bioluminescence (Galt, Grober and Sykes, 1985).
Other appendicularians: Mesochordaeus (Fenaux and Youngbluth, 1990), etc.

Karyotype

In individuals sampled in the Wadden sea, Körner, 1952 reported that germ cells contain 3 haploid chromosomes. This is a low number in the animal reign, although at least one mammal has a similar number (Wurster and Benirschke 1970), and some insects have even less.
There are also intriguing observations of somatic mitotic cells with 7 chromosomes (Körner, 1952)
In individuals captured in Villefranche-sur-Mer (Mediterranean sea), meiotic cells were reported to have8 haploid chromosomes by Colombera & Fenaux, 1973.
Several manuscripts using animals from the SARS laboratory include fluorescent microscopy pictures supporting the 3 × 2 karyotype. For instance: centromere marking in Feng and coll., 2019.
Each cell only contains 70 fg of DNA (Animal Genome Size Database).

Genome

Genome size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by Seo et al, 2001. A 70.4 Mb genome "reference assembly" was later produced from the shotgun sequencing of sperm DNA from ~200 partially inbred males (11 successive sib-matings). Two distinct haplotypes were found (Denoeud et al., 2010). In 2019, it is the smallest sequenced chordate genome, but some nematodes have been found with smaller genomes.
The OSAKA2016 genome assembly (PacBio) from the North Pacific species is ~65 Mb-long Wang and coll., 2020.
Other oikopleuid genomes have been sequenced by Naville and coll. (2019): small genomes are also found in O. longicauda (131 Mbp) and F. borealis (91 Mbp). There is an apparent correlation between organism size and genome size: O. albicans (356 Mbp), Bathochordaeus sp. (396 Mbp), O. vanhoeffeni (632 Mbp) and M. erythrocephalus (874 Mbp) all have larger body sizes than O. dio., O. lon. and F. bor.
“No signal of synteny conservation is detected between Oikopleura and Ciona intestinalis. (...) Oikopleura showed a local gene order that is indistinguishable from random for distances smaller than 30 genes and a modest level of conserved synteny at larger distances.” (Denoeud et al., 2010)
Telomere sequence is (TTAGGG)n, as evidenced by successful FISH stainings by Schulmeister, Schmid and Thompson, 2007.
Genome compaction in Oikopleura and Ciona have been reviewed in parallel by Berná and Alvarez-Valin (2014).
Analysis of sex-linked markers supports genetic sex determination with male heterogamety – that is: X chromosomes for females and Y for males. (Denoeud et al., 2010)
The major spliceosome is hypothethised to have evolved to become more permissive in order to splice G*/AG sites. ”A large fraction (more than 10%) of the (...) introns displayed non-canonical (non GT-AG) splice sites, whereas the usual proportion is around 1%-1.5% in other genomes” (Denoeud et al., 2010).
The consensus sequence around non-canonical GA/AG splice sites is AG|GAA/AG (Denoeud et al., 2010, Frey and Pucker, 2020).
Operons are enriched for houskeeping genes and depleted for developmental genes (Denoeud et al., 2010).
“Highly conserved elements (HCEs) lie around these developmental genes.” “Spots of sequence ultraconservation are almost systematically located in non coding regions, including introns that are larger than average in such genes than in others.” (Denoeud et al., 2010).
Transcriptome comparisons between Atlantic and Pacific strains showed nucleotide and amino acid sequence similarities of 91.0 and 94.8 %, respectively (Wang and coll., 2015).
Regulatory genes evolve faster. All aminoacids, including cystein, show reduced conservation, suggesting relaxation of functional constraints. Compared with Ciona, 10% of the cysteins are lost (Berná and coll., 2012). Cystein loss happened in both the disordered and ordered protein domains (Berná and Alvarez-Valin, 2015).
Proteins of O. dioica are shorter and contain less disordored domains than proteins from other chrodates (Berná and Alvarez-Valin, 2015).
Nash and Lenhard (2019) proposed a kurtosis-based measure of pairwise non-coding conservation that “may have utility in the analysis of” conserved non-coding elements in Oikopleura.

Mitogenome

A partial mitochondrial genome was reconstituted in Denoeud et al., 2010, where edited oligo-dT stretches were discovered. A/T-rich codons are more frequent than in human.
Long-read mitochondrial assemblies confirmed the gene content (atp6, cob, cox1, cox2, cox3, nad1, nad4, nad5 and a putative nad2 ORF), and showed that the poly-T regions could contain Cs that do not interrupt editing (Dierckxsens and coll, 2024, Klirs et and coll., 2024).
The nad3 gene was transferred to the nuclear genome (Klirs et and coll., 2024).
In other tunicates, all mitochondrial genes are on the same DNA strand and 24 tRNAs are present, instead of 22 in other chordates (reviewed by Gissi and coll., 2008).
The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014 in Genbank are probably a contamination and a misidentification, respectively (Sakaguchi and coll., 2017).
Pichon, Luscombe and Plessy, 2019 confirms that O. dioica's mitochondrial sequences can be translated with the ascidian genetic code, and suggests that O. lon, B. sty and perhaps M. ery (all in the Coecaria genus) use different code(s).

Repeat elements

The main groups of retrotransposons present in O. dioica are Odin (Oikopleura dioicanon-LTR), Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like Volff and coll., 2004. “F. borealis has no Odin elements but has members of other LINE families.” (Naville and coll., 2019)
Tor elements are expressed in somatic tissues in proximity to the germline (Henriet and coll., 2015).
“LTR retrotransposons account for a significant part of the indel polymorphism in the Oikopleura genome.” “Tor-3G elements are frequently inserted into exons and can be transcribed together with their host gene, although transcripts initiated in the LTR are also detected (Figure S11).” “The low allelic frequency of Tor-3G insertions is correlated with the almost exclusive occurrence of heterozygous genotypes in the populations. Moreover, experimental crosses between selected heterozygous parents for the same insertion have thus far not resulted in homozygous offsprings.” (Denoeud et al., 2010).
SINE and MITE account for a large part of genome expansion in larger oikopleurid species (Naville and coll., 2019).
O. dioica's Y chroomosome contains 43% of the TOR insertions (Naville and coll., 2019).

Genes and pathways

Present or gained

(See also other sections)

~80 "house proteins" have been identified and more than half lack similarity to known proteins (Hosp et al., 2012).
Histones: “Densitometric analyses of Southern blots yielded estimates of 9–11 H4 genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1 genes” (Chioda, Eskeland and Thompson, 2002). “47 histone genes (6 H4, 10 H3, 15 H2A, 11 H2B and 5 H1 genes) encoding 31 different histone proteins (2 H4, 6 H3, 11 H2A, 7 H2B and 5 H1) were identified”. The centromeric CenH3 is present (Moosmann and coll., 2011).
2 cellulose synthase genes CesA1 and CesA2, possibly acquired by horizontal gene transfer from an actinobacteria (Nakashima and coll., 2004), were found by Sagane et al. (2010) and Nakashima et al. (2011). They are used to produce different crystalline forms of cellulose (Nakashima et al., 2011). Crystalline cellulose Iβ was also found in O. rufescens by Kimura and coll (2001). The CesA gene is trans-spliced in the ascidian Ciona intestinalis (Matthysse and coll., 2004).
A GH6 (glycosyl hydrolase family 6) domain is found in the CesA genes, as well as an independent genes, in Tunicates (Inoue, Nakashima and Satoh, 2019). In Oikopleura, it lacks a conserved catalytic aspatate, and does not share ancestral introns with other tunicates (Li and coll., 2020).
O. dioica has multiple CDK1 and Cyclin B paraplogs, some of which are implicated in oogenesis (Øvrebø and coll., 2015, Feng & Thompson, 2018).
O. dioica CDK1a and b locate on LG2; CDK1c and is CDK1e on LG1. CDK1d is on the X chromosome near CycBa. In O. albicans, CDK1a,b and c are on the same chromosome (Ma, Øvrebø and Thompson, 2022),
O. dioica, like other deuterostomes, has acid-sensing ion channels (ASICs). They are expressed in the nervous system (Lynagh et al., 2018).
Some muscle genes were duplicated in the Oikopleura stem lineage (Inoue & Satoh), prehaps reflecting the importance of tail movements at larval and adult stages.
Defensome genes such as dehydrogenases and (Glutamate-cysteine ligase modifier subunit; Gclm) are activated by polyunsaturated aldehydes produced by diatoms (Torres-Águila and coll., 2018).
The Hox cluster has been split up in Oikopleura (Seo and coll., 2004).
O. dioica has 83 homeobox genes, according to Edvardsen and coll., 2005. Illustrating how diverged are the sequences, earlier attempts to clone Hox genes yielded only a single clone (Holland and coll. 1994).
Southern blot analysis suggest the presence of a SCO-spondin gene in O. dioica (Gobron and coll., 1999).
A single ortholog of Brachyury (TBXT, or T) was cloned by Bassham and Postlethwait (2000). Accession number: AF204208.
7 actin genes were found by Almazán and coll. (2018). 4 of them are muscular arouse after the separation of the appendicularian and ascidian lineages, and 3 are cytoplasmic, one of them being intronless and possibly originated by retrotransposition.
Duplications in the Rab family: Rab5/17, Rab6, Rab7, Rab10, Rab35. The EF-Rab chimera Rab46 is kept (Coppola and coll., 2019). See below for the losses.
INCENP and Plk1 are duplicated (Feng and coll., 2019).
Two connexins, CxA and CxB are expressed during embyogenesis (Mikhaleva, Tolstenkov and Glover 2019).
Piwi (Henriet and coll., 2015).
Metallothioneins OdMT1 and OdMT2 (Calatayud and coll., 2018). Their cysteins are organised in a way that is not found in other branches of the evolutionary tree (Calatayud and coll., 2021a). They bind cadmium ions and display variations of number of tandem repeats between dioceous species. Non-functional alleles were found, raising the possibility that some individuals lack MT genes (Calatayud and coll., 2021b).
2 NUMB genes were found; both are closer to Vertebrate NUMB than to Vertebrate NUMB-Like (Confalonieri and coll., 2019).
Genes related to thyroid functions (vWFL, Nkx2-1, FoxE, TPO and Duox) were studied by Onuma and coll., 2020.
8 Wnt genes were found, belonging to 4 families. Intronless Wnt11 genes were found; they might have been created by retrotransposition (Martí-Solans and coll., 2021).
Nk4, Hand1/2 and FoxF (heart development, Ferrández-Roldán and coll., 2021).
O. dioica has the miRNA machinery and some miRNAs such as let-7a were detected. 36 % of the miRNAs had a length of 22 nt in Fu, Adamski and Thompson, 2008.
6 FGF genes were detected by Oulion, Bertrand and Escriva (2012).
Eya, Pitx, Six1/2, Six3/6a and Six3/6b, with expression patterns supporting homology of larvacean and vertebrate placodes (Bassham and Postlethwait, 2005).
There are two copies of Aurora, OdAur1 and OdAur2. In meiosis, they localise to the centrosomes and the spindle respectively (Feng and Thompson, 2023).

Lost

O. dioica lacks Dnmt1 and Dnmt3 (Cañestro, Yokoi and Postlethwait, 2007, Albalat, Martí-Solans and Cañestro, 2012). It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly. ?Jurkowski and Jeltsch (2011) did not find Dnmt2 in O. dioica.
O. dioica lost CDCA7, HELLS, UHRF1 and other genes related to DNA methylation (Funabiki and coll., 2023).
CYP1 family genes and their regulator AhR are not detectable (Yadetie et al, 2012).
No olfactory receptors have been found in Oikopleura nor in Ciona (Niimura, 2009).
Most members of retinoic acid pathway gene network (biosynthesis, signalling and degradation) are lost in O. dioica (Martí-Solans et al., 2016).
APEX2 (encoding for the APE2 protein involved in base excision repair and microhomology mediated end-joining (MMEJ) was not found, but APEX1 was found (Denoeud et al., 2010).
The entire machinery required for performing classical NHEJ repair of DSB (which is conserved from yeast to mammals) is undetectable (Denoeud et al., 2010). An alternative or microhomology (MH)-driven end joining pathway is active and triggers microdeletions at the joining site (Deng, Henriet and Chourrout, 2018). Loss of C-NHEJ is often associated with parasitism, which is not the case in Oikopleura (review in Nenarokova and coll., 2019).
In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is implicated in DNA repair). Moosmann and coll., 2011
The minor spliceosome could not be found in Oikopleura's genome (Marz et al., 2008), Denoeud et al., 2010), nor in F. borealis (Henriet and coll., 2019). It is found in Ciona but not in C. elegans (Marz et al., 2008).
More than 50 % of the Rab family is lost (Coppola and coll., 2019): Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the the EF-rab chimera Rasef and EFcab4/Rab44.
Components of the constitutive centromere-associated network (CCAN) of the inner kinetochore cound not be found in the genome by (Feng and coll., 2019).
Nodal is not found in O. dioica's genome (Onuma and coll., 2020).
Peroxisomes and genes related to them (Žárský and Tachezy, 2015; Kienle, Kloepper and Fasshauer, 2016).
Mesp, Ets1/2b, Gata4/5/6, Mek1/2, Hand-r and Tbx1/10 (heart development, Ferrández-Roldán and coll., 2021).
None of the genes encoding Bcl-2 proteins or their BH3-only ligands could be found in O. dioica Suraweera and coll., 2022.
Three caspases related to the CSP3/7 family were found by Weil and coll, 2005.

Epigenome

“Knobs” of heterochromatin strongly marked by H3K9me3 and enriched in H3K4me3 are prominent in endocycling cells (Spada, Vincent and Thompson (2005)). H4K20me2 also seems to be enriched (Spada, Chioda and Thompson (2006)).
Histone 3.3 phosphorylation is seen in mitotic and meiotic cells, but not in endocycling ones (Schulmeister, Schmid and Thompson, 2007).
Some 5-methylcytosine was detected by MeDIP-chip by (Navratilova et al., 2017).
Chromatin domains are rarely longer than 7 nucleosomes (Navratilova et al., 2017).
H4K20me2 decreases during S phase. In mitotic cells, it then increases at M phase, while in endocycling cells, it increases directly after the end of the S phase (Spada, Chioda and Thompson (2006)).

Transcriptome

O. dioica is the first chordate where gene operons have been described. A 40-nt 5′ splice leader (SL) bearing a trimethylated cap is found in some RNAs. The SL gene is found downstream of the 5S RNA gene, which is repeated multiple times in the genome. The 3′ acceptor site has a strong UUU(C/U/A)AG consensus. Reported intercistronic regions are short: <30 nt (Ganot et al., 2004) or ~33 nt (Wenzel, Mueller and Pettitt, 2020).
The splice leader found in the Norwegian strain by (Ganot et al., 2004) was found indentical in a Japanese strain by (Wang and coll., 2015).
A study using CAGE found that 39% of annotated gene models are trans-spliced with the SL and that 42% of SL transcripts are monocistronic (Danks et al., 2015).
Embryonic RNAs are more trans-spliced than larval RNAs (Danks et al., 2015, Wang and coll., 2015).
A TCTAGA promoter element is found in 73.5% of the non-trans-spliced genes detected with CAGE in testis (Danks et al, 2018).
“Maternal promoters in O. dioica were located on the X-chromosome more frequently than expected” (Danks et al, 2018).
Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, Denoeud et al., 2010) and subjected to a large turnover: many ancestral introns are lost, and many new species-specific introns found (Edvarsen et al., 2004). Introns are gained by insertion of transposon-like elements and by reverse splicing, (Denoeud et al., 2010). Larger introns tend to be older, and among the large introns, the older contain repeat elements less frequently than the newer (Denoeud et al., 2010). In Fritilaria borealis, most introns are derived from the insertion of MITE elements and are AG/AR non-canonical (Henriet and coll., 2019).
HEK293T cells can only splice canonical GT/AG O. dioica (and F. borealis) introns, but not the non-canonical AG/AR ones (Henriet and coll., 2019).
12 developmental stages were studied with tiling arrays by Danks et al., 2013.
On the histone mRNAs, no purine-rich histone downstream element (HDE) was found by Chioda, Eskeland and Thompson in 2002.

Tools

DNAi was used to screen for maternal genes (Omotezako et al., 2017).
CRISPR-Cas9 was used to induce genomic microdeletions (Deng, Henriet and Chourrout, 2018).

Development

Gametes

The oocytes originate from a specialised syncitium, the coenocyst, in which nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels (Ganot and coll., 2007).
The gonad syncytium forms as early at 10 hpf (Nishida and coll., 2021).
Oocytes lacking odCDK1d can not resume from meiosis from prophase I arrest, and therefore are non-viable after spawning (Øvrebø and coll., 2015).
Oocytes are in metaphase I stage at the time of spawning (Ganot, Kallesøe and Thompson (2007)).
Inhibition of the MAPK pathway cause some nurse cell nuclei to enter the oocyte through the ring channels (Ganot, Moosmann-Schulmeister and Thompson, 2008).
Egg diameter in females from (probably) Villefranche-sur-mer: 97 to 107 µm (Fenaux, 1976).
Increased food abundance increases egg number but does not change diameter nor generation time (Troedsson and coll., 2002). Food reduction before day 4 causes growth arrest (GA), in which all cell cycles eventually pause. Animals in GA can survive ~18 days at 15°C. GA can also be induced by inhibiting the TOR pathway (Subramaniam, Campsteijn and Thompson, 2014).
Meiosis is resumed by change of extracellular pH when the oocytes are released in seawater. Partenogenesis starts if PP2A is inhibited by DNAi or with okadaic acid (Matsuo and coll., 2020).
Colchicine treatment induced early differenciation of the oocytes (Ganot, Kallesøe, Thompson (2007)).
In mesocosms under high-CO2 (low-pH) conditions, femals produce more eggs (278 ±11 vs 334 ±14), Taucher and coll. (2023).

Fertilization and early stages

The sperm's mitochondrion enters the oocyte together with the nucleus (Holland, Gorsky and Fenaux, 1988).
The first and second polar bodies are visible 5 and 15 min after fertilisation, respectively (Nishino and Morisawa, 1998).
First embryonic cleavages are deterministic and “Clonal organization of the tissues is essentially invariant among individuals” (Stach and coll., 2008).
Fertilization in high sperm concentration leads to polyspermia (Fenaux, 1976).

Other

Generation times shortens when temperature rises. First spawnings are seen on day 6 at 14.2 °C, and on day 8 at 17.2 °C (Bouquet and coll., 2018). Reported generation times in the litterature: 149 ± 2 h at 14.2 °C and 120 ± 6 h at 17.2 °C (Bouquet and coll., 2018), and 132 ± 13 h (5.5 d) at 20 °C and 159 ± 20 h (6.9 d) at 15 °C (Troedsson and coll., 2002). Note that culture conditions might differ. ~1 day generation time reported in microcosms at 29°C in Jamaica (Hopcroft and Roff, 1995). ~1.2 day generation in the Seto inland sea (Uye and Ichino, 1995). Tôkyô bay O. dioica under laboratory condiditons: 6 days at 15°C, 4 days at 20°C and 3 days at 25°C (Sato, Tanaka and Ishimaru, 2001).
Large animals (~5 mm body length) could be cultivated when provided with large amounts of food (Li and Zhang, 2021).
Telomeres are localised at the nuclear envelope and do not overlap with nuclear pore complexes in early meiotic oocytes before H3S10 phosphorylation. In nurse cells at a later stage of oocyte development, the telomeres localise in silent chromatin at the nuclear periphery (Ganot, Kallesøe, Thompson (2007)).
The Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain. No expression of pax2/5/8 is detected between the otxa + otxb and the hox1 territories. (Cañestro et al., 2005).
A centromere-attracting body is resoponsible for asymetric cell division in primordial germ cells (Nishida and coll., 2021). The snail mRNA co-localises with it.
The pum1 and vas4 RNAs show localised expression during development. Prior hatching, pum1 is found outside the embryo (Olsen et al., 2018).
Duplicated developmental genes were found by Denoeud et al., 2010, who noted that it is exceptional in invertebrates, and hypothethise that it may be caused by neofunctionalisation (house production, ...) or by the small size of the genome (doubling the genes would then double the amount of regulatory sequences).
Regular calcium waves are pulsing during embyogenesis. Their propagation and synchronicity is severly disrupted by the knockdown of the connexins CxA and CxB (Mikhaleva, Tolstenkov and Glover 2019). The calcium waves are required for Bmp.a expression in descendants of the R (Right) blastomere (Onuma and coll., 2020).
The tandem propA and propB genes control directly or indirectly oik41a and proper development of the house-secreting epithelium (Mikhaleva et al., 2018).
The endodermal strand is the strand of 16 cells that lie in a single line. The endodermal cells strand migrate from the tail to the trunk and give rise to the posterior part of the digestive tract (rectum), but not the anus. Removal of the trunk suggests that it is not necessary for initiation of the migration (Kishi and coll, 2014).
The oral gland precursor is a syncytium with 4 nuclei that migrates anteriorly. The two differentiated oral gland cells have two nuclei each, as demonstrated by a co-staining of nuclei (H2B-mCherry) and cell membrane (PH-YF) by Kishi and coll, 2014, as well as SEM tomography (Nishida and coll., 2021). O. Gorskyi also has two cells with 2 nuclei each (Flood 2000).
Oral gland and subchordal cells, which were thought to be related, do not originate from the same blastomere (Onuma and coll., 2020).
The subchordal cell precursors migrate along the right side of the notochord in the space that has been filled with endodermal strand cells. Amputation experiments indicate that the posterior portion of the tail is required for posterior migration of subchordal cell precursors (Kishi and coll, 2014). They express Brachyury (Bassham and Postlethwait (2000)).
Notochord cell precursors express Brachyury like in other chordates (Bassham and Postlethwait (2000)).
Adult notochord cells proliferate (Søviknes and Glover, 2008).
Expression of development genes is retarded by polyunsaturated aldehydes produced by diatoms (Torres-Águila and coll., 2018).
Bisphenol A (BPA) reduces fitness at concentration that are defined as ”environmentally safe” by the European Union (Li, Liang and Zhang, 2024).
Epithelial cells divide by mitosis during embryogenesis. Once the final number of cells is produce, they grow by endomitosis, with final ploidy ranging between ~30 to ~1300 C. Cells with higher ploidy have shorter gap phases. Endomitoses stop when gamete differentiation starts. Ganot and Thompson, 2002
Endocycling cells show no polytenisation nor in loco amplifications. Deep invaginations of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes (Spada and coll., 2007).
Knock-out of Pax37B shows it is essential to the proper patterning of the oikoblastic epithelium (Lagman an coll., 2024).

Anatomy

The adult tail is made of three layers of cells: epithelium, muscle, notochord. The fins of the tail are made from single epithelial cells joining each side with tight junctions (Nakashima and coll, 2011).
Onuma and coll., 2017 published a comprehensive collection of surface electron microscopy pictures from external and internal organs.
Two subchordal cells are found in the haemocel of the tail. Utrastructure analysis suggests the alternance of highly exocytic and highly endocytic states (Fredriksson and Olsson, 1991).
The tail's neural tube has a ”fibrogen cell” at its anterior ends, which is secreting the Reissner's fiber (reviewed in Olsson, 1993). Electron microscopy shows a large perikaryon, cisternas and a cilium which is inserted in the central canal (Holmberg and Olsson, 1984).
In contrary to Kowalevskiidae, (Brena, Cima and Burighel, 2003), Oikopleura do have a heart. The genes Mesp, Ets1/2b, Gata4/5/6, Mek1/2, Hand-r and Tbx1/10, which are essential to heart development in other chordates are lost in appendicularians (Ferrández-Roldán and coll., 2021).
A 3D reconstitution of hatchlings and jufeniles was done by SEM tomography by Nishida and coll., 2021.
The brain of B. stygius contains a number of cells comparable to the one of O. dioica (Zemann and coll., 2003).

Physiology

Searching for an immune system, Denoeud et al., 2010 excluded LRR proteins, as none of the 74 models found had a transmembrane domain.
Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in Oikopleura (like in other non-vertebrates). Conservation of critical residues and similarity in expression pattern suggest that its metabolic targets are the same as in other species.
Some members of retinoic acid pathway gene network that were not lost in O. dioica show signs of neofunctionalisation or specialisation in their ancestral activity in digestion or chemical defence (Martí-Solans et al., 2016).
Ciliated cells move the food through the digestive system. Protein production, probably digestive enzymes, is strong in the gastric band of both stomach lobes. Endocytosis is visible in the left lobe of the stomach and the rectum. Lipid uptake might happen in the right lobe of the stomach (Burighel, Brena, Martinucci and Cima (2005)).
Yellow color can be caused by bacterial infection. Flood (1991) observed rod-shaped bacteria (0.6 or 0.4 µm-wide) in O. doica or O. vanhoeffeni.
Oxygen consumption increases with temperature (15°C vs 22°C) and activity (anesthesised vs control animals). It scales with body weigth, and not with food concentration after correcting for body weight (Lombard, Sciandra and Gorsky, 2005).
In line with the absence of peroxisomes in O. dioica, no wax esters (storage lipids) were found in O vanhoeffenni, which is mostly containing phospholipids Deibel and coll.,1992.

House

O. dioica individuals produce ~50 houses in their life (Sato, Tanaka and Ishimaru, 2001).
The house was observed in details with India ink coloration by Fenaux 1986. He also observed that, when in the house, “the tails beat slowly when the suspended particles were numerous and rapidly when they were few”.
The master thesis of E. Spriet (1997) provides high-resolution pictures of nuclar stains of the oikoblastic epithelium for O.labradoriensis, O. vanhoeffeni, O. dioica, O. villafrancae and O. albicans. The complexity of nuclear ramifications varies between species. (Interstingly, it might correlate with genome size).
The food collecting filter in the house was described as a “self-cleaning filter” by Conley and coll., 2017, who observed its expansion and contraction at high spatial and temporal resolution.
In O. labradorensis, Flood (1991) estimated that 35 ml of water were filtered per hour. In comparison, the giant species Bathochordaeus mcnutti was reported to filter as much as 76 L/h (Katija and coll., 2018).
The clearance rate of O. longicauda and O. fusiformis are similar (36 and 39 ml/h respectively). O. lon. has a lower rate on bacteria, but as their biomass is less than the one of eukaryotes, this does not result in a significant difference in terms of carbon updake (Scheinberg, Landry and Calbet, 2005).
The inner house of Bathochordaeus has been modeled in 3D by Katija and coll., 2020.
Filter-feeding in marine animals has been reviewed by Conley, Lombard and Sutherland (2018).
Bathochordaeus may produce one house per day (Robison, Reisenbichler and Sherlock, 2005).
Mesochordaeus erythrocephalus (Hopcroft and Robinson, 1999): mesopelagic species with a large (~30 cm) house.
Houses of O. dioica and related species that have oral glands have granular inclusions that are bioluminescent (Galt and Sykes (1983), Galt, Grober and Sykes, 1985). In these species, light is produced by granular inclusions in the house. In species without oral glands, bioluminescence might be caused by dinoflagellates.
A 8th cell was seen in the Fol area at 10 hpf in the 3D tomography analysis of Nishida and coll., 2021. It is possible that this cell is lost during later development.
Study of the O. dioica house and the origin of its components on the oikoblastic epithelium, using multiple microscopy techniques Razghandi and coll., 2020.
Abandonned houses bring nanoplankton into the copepod food chain (Alldredge AL, 1972).
O. dioica discards houses for new ones even in artificial seawater with no clogging particles. An individual stuck to the culture vessel could not inflate new houses, but nevertheless synthesised 7 rudiments (stacked on each other) before starving (Fenaux 1985.
Temperature and food availability increase house production from ~0.2 /h to ~0.4 / h (Fenaux 1985, of from ~0.4 /h to ~0.8 / h Sato, Tanaka and Ishimaru, 2001.
The tail acts as a peristaltic pump to generate the flow in the house. Tail beat and particule speed increased with temperature (5, 15 and 25 ºC) (Hiebert and coll., 2023).

Phenotypes

A low-frequency variant providing natural tail fluorescence late stages shortly before sexual maturation was found to have X-like inheritance (Denoeud et al., 2010, Fig. S20). It deviates from mendelian inheritance (Table S10), but is is recovered after sperm cryopreservation of male carriers.
Blue pigmentation may arise from the conversion of β‐carotene from the dietary algae into astaxanthin with cytochrome‐P450 hydroxylases, and binding to protein from the lipocalin family, to change the color from red to blue (Mojib and coll., 2014).

Ecology

The ecological role of appendicularians was reviewed by Jaspers and coll, 2023.
Luo and coll. (2022) reported that pelagic tunicates indirectly shunt the microbial loop.
O. dioica grazes on bacterioplankton, which can be a significant share of its own diet, but the grazing has only “minimal influence on the population dynamics of the free-living bacteria” (King, Hollibaugh and Azam, 1980)
In a rRNA metabarcoding study López-Escardó and coll, 2018 report that 28 % of the RNA reads in oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
O. dioica populations may have a higher fitness in warmer and more acid oceans (Bouquet et al., 2018). Another mesocosm study that took place in the Gullmar Fjord (Algueró-Muñiz M and coll., 2017) did not predict major changes in mesozooplankton community structure and provides raw data including O. dioica, for which no significant changes are visible.
O. dioica has “a very large mutation rate, and/or a very large effective population size” (Denoeud et al., 2010, according to a study of silent and non-silent substitution rates in coding sequences).
Meta-transcriptomic analysis in the Red sea showed a decrease of appendicularians during a Trichodesmium bloom in 2012 (Mojib and coll., 2017).
As of August 2018, O. dioica is not yet found in the BOLD database of DNA barcodes.
Carbon output of O. dioica is either their house or fecal pellets, the ratio of which may depend on food concentration (Acuña and Kiefer, 2000).
Gravid B mcnutti individuals are found at down to 800 m, but spawning is supposed to happen closer to the surface (Sherlock and coll., 2017).
Oikopleuridae have been reported to be able to ingest microplastics. Example(s): B. stygius (Katija and coll., 2017b). 3 to 17 microplastic particles were found in sinking houses in the Monterey Bay Choy and coll., 2019.
The development of O. dioica is comparatively less affected by microplastic leachates than some other invertebrates (?Guri and coll., 2024).
O. dioica can filter, ingest and defecate the Emiliania huxleyi virus (Lawrence and coll., 2018). This study does not assess whether the viruses are digested.
Houses and fecal pellets of Oikopleura species are consumed by eel larvae (Mochioka and Iwamizu, 1996).
O. dioica and O. fusiformis are eaten by anchovies (Capitanio, Pájaro and Esnal, 2005).
In the Black Sea, invasion of O. dioica's predator Mnemiopsis leidyi (a ctenophore) decimated its population, which was restored to higher levels by the subsequent invasion of the predator's predator Beroe ovata. Shiganova, 2005.

Distribution in and near Japan

O. dioica was reported to be abundant in Tokyo bay except in summer (Sato and coll, 2008).
O. dioica was reported in the Omura (Nagasaki) bay by Ito and Iizuka (1980).
It was already reported to be frequent in Japanese waters in 1907 by T. Aida.
O. dioica, longicauda and cophocerca April 1997 in Moroiso Bay, Misaki, Miura-peninsula, Kanagawa (Nishino and Morisawa, 1998).
Oikopleuridae can be found in the deep see. For instance, Lindsay and coll., 2014 reported Oikopleura, Mesochordaeus and Bathochordaeus individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
Two blooms taking place in summer 1997 in the Seto inland sea, Japan, were reported by Nakamura (1998).
O. dioica was found all year in the Fukuyama harbour, Japan in 1986—7 (Uye and Ichino, 1995). Mature stages were also found all year, and trunk length was shorter in summer.
In 1972, 1976, 1977, 1978, 1982 or 1986, O. dioica was rare but relatively more abundant in slope waters, compared with Kuroshio and subtropical waters, on the Pacific side of the Japan coast (Hidaka, 2008).

Distribution near Taiwan and China

In Taiwan, O. dioica was reported in north east costal waters in summar 2005 by ?Hsiao and coll. and in 2009 (plus near the Kueishan island) by Kâ and Hwang, 2011. In a coastal sampling sites visited in 2014, 2015, and 2017, it was almost always the most abundant appendicularian. It was most abundant in summer (Franco and coll,. 2016, Franco and coll., 2017).
In the northern south China sea, O. longicauda and O. rufescens were reported to be more abundant than O. dioica in 2006 by (Li and coll., 2012).
O. dioica captured in 2017 from Jiaozhou Bay, Qingdao, China (35°03′N, 120°20′E) could be cultivated at 18 °C (Li and Zhang, 2021).
O. dioica and O. longicauda were found throurought 2006-2007 in the Yellow sea (Franco, Chen and Li, 2014). Abundance peaked is spring, but the animals could also be found in winter when water temperature went below 10°C.

Elsewhere in the Pacific ocean

California (C. Essenbergm, 1922); rare in summer's warm (> 20ºC) waters and more abundant in winter's cool (13~16 ºC) waters.
Also found in eDNA form Monterey bay (Djurhuus and coll., 2020).
Throurought the North Pacific (Tokioka, 1960).
Alaska, where it is more abundant in summer and near the coast (Doubleday and Hopcroft, 2015).
Giant appendicularians could be observed in high abundance from deep submersibles near Californian and middle American coasts (Barham, 1979, ?Galt, 1979).
Northern Chile: Aravena and Palma, 2002.
Might have been observed by Huxley (1851) in New Guinea and the South Pacific.

Elsewhere in the World

Bay of Bengal (Bhavanarayana and Ganapati in 1972).
While O. dioica was not reported on the atlantic and pacific coasts of Costa Rica, its presence is considered plausible (Castellanos, Morales-Ramírez and Suárez-Morales, 2009).
Jamaica, where it was less abundant than O. longicauda (Hopcroft and Roff, 1995, Hopcroft and Roff, 1998).
South Atlantic: found all year near Mar del Plata in 2000—1, where it was most abundant in summer (Viñas and coll., 2013), Caravelas river estuary and adjascent costal areas (Carvalho and Bonecker, 2010).
Found near Argentina (Capitanio, Pájaro and Esnal, 2005).
Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature = 30 °C; night dives), O. dioica was found but not as abundant as other larvaceans (Galt, Grober and Sykes, 1985).
Mesopelagic oikopleura were described by R. Fenaux (1993) in Bahamian and Bermudian and in mediterranean waters.
Oikopleuridae can be found in polar waters. Capitanio, Daponte and Esnal (2003) proposed that O. gaussica, O. valdiviae, O. drygalskii, and O. weddelli are actually a single species (with oral gland cells and ~8 to 14 subchordal cells).
Indian ocean near Australia: detected in eDNA sequencing of 18S rRNA (Berry and coll., 2019)
TARA Oceans (Vorobev and coll., 2020), ?10.1101 2020.10.15.341214v2.
In the southern Black sea in 2006–2007 (Üstün, Bat and Besiktepe, 2016) and in the northern Black sea (Shiganova 2005.

In the past:

Fossils in China: Zhang Aiyun, 1987. Body rich in vanadium but not the house.

Not found in:

Admirality bay, King George island, Antarctica, where the two most abundant appendicularians were F. borealis and O. gaussica ([[Panasiuk and Kalarus, 2021|biblio/10.3390_d13120675]).

Laboratory culture

Culture protocols (incomplete list):

G.-A. Paffenhöfer, 1973.
Fenaux and Gorsky (1985) published a method using a helicoidal paddle to stir the culture.
Rotating vessels: Sato and coll, 1999.
Tested once in Ctenophore tubes (Patry, Bubel, Hansen and Knowles, 2020).
Nishida lab protocol: ?Nishida 2008.
Thompson lab protocol: ?Bouquet and coll., 2009.
Cañestro lab protocol: ?Martí-Solans and coll., 2015.
OIST's culture protocol: Masunaga and coll., 2020.
Fritilaria culture: Henriet, Aasjord and Chourrout, 2022, Sato, 2023.
Rotating cylinders instead of paddles: Sato, 2023.

Food tested in laboratory (totally incomplete list):

Fenaux 1976 reported the use of Nanochloropsis oceanica (under the name Nanochloris occulata) (2 to 3 µm according to Wikipedia).
Flagellates Isochrysis galbana (4 µm width) and Monochrysis lutheri (4 µm width), and the diatom Cyclotella nana (Thalassiosira pseudonana) which had a width of 5 µm (G.-A. Paffenhöfer, 1973).
Isochrysis galbana (5.5 µm in size), Tetraselmis suecica (9.5 µm), and the chlorophyte Chlorella sp. (3.5 µm) Acuña and Kiefer, 2000.
I. gal, Tetraselmis sp for O. dioica and the same plus an “unidentified flagellate of 2 µm cell diameter” for O. longicauda ([[Sato and coll, 1999|biblio/10005415955]).
The diatom Chaetoceros calcitrans, often used as a food, can be toxic at high concentrations, probably because of the production of biotoxins (Torres-Águila and coll., 2018).
The Postlethwait lab has been feeding their animals with (Dunaliella tertiolecta, Isochrysis galbana, Rhodomonas lens, Nanochloropsis sp., and Micromonas sp. (strain Dw-8)) Bassham and Postlethwait (2000)).
The Luscombe lab (Masunaga and coll., 2020) uses Chaetoceros calcitrans, Isochrysis galbana, Rhinomonas reticulata, and Synechococcus sp..

RSS Atom

An improved cultivation device for appendicularians with notes on the biology of Fritillaria sp. collected in Sagami Bay, Japan.

Sato Riki

Journal of the Marine Biological Association of the United Kingdom. 2023;103:e68. doi:10.1017/S0025315423000541

Uses rotating cylinders to circulate water in buckets. The cultivated Fritillaria sp. do not survive the use of rotating paddles. Its house covered the body entirely.

Li S, Liang Y, Zhang G.

J Hazard Mater. 2024 Aug 16;479:135552. doi:10.1016/j.jhazmat.2024.135552.

Growth and reproductive toxicity of bisphenol A in Oikopleura dioica at environmentally relevant concentrations.

“Evaluation of the toxicity of environmentally relevant levels of BPA [(bisphenol a)] (2.5–150 μg/L) on the appendicularian Oikopleura dioica” LC50 of 142 μg/L. “125 μg/L BPA significantly inhibited the somatic growth, gonadal development and reproduction” ”exposure to an environmentally safe concentration (2.5 μg/L) affected female fecundity and fitness” “BPA exposure […] led to abnormal secretion of digestive enzymes and phospholipase A2”

David Lagman, Anthony Leon, Nadia Cieminska, Wei Deng, Marios Chatzigeorgiou, Simon Henriet, Daniel Chourrout

Dev Biol. 2024 Aug 22:S0012-1606(24)00217-3. doi:10.1016/j.ydbio.2024.08.012.

Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory

Knock-out of Pax37B and Pax37A using CRISPR-Cas9. Pax37B is essential to the proper patterning of the oikoblastic epithelium but not Pax37A. Based on the analysis of single-cell and transcriptomic data in Oikopleura and Ciona, the authors propose a parallel between oikoblastic cells in Oikopleura and the neuroepithelial cells that produce gluing collocytes in Ciona.

Tracing Homopolymers in Oikopleura dioica's mitogenome.

Dierckxsens N, Watanabe K, Tan Y, Masunaga A, Mansfield MJ, Miao J, Luscombe NM, Plessy C.

Genome Biol Evol. 2024 Aug 20:evae182. doi: 10.1093/gbe/evae182

Our PacBio I25 assembly

Klirs Y, Novosolov M, Gissi C, Garic R, Pupko T, Stach T, Huchon D.

Genome Biol Evol. 2024 Aug 20:evae181. doi:10.1093/gbe/evae181

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.

“the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal“ Cs are occasionally found in edited poly-T regions.

R. D. Scheinberg, M. R. Landry, A. Calbet

MEPS 294:201-212 (2005) doi:10.3354/meps294201

Grazing of two common appendicularians on the natural prey assemblage of a tropical coastal ecosystem

Trunk length 0.7 ± 0.2 for O. longicauda and 0.8 ± 0.2 for O. fusiformis. House length 3.9 ± 0.5 mm vs 7.0 ± 1.3, respectively. Clearance rate 35 and 39 ml/ind/h respectively. “The mean clearance rates of these 2 species on total sub-micron cells in Kaneohe Bay were not significantly different; however, O. fusiformis cleared Hbact at a marginally higher rate”

Fenaux R, Youngbluth MJ.

Journal of the Marine Biological Association of the United Kingdom. 1990;70(4):755-760. doi:10.1017/S0025315400059038

A new mesopelagic appendicularian, Mesochordaeus bahamasi gen. nov., sp. nov.

10.1017/S0025315400059038desc="Primary publication for the Mesochordaeus genus. “collected […] on 5 October 1981, off the Bahamas (Dive no. 634, 25°58-2'N, 77°25-6'W) at a depth of 595 m” “In dorsal view, the trunk is oval, 3360 µm long and 1800 µm wide. Maximum height (in pharyngeal region) is 1400 µM”"

Jessica Y Luo, Charles A. Stock, Natasha Henschke, John P. Dunne and Todd D. O'Brien

Progress in Oceanography Volume 205, July 2022, 102822

Global ecological and biogeochemical impacts of pelagic tunicates

“Our results suggest that pelagic tunicates play important trophic roles in both directly competing with microzooplankton and indirectly shunting carbon export away from the microbial loop.”

Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Aleksandra Bliznina, Paolo Barzaghi, Tamara L. Hodgetts, Alfonso Ferrández-Roldán, Cristian Cañestro, Takeshi A. Onuma, Charles Plessy & Nicholas M. Luscombe.

The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe.

Three (cryptic) O. dioica species. The only robust morphological change found was egg diameter.

Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM.

Genome Res. 2024 Apr 25;34(3):426-440. doi:10.1101/gr.278295.123

Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species.

Gene order is scrambled between O. dioica species. Molecular clock analysis of 177 single-copy orthologs places appendicularian sister to all tunicates.

Eva Jimenez Guri, Periklis Paganos, Claudia La Vecchia, Giovanni Annona, Filomena Caccavale, M Dolores Molina, Alfonso Ferrandez-Roldan, Rory Daniel Donnellan, Federica Salatiello, Adam N Johnstone, Maria Concetta Eliso, Antonietta Spagnuolo, Cristian Canestro, Ricard Albalat, Jose M Martin-Duran, Elisabeth A Williams, Enrico D'Aniello, Maria Ina Arnone.

bioRxiv 2024.01.10.574808; doi: https://doi.org/10.1101/2024.01.10.574808

O. dioica's development less affected by leachates than other tested animals.

Feng H, Thompson EM.

Front Cell Dev Biol. 2023 Dec 7;11:1323378. doi:10.3389/fcell.2023.1323378

Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica.

“a C-terminal GFP fusion [of OdAur1] was localized on centrosomes throughout mitosis” “a commercial phospho-Aurora antibody that can recognize the phosphorylated forms of both Aurora1 and Aurora2 in O. dioica [localised] on centrosomes and chromosomes in prophase and metaphase, and on centrosomes and the central spindle in anaphase” “This suggests that Aurora1 and Aurora2 in O. dioica represent the polar and equatorial forms of Aurora kinases”. “[Knockdown] suggests that Aurora1 is involved in promoting the progression of prometaphase I. In all the Aur2 KD oocytes, both H3-pS10 and H3-pS28 were absent, and chromosomes were decondensed, reminiscent of INCENPa knockdown phenotypes”

Taucher J, Lechtenbörger AK, Bouquet JM, Spisla C, Boxhammer T, Minutolo F, Bach LT, Lohbeck KT, Sswat M, Dörner I, Ismar-Rebitz SMH, Thompson EM, Riebesell U.

The appendicularian Oikopleura dioica can enhance carbon export in a high CO2 ocean.

Glob Chang Biol. 2023 Nov 10:e17020. doi: 10.1111/gcb.17020.

“pelagic mesocosms [...], each extending to a depth of 21 m (19 m cylindrical bag and 2 m full size/diameter conical sediment trap attached to the bottom of the bag) and enclosing about 60 m3 of the natural water column.” “Average pCO2 during the experiment ranged between ~320 (“ambient”) and 1700 μatm (“high CO2,” corresponding to a drop in pH by 0.57 units compared to ambient conditions).” “a custom-built net (50 μm mesh size; 20 cm in diameter) with a modified, non-filtering cod end (3.8 L clear polycarbonate beaker) and reduced towing speeds (0.15 m s−1) was applied in order to collect alive and undamaged O. dioica specimen.” “The peak biomass of O. dioica was approximately twice as high in the high CO2 mesocosms (2.5 vs. 1.3 μgC L−1) and occurred earlier (days 13–17) than under ambient conditions (day 21)”. “female O. dioica were cultured in mesocosm water (pre-filtered through a 50-μm mesh) of the respective CO2 conditions until they achieved maturity and produced eggs.” “The fecundity of O. dioica was significantly elevated under lower pH, with females producing 278 (±107) eggs under ambient and 334 (±14) eggs in the OA treatment“

Hiebert TC, Gemmell BJ, von Dassow G, Conley KR, Sutherland KR.

J R Soc Interface. 2023 Nov;20(208):20230404. doi:10.1098/rsif.2023.0404

The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping.

“Flow tracers consisted of live, unicellular microalgae. Rhinomonas reticulata was used for observations at low magnifications (4×) and Isochrysis galbana was used for observations at high magnifications (40×).” “Our micro-videography confirms that the beating tail in O. dioica acts as a positive displacement peristaltic pump when filtering” “Temperature had a significant effect on tail beat frequency, which increased by 366% from 5 to 25°C.” “Likewise, inlet particle speeds increased with increasing temperature”

Robert Fenaux

Cycle vital d'un Appendiculaire Oikopleura dioica Fol, 1872 : description et chronologie

Ann. Inst. Oceanogr. Paris (1976) 52, 89-101 https://cir.nii.ac.jp/crid/1571417125678584576

[[!url https://cir.nii.ac.jp/crid/1571417125678584576 desc="High sperm concentration leads to polyspermia, aborted cell divisions, and early developmental arrest. Egg diameter between 97 and 107 µm. The trunk / tail length ratio varies with age and can be matched with a Bertalanffy model. Fed with Nannochloris occulata."]]

Holland, L.Z., Gorsky, G. & Fenaux, R.

Zoomorphology 108, 229–243 (1988). doi:10.1007/BF00312223

Fertilization in Oikopleura dioica (Tunicata, Appendicularia): Acrosome reaction, cortical reaction and sperm-egg fusion.

“Males [...] were placed in cold (4° C) seawater to induce testicular rupture.” “Each egg is about 80-100 µm in diameter and is surrounded by a thin vitelline layer 80-100 nm thick [...] There is an asymmetrical perivitelline space ranging from 2 to 7 µm in width”. “The maximal diameter of the chromosomes in our section is about 150 nm”. “By 60 s after insemination, when the egg is regaining its spherical shape, the sperm nucleus, centriole, axoneme and mitochondrion have moved into the egg cortex”. “Fertilization [...] occurs almost simultaneously throughout an egg population after the addition of sperm”. “The central cytoplasm of the unfertilized appendicularian egg contains a preponderance of multivesicular bodies and the periphery has alternating areas rich in mitochondria and rich in endoplasmic reticulum”. “the anterior portion of the nuclear envelope evaginates together with the acrosomal membrane and may help to stiffen the resulting acrosomal tubule. The lumen of the tubule, which is consequently lined by the nuclear envelope, contains some fine fibrils that extend back into the nucleus.”

Jaspers C, Hopcroft RR, Kiørboe T, Lombard F, López-Urrutia Á, Everett JD, Richardson AJ.

Trends Ecol Evol. 2023 Oct;38(10):980-993. doi:10.1016/j.tree.2023.05.005

Gelatinous larvacean zooplankton can enhance trophic transfer and carbon sequestration.

Role of appendicularians in the biological pump to the sea floor. “Larvacean shunt” in the food chain.

Zemann B, Le MV, Sherlock RE, Baum D, Katija K, Stach T.

J Morphol. 2023 Jul;284(7):e21598. doi:10.1002/jmor.21598

Evolutionary traces of miniaturization in a giant-Comparative anatomy of brain and brain nerves in Bathochordaeus stygius (Tunicata, Appendicularia).

102 cells in the brain, a number comparable to one in O. doica.

William Abbott Herdman

Journal of The Linnean Society of London, Zoology, vol 23, 558-652, Feb 5th 1891. ark:/13960/t5q898f4x, biostor-236874.

A revised classification of the Tunicata, with definitions of the orders, sub-orders, families, sub-families and genera, and analytical keys to the species

Defines:

Order Larvacea, Herdman, 1882
- Family Appendiculariidae, Bronn, 1862
  - Genus Appendicularia (Chamisso 1821), Fol, 1874
  - Genus Oikopoleura (Mertens 1831), Fol, 1872 synonym: Vexillaria, J. Müller
  - Genus Stegosoma, Chun 1888
  - Genus Fritillaria (Q. & G. 1833), Fol, 1872 synonym: Eurycercus, Busch
  - Genus Kowalvskia, Fol, 1872 Herdman speculates that it may be a Family.

Hironori Funabiki, Isabel E. Wassing, Qingyuan Jia, Ji-Dung Luo, Thomas Carroll

bioRxiv 2023.01.30.526367 doi:10.1101/2023.01.30.526367

Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases

In addition to DNA methyltransferases, Oikopleura dioica has also lost “SNF2 family ATPase HELLS” and “its activator subunit CDCA7”, as well as the DNMT1 activator UHRF1.

Huxley, Thomas Henry.

Philosophical Transactions of the Royal Society of London, vol. 141, 1851, pp. 595–605.

Remarks upon Appendicularia and Doliolum, Two Genera of the Tunicata

https://www.jstor.org/stable/108414

Observed appendicularians in New Guinea and in the South Pacific. Found testis but no ovary. Sampled animals did not have their house. Recognised that Appendicularians are Tunicates.

Hermann Fol

Archives de zoologie expérimentale et générale (Notes et revue) 3: XLIX-LIII

Note sur un nouveau genre d'Appendiculaires.

First description of Appendicularia sicula. Not assigned to one of the 3 tribes defined in 1872 because it shares features with all of them.

Includes corrections to the 1872 paper: Kowalewskaia → Kowalewskia, aplostoma → haplostoma, ectothélium → ectoderme, endothélium → endoderme.

SourceID 354924

Bibliographic reference and link to biodiversity library: https://marinespecies.org/aphia.php?p=sourcedetails&id=354924

Maurice Bedot

Revue suisse de zoologie, 2, 1894, pp 1–21

Hermann Fol, sa vie et ses travaux, avec un portrait

Éloge et bibliographie d'Hermann Fol après sa disparition.

F. L. Capitanio, M. Pájaro, G. B. Esnal

Journal of Applied Ichthyology Volume 21, Issue 5 p. 414-419. 10 October 2005 doi:10.1111/j.1439-0426.2005.00657.x

Appendicularians: an important food supply for the Argentine anchovy Engraulis anchoita in coastal waters

Oikopleura dioica and O. fusiformis found in the stomach of anchovies. The two Oikopleura and Fritillaria borealis were also found in plankton samples.

Anna Panasiuk and Marcin Kalarus

Diversity 2021, 13(12), 675. doi:10.3390/d13120675

Appendicularia (Tunicata) in an Antarctic Glacial Fjord–Chaotic Fjordic Structure Community or Good Indicators of Oceanic Water Masses?

Fritillaria borealis was the most abundant and found mainly in summer, Oikopleura gaussica was the second most abundant and found mainly in winter. F. antartica, F. aberrans, O. fusiformis and O. parva were also found.

Simon Henriet, Anne Elin Aasjord, Daniel Marc Chourrout

Front Zool. 2022 Oct 28;19(1):26. doi:10.1186/s12983-022-00471-y

Laboratory study of Fritillaria lifecycle reveals key morphogenetic events leading to genus-specific anatomy.

Possibly parasited by a Syndiniale from the genus Sphaeripara and Oodinium. Fed with Micromonas pusilla or Synechococcus sp in culture at a density between 2 and 8 × 10⁷ depending on the developmental stage. 4 chromosomes are visible in oocytes by DAPI staining. Self-fertilization was never observed. In vitro fertilized oocytes frequently aborted development when left in vessels without water flow. Embryos hatch between 4 and 6 h at 15 °C. Cellulose-producing cells identified by staining with a carbohydrate-binding-module (CBM).

Bassham S, Postlethwait JH.

Development. 2005 Oct;132(19):4259-72. doi:10.1242/dev.01973

The evolutionary history of placodes: a molecular genetic investigation of the larvacean urochordate Oikopleura dioica.

Animals fed with algal concentrates. O. dioica has one orthologue of eyes absent, Eya, and one orthologue of the vertebrate Pitx genes, with multiple promoters and alternative splice sites, and lacking an OAR domain. It has three sine oculis orthologues, Six1/2, Six3/6a and Six3/6b. They are not clustered like vertebrate genes, but the two Six3/6 share an intron position in their homeodomain. Expression pattern of these genes support the hypothesis that O. dioica has a placode that is homologous to the vertebrate olfactory placode.

Thomas Henry Huxley

Philosophical Transactions of the Royal Society of London Vol. 141 (1851), pp. 595-605 doi:10.1098/rstl.1851.0028

Remarks upon Appendicularia and Doliolum, Two Genera of the Tunicata

https://www.jstor.org/stable/108414

One of the appendicularian species found in the Bering Sea was called Appendicularia flagellum by Chamisso (1821), Oikopleura Chamissonis by Mertens (1830) and Oikopleura bifurcata by Quoy and Gaimard. Huxley id not see houses, even when keeping the animals in vessels for multiple hours. He identified appendicularia as tunicates, and notes “... so does Appendicularia typify, in the larval state of the Ascidians.” ”In young specimens the testis is greenish, and contains nothing but small pale circular cells; but in adults it assumes a deep orange red-colour“ “The animal has an ovoid or flask like body, one- fourth of an inch in length, to which is attached a long curved lanceolat tail.”

Oulion S, Bertrand S, Escriva H.

Int J Evol Biol. 2012;2012:298147. doi:10.1155/2012/298147

Evolution of the FGF Gene Family.

“In another urochordate, the larvacean Oikopleura dioica, we found six FGF coding genes, among which two can be assigned to the FGF11/12/13/14 subfamily, and one to the FGF9/16/20 subfamily”

Deibel, D., Cavaletto, J. F., Riehl, M., Gardner, W. S.

Lipid and lipid class content of the pelagic tunicate Oikopleura vanhoeffeni.

MEPS 88:297-302, 1992

Phospholipids represent the large majority of O. vanhoeffeni's lipids. “Sterol esters, wax esters, methyl esters and diglycerides were never found”.

https://www.int-res.com/abstracts/meps/v88/ https://www.int-res.com/articles/meps/88/m088p297.pdf

Søviknes AM, Glover JC.

Biol Bull. 2008 Feb;214(1):17-28. doi:10.2307/25066656

Continued growth and cell proliferation into adulthood in the notochord of the appendicularian Oikopleura dioica.

Actin stained with phalloidin, DNA stained with To-Pro-3, and BrdU stained with antibodies. Dual H2S10p and BrdU staining in the adult notochord suggest cell proliferation.

Robert Fenaux

Rhythm of secretion of Oikopleurid's houses

Bulletin of Marine Science, Volume 37, Number 2, September 1985, pp. 498-503(6)

An individual unable to expand its houses and feed was shown to have secreted 7 house rudiments stacked on each other before dying. Number of houses secreted by hour in a 12 h period: 0.17 ± 0.04 at 14°C; 0.23 ± 0.04 at 16°C; 0.30 ± 0.04 at 18°C; 0.36 ± 0.06 at 20°C and 0.44 ± 0.04 at 22°C. Increase of food supply increases house production. Individuals in artificial seawater still produce and discard houses before dying of starvation.

https://www.ingentaconnect.com/content/umrsmas/bullmar/1985/00000037/00000002/art00012

No PMID, no DOI found. WOS ID: A1985AYN8600012

Marius Wenzel, Berndt Mueller, Jonathan Pettitt

BMC Bioinformatics. 2021 Mar 22;22(1):140. doi:10.1186/s12859-021-04009-7

SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two “gene” annotations.

Weill M, Philips A, Chourrout D, Fort P.

Biol Cell. 2005 Nov;97(11):857-66. doi:10.1042/BC20050018

The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans.

O. dioica has three caspases, all related to the CSP3/7 family.

Suraweera CD, Banjara S, Hinds MG, Kvansakul M.

Int J Mol Sci. 2022 Mar 28;23(7):3691. doi:10.3390/ijms23073691

Metazoans and Intrinsic Apoptosis: An Evolutionary Analysis of the Bcl-2 Family.

Oikopleura dioica has lost all the Bcl-2 genes as well as their BH3-only ligands.

Shiganova, T. (2005).

Journal of the Marine Biological Association of the United Kingdom, 85(3), 477-494. doi:10.1017/S0025315405011410

Changes in appendicularian Oikopleura dioica abundance caused by invasion of alien ctenophores in the Black Sea.

Comparison of O. dioica populations before and after invasion of the ctenophores Mnemiopsis leidyi and Beroe ovata. In 1957, O. dioica peaked in May in the Western Black sea. In 1979 in peaked from June to November near Sevastopol. In 1969 there was one peak in May–June and one in August. In 1991–6, abundance of O. dioica was strongly reduced while M. leidyi was proliferating. In 1999 and following years, after B. ovata invastion, M leidyi populations were strongly reduced and O. dioica abundance returned to high levels.

Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.

Mol Biol Evol. 2008 Jun;25(6):1067-80. doi:10.1093/molbev/msn060

Fu X, Adamski M, Thompson EM.

miRNA array spotted on N+ membranes. Confirms the existence of Drosha, DGCR8, Dicer, and 3 AGO proteins. “Five compact clusters containing 15 miRNAs were identified, and the distance between adjacent members was systematically less than 100 bp.” 36% of the miRNAs were long of 22 nucleotides. “many O. dioica miRNAs were found to be located in the antisense orientation of a protein-coding gene, often opposite the sense strand of an intron.” “let-7a [...] was not detected during embryogenesis but was observed in the postmetamorphic oikoplastic epithelium.”

Nenarokova A, Záhonová K, Krasilnikova M, Gahura O, McCulloch R, Zíková A, Yurchenko V, Lukeš J.

mBio. 2019 Jul 16;10(4):e01541-19. doi:10.1128/mBio.01541-19

Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes.

Reviews possible advantages of losing the C-NHEJ pathway, such as reduction of transposon movement, reduction of genome size and change of genome structure, and insertion of short new sequence in proteins. Focus on parasites but some facts about Oikopleura are highlighted for comparison purposes.

Fabien Lombard, Antoine Sciandra and Gabriel Gorsky

MEPS 301:149-158 (2005) doi:10.3354/meps301149

Influence of body mass, food concentration, temperature and filtering activity on the oxygen uptake of the appendicularian Oikopleura dioica

Using the Bergen lab strain. Culture at 15 ± 1°C. Fed with Isochrisis galbana and Thalassiosira pseudonana. Food was lyophilised for oxygen measurements, so that it does not respirate. Animals with new house and empty stomach were used in the experiments. Animals and food were placed in oxygen-saturated water, and the remaining oxygen was measured with a polaro-graphic oxygen meter at the end of the experiment. Some animals wer aesthetized with tricaine methanesulfonate (Sandoz MS-222). Animals receiving more food consume more oxygen, but also become larger. After correction for body weight, food concentration did not influence respiration. Anesthesia reduces respiration by 33%. Animals consume more oxygen at 22°C than at 15°C.

Ma X, Øvrebø JI, Thompson EM.

Front Cell Dev Biol. 2022 Jan 28;9:770939. doi:10.3389/fcell.2021.770939

Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos.

The last common ancestors of all oiks probably had only one CDK1 as Fritillaria borealis also has only 1. Oiks in general have 3 paralogs (a, b, c), and O. dioica has 5 (a, b, c, plus d and e which appear to originate from c). They are found on chr1 (c, e), chr2, (a, b) and the XSR of chr3 (d). CycBa is also found on the XSR, and interacts with CDK1d for functions essential to meiosis of oocytes. In contrary to the ancestral CDK1 in other animals, the levels of CDK1d oscillate. “Interspecies clustering of CDK1 paralogs [show] conservation of their intron-exon structures” “O. dioica CDK1a and b locate on the same autosome whereas CDK1c is present on a different autosome that also contains CDK1e. CDK1d is found on the X chromosome where, at a distance of 5 MB, the CycBa locus is also located.” “The PSTAIRE helix is modified in all Oikopleura CDK1 paralogs whereas Oikopleura CDK2s retain the canonical PSTAIRE sequence. All of the 17 identified Oikopleura CDK1 sequences share the A48S substitution.”

Dev Biol. 2022 Jan;481:188-200. doi:10.1016/j.ydbio.2021.10.009

Nishida H, Matsuo M, Konishi S, Ohno N, Manni L, Onuma TA.

Germline development during embryogenesis of the larvacean, Oikopleura dioica.

Identified a CAB (centrosome-attracting body) “for the following reasons. (1) There was a clear boundary between the CAB-like region and the general cytoplasm, but the membrane structure did not surround the CAB. (2) It contained an electron-dense matrix that resembled a germplasm. (3) The region was devoid of mitochondria but contained ER. (4) It was present beneath the cell membrane, and the cell surface exhibited microvilli. (5) It was present in the germline lineage cells.” ”The longest diameter of the CAB was approximately 10 μm.“ It was observed between the late 8-cell stage and some 1.5-h embryos, but not after 2h. It was stained by the H3S28p rat monoclonal antibody (Abcam ab10543) but not by DAPI. The snail mRNA also colocalises with the CAB's H3S28p staining. A germ body (GB) “appeared [in PGCs] 13 min after the 5th cleavage [and] disappeared 1.5 h after fertilization at 20 °C. It is discussed whether the GB and the CAB are or are not the same structure.

Ferrández-Roldán A, Fabregà-Torrus M, Sánchez-Serna G, Duran-Bello E, Joaquín-Lluís M, Bujosa P, Plana-Carmona M, Garcia-Fernàndez J, Albalat R, Cañestro C.

Nature. 2021 Nov;599(7885):431-435. doi:10.1038/s41586-021-04041-w

Cardiopharyngeal deconstruction and ancestral tunicate sessility.

Mesp, Ets1/2b, Gata4/5/6, Mek1/2, Hand-r and Tbx1/10 are absent from appendicularian genomes. Nk4, Hand1/2 and FoxF were found.

Funda Üstün, Levent Bat and Sengül Besiktepe

Rapp. Comm. int. Mer Médit., 41, 2016, p485

Distribution of Oikopleura (Vexillaria) Dioica Fol, 1872 (Class: Appendicularia) in the southern Black sea in 2006-2007

https://ciesm.org/online/archives/abstracts/pdf/41/#

O. dioica found in June 2006, October 2006 and May 2007, in 4 size classes infour size class (<0.5, 0.5-1, 1-2 and 2-3 mm).

Tom O. Delmont, Morgan Gaia, Damien D. Hinsinger, Paul Fremont, Chiara Vanni, Antonio Fernandez Guerra, A. Murat Eren, Artem Kourlaiev, Leo d’Agata, Quentin Clayssen, Emilie Villar, Karine Labadie, Corinne Cruaud, Julie Poulain, Corinne Da Silva, Marc Wessner, Benjamin Noel, Jean-Marc Aury, Tara Oceans Coordinators, Colomban de Vargas, Chris Bowler, Eric Karsenti, Eric Pelletier, Patrick Wincker, Olivier Jaillon

bioRxiv 2020.10.15.341214; doi: https://doi.org/10.1101/2020.10.15.341214

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Assembled more than 700 eukaryotic metagenomes. 37 of them are Appendicularian. A phylogeny was made using DNA-dependent RNA polymerases.

Matsuo M, Onuma TA, Omotezako T, Nishida H.

Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica.

Dev Biol. 2020 Apr 15;460(2):155-163. doi:10.1016/j.ydbio.2019.12.005

“PP2A is essential for the maintenance of meiotic arrest and prevention of parthenogenesis at spawning event in O. dioica. When PP2Ac is lost, the pH rise at spawning brings about an aberrant Ca burst by still unknown molecular mechanisms, and it activates eggs via CaMK II, reinitiates meiosis, and eventually results in improper initiation of embryogenesis.” Okadaic acid also induced parthenogenesis. Termination of parthenogenetic migth be explain by failure to complete the cleavages because of the absence of the centrosome that should have been brought by the sperm.

Alldredge, Alice

Scientific American Vol. 235, No. 1 (July 1976), pp. 94-105 (12 pages)

Appendicularians

JSTOR ID 24950396

Li KL, Nakashima K, Inoue J, Satoh N.

Genes (Basel). 2020 Aug 13;11(8):937. doi:10.3390/genes11080937

Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer.

Comparison of primary sequence and of intron position suggests that GHC6-1 was transferred in a common ancestor of all living tunicates. O. dioica's GH6-1 gene lacks a conserved catalytic aspartate, and does not share introns with the other tunicate genes.

“We found that in many tunicate GH6-1 proteins, an aspartic acid can be aligned to the catalytic H. jecorina D221, except for SthGH6-1b (E197) and OdiGH6-1 (K211). However, the catalytic aspartic acid was not conserved in tunicate CesA.”

“In this study, although we found no other sites shared between genes of O. dioica and other tunicates, we found that many shared splice sites are present among GH6-containing genes from three other major clades of tunicates (Thaliacea + Phlebobranchia + Stolidobranchia). It is reasonable to assume that many shared introns were acquired after the branching of larvaceans and before the subsequent divergence of major tunicate clades.”

Calatayud S, Garcia-Risco M, Capdevila M, Cañestro C, Palacios Ò, Albalat R.

Front Cell Dev Biol. 2021 Jul 2;9:702688. doi:10.3389/fcell.2021.702688

Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins.

“we concluded that the 11C/12C domain of OdiMTs formed stable clusters with four Cd(II) ions” “protein sequence comparisons reveal amino-acid identities ranging from 94.4% between Norway and Barcelona, up to 63.9% when compared with the sequence of Okinawa” “amino acid identities persistently were slightly lower than nucleotide identities [...] indicated that nucleotide substitutions are significantly affecting non-synonymous positions, which can be considered an indication [of] positive selection.” “The presence of [...] non-functional alleles for both MTs [...] opened the possibility that some O. dioica specimens might lack functional MTs” “The most conspicuous difference of OdiMT genes between O. dioica populations was the identification of OdiMT2 encoding proteins with variable number of RUs (i.e., t-12C/12 pairs). OdiMT2ORE with seven repeats (RU1–RU7) was the longest one, followed by OdiMT2NOR, with six repeats, OdiMT2OSA, with five repeats, OdiMT2CAT, with four repeats, and OdiMT2OKI, with three repeats.”

Alldredge AL.

Science. 1972 Sep 8;177(4052):885-7. doi:10.1126/science.177.4052.885

Abandoned larvacean houses: a unique food source in the pelagic environment

The copepod Oncaea mediterranea can feed on appendicularian houses (lab experiment with starved copepods). As some nanoplankton is caugt in the abandonned houses, this brings back the nanplankton in the copepod food chain.

Calatayud S, Garcia-Risco M, Palacios Ò, Capdevila M, Cañestro C, Albalat R.

Mol Biol Evol. 2021 Jun 19:msab184. doi:10.1093/molbev/msab184

Tunicates illuminate the enigmatic evolution of chordate metallothioneins by gene gains and losses, independent modular expansions and functional convergences.

Ancestral two-domain organisation found in Cephalochordates and Vertebrates. Ascidians appear to have lost one domain and larvaceans proteins ressemble no other.

Martí-Solans J, Godoy-Marín H, Diaz-Gracia M, Onuma TA, Nishida H, Albalat R, Cañestro C.

Front Cell Dev Biol. 2021 Jun 9;9:700827. doi:10.3389/fcell.2021.700827

Massive Gene Loss and Function Shuffling in Appendicularians Stretch the Boundaries of Chordate Wnt Family Evolution.

Localised subcellular expression in the “postplasm” during early embryogenesis. Gene amplification by retrotranscription.

”8 O. dioica Wnts belonged to 4 Wnt subfamilies—i.e., Wnt5, Wnt10, Wnt11 (5 sequences) and Wnt16 subfamilies). The results, therefore, show that O. dioica have lost 9 Wnt subfamilies during its evolution. On the other hand, our results revealed that O. dioica has expanded the Wnt11 subfamily to at least 4 paralogs, named Odi_Wnt11a to Odi_Wnt11d.” “Odi_Wnt11b, Odi_Wnt11c, and Odi_Wnt11d, had no introns, pointing to the possibility of a retrotranscriptional origin during the evolution of the appendicularian lineage.”

Mochioka, N., Iwamizu, M.

Marine Biology 125, 447–452 (1996). doi:10.1007/BF00353257

Diet of anguilloid larvae: leptocephali feed selectively on larvacean houses and fecal pellets.

Proposes that “that the peculiar, large, fang-like teeth of leptocephali are used for feed- ing, and evolved to pierce and grasp the mucous houses of larvaceans”. Found houses and fecal pellets that may be from O. longicauda.

Li, S., Zhang, G.

J. Ocean. Limnol. 39, 609–622 (2021). doi:10.1007/s00343-020-0071-0

Role of intraspecific competition in intrinsic growth rate regulation in an Oikopleura dioica (Tunicata) population.

O. dioica found in Jiaozhou Bay, Qingdao, China and cultured at 18 °C. Generation time of 4.5 days. Largest animals tend to appear with low density of individuals and large amounts of food.

“Individuals of Oikopleura dioica (Tunicata, Appendicularia) were collected in the Jiaozhou Bay, Qingdao, China (35°03′N, 120°20′E) on June 20, 2017, using a plankton net with a large-volume cod-end (10L). The samples were diluted into 50 L buckets and transported immediately to the laboratory, where healthy individuals were sorted and cultured in a small room (approximately 10 m2) maintained at 18 ± 1°C using a standard air conditioner.”

“parental animals were forced to release their gametes by gentle aspiration in a pipette. Then, all dishes were placed in a speed-regulating vibrator (HY-4H) rotating at 60 r/min for 5 min to mix the eggs and male gametes together, and this time was considered time zero (D0).”

“To control the food concentration, a mono-diet of Isochrysis galbana was adopted for all treatments.”

“From gamete production, the entire incubation duration was 4 d and 12 h.”

“The body length of O. dioica was 145 ± 17 μm on average after 15 h of metamorphosis.” “ On average, body lengths of 324–549 μm were achieved at the end of the experiments.” “At each food level, both the final body and gonad length decreased on average with density.”

“Calculated with a fixed generation duration of 4.5 d, the mean maximal intrinsic rate of natural increase (rmax) varied between 0.25 and 0.65/d”

“In general, the population growth was significantly regulated by the PFS. The rmax was increased with the PFS and was saturated at values higher than 8.1 μg C/ind.”

“Though the mortality recorded in our experiments was generally higher at low food concentrations, it is uncertain whether mortality increased with increased competition stress.”

Onuma TA, Nakanishi R, Sasakura Y, Ogasawara M.

Dev Biol. 2021 Jun 6:S0012-1606(21)00142-1. doi: 10.1016/j.ydbio.2021.05.021.

Nkx2-1 and FoxE regionalize glandular (mucus-producing) and thyroid-equivalent traits in the endostyle of the chordate Oikopleura dioica.

Found vWFL (von Willebrand factor-like, a single gene, whereas Ciona has two), and the thyroid-related peroxidases, TPO and Duox, and the thyroid-related TFs Nkx2-1 and FoxE. Also reported a SCO spondin in the supplemental material. “Nkx2-1 knockdown suppressed vWFL expression in 8 hpf larvae. In contrast, FoxE knockdown had no effect on vWFL expression.” “Nkx2-1 knockdown decreased TPO expression in the endostyle of over 90% of larvae.” “FoxE knockdown did not affect Duox expression.” “Nkx2-1 knockdown caused malformation of the endostyle in 80% of the larvae. In contrast, FoxE knockdown did not affect endostyle morphology.” “Nkx2-1 expression was decreased by Nkx2-1 knockdown, but not by FoxE knockdown. On the other hand, FoxE expression was decreased in two-thirds of the Nkx2-1 knockdown larvae as well as in FoxE knockdown larvae.”

The filter-house of the larvacean Oikopleura dioica. A complex extracellular architecture: from fiber production to rudimentary state to inflated house.

J Morphol. 2021 May 26. doi:10.1002/jmor.21382

Razghandi K, Janßen NF, Le Mai-Lee V, Stach T.

Developmental origin of the escape slot and the outlet valve.

Bliznina A, Masunaga A, Mansfield MJ, Tan Y, Liu AW, West C, Rustagi T, Chien HC, Kumar S, Pichon J, Plessy C, Luscombe NM.

BMC Genomics. 2021 Mar 29;22(1):222. doi: 10.1186/s12864-021-07512-6.

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing.

The OKI2018_I69 assembly.

Sato Riki, Yu Jingshan, Tanaka Yuji, Ishimaru Takashi

Plankton Biology and Ecology 46(2), 162-164, 1999-08-01

New apparatuses for cultivation of appendicularians

Culture of O. dioica and O. longicauda in rotating vessels. O. lon required an “unidentified flagellate of 2µm cell diameter”.

PDF at: http://www.plankton.jp/PBE/issue/vol46_2/vol46_2_162.pdf

Beaufortia, 2000, Volume 50 - Issue 2 p. 69-77 urn:nbn:nl:ui:19-505187

Flood (Per R.)

A new appendicularian, Oikopleura gorskyi n. sp. (Tunicata), from norwegian fjords

2 oral gland cells with 2 nuclei each. 5–7 Eisen oikoblasts surrounded by an unusually low number of neben cells. Luminosomes (inclusion bodies) found on the house. ~8 + ~13 subchordal cells lie ventrally in the tail. Found in Sognefjorden at 400 to 1200 m depth and in Herdlefjorden below 270 m. Tempeature: ~7.1°C. Might be found at shallower depth as well.

3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM.

Nishida H, Ohno N, Caicci F, Manni L.

Sci Rep. 2021 Mar 1;11(1):4833. doi:10.1038/s41598-021-83706-y

“The bilateral arrangement of precursor cells of the oikoplastic epidermis was already attained by the hatching stage.” “Upon 3D construction, additional single cells, which showed similar features to giant Fol cells, albeit slightly smaller, were present in the lateral part. It is possible that this cell will be lost after larval development.” “The gonad syncytium formation already starts as early as in 10 hpf juveniles by the cell fusion of germ cells, although it is not possible to discern males or females at this stage.”

Savelieva, A.V.

Russ J Mar Biol 45, 145–151 (2019). doi:10.1134/S1063074019020111

The First Ultrastructural Description of Appendicularians (Chordata: Tunicata) Infected by Microsporidia-Like Protists

Parasites ressembling to microsporidia and their spores found in O. gracilis.

Carlo Brena, Francesca Cima, Paolo Burighel

Volume 258, Issue 2, November 2003, Pages 225-238, doi:10.1002/jmor.10145

Alimentary tract of kowalevskiidae (appendicularia, tunicata) and evolutionary implications

No heart was found.

Zhang Aiyun (张爱云)

Citation: Science in China Series B-Chemistry, Biological, Agricultural, Medical & Earth Sciences 30, 888 (1987); doi: 10.1360/yb1987-30-8-888

Fossil appendicularians in the early cambrian

“The content of fossil animal's coats increases with the quantity of algae.” “The coat of fossil animals does not contain vanadium.” “There is also a highly concentrated vanadium compount in the body of fossil animals.”

Nash AJ, Lenhard B.

Bioinformatics. 2019 Jul 15;35(14):2354-2361. doi: 10.1093/bioinformatics/bty1014.

A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates.

“our method may have utility in the analysis of GRB developmental gene regulation in species that have undergone extreme genome compaction such as the puffer fish, Tetraodon nigroviridis, and the sea squirt, Oikopleura dioica”

“The kurtosis of the distribution of the lengths of all identical sequences was calculated in [30 kbp] bins across the genome.”

“Runs of 100% sequence identity were [...] filtered for annotated repeats and exonic sequences.”

“The kurtosis of the distribution of lengths in each bin was then calculated as [...] R(F) = q0.99(F) − q0.01(F) / G50 where F is the distribution of the lengths of runs of perfect sequence identity in a bin, and G50 is the range of the middle 50% of the distribution of lengths of all runs of identity, from all bins (background distribution); calculated as [...] q0.75(J) − q0.25(J) where J is the distribution of the lengths of runs of perfect sequence identity across the whole genome.”

“This is an adaptation of the robust kurtosis measure proposed in Ruppert (1987).”

“There is a strong correlation between kurtosis and CNE density, and this correlation is greater within GRBs than outside GRBs”

Jurkowski TP, Jeltsch A.

On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2.

PLoS One. 2011;6(11):e28104. doi:10.1371/journal.pone.0028104

Did not find Dnmt2 in O. dioica.

Albalat R, Martí-Solans J, Cañestro C

Brief Funct Genomics. 2012 Mar;11(2):142-55. doi:10.1093/bfgp/els009

DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates.

Only Dnmt2 (Trdmt1) is found in Oikopleura.

Katrin Braun, Fanny Leubner, Thomas Stach

Cladistics Volume36, Issue3, June 2020, Pages 259–300 doi:10.1111/cla.12405

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

Places appendicularians basal in tunicates. Detailed summary of past studies pro and con that placement.

Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2.

Confalonieri S, Colaluca IN, Basile A, Pece S, Di Fiore PP.

G3 (Bethesda). 2019 Oct 7;9(10):3359-3367. doi: 10.1534/g3.119.400494.

Ciona NUMB can inhibit ubiquitination of P53 by MDM2. This and a phylogenetic analysis demonstrates that PTB-long isoform encoded by Exon3 is a Chordate invention. O. dioica has 2 NUMB genes, more similar to NUMB than to vertebrate-specific NUMBL. Their intron/exon structures are different from any other organism.

Glover JC.

Curr Biol. 2020 Oct 19;30(20):R1243-R1245. doi:10.1016/j.cub.2020.07.075

Oikopleura.

Introduction for non-specialists. Mentions the ideas that the CesA gene could have been transferred from an endosymbion.

Wada H.

Mol Biol Evol. 1998 Sep;15(9):1189-94. doi:10.1093/oxfordjournals.molbev.a026026

Evolutionary history of free-swimming and sessile lifestyles in urochordates as deduced from 18S rDNA molecular phylogeny.

Phylogenetic study that places Oikopleura at the base of the tunicate tree. Two Oikopleura 18S sequences were recovered from screening an O. dioica genomic DNA library: a major one (7/8 clones, AB013014), labelled as O. dioica and a minor (1/8 clones, AB013015), interpreted as a contamination an unknown species similar to the one of D14366.

Riki Sato, Yukiko Ishibashi, Yuji Tanaka, Takashi Ishimaru, Michael J. Dagg.

Journal of Plankton Research, Volume 30, Issue 3, March 2008, Pages 299–309 doi: 10.1093/plankt/fbn001

Productivity and grazing impact of Oikopleura dioica (Tunicata, Appendicularia) in Tokyo Bay

Rare in July to September, where surface temperatures are higher than 25 °C. Homogeneously distributed from 0 to 25 m in the water column from December to March, when temperatures were around 10 °C or below. Rarity in summer interpreted as the result of predation.

DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF.

Genome Biol Evol. 2020 Jun 1;12(6):948-964. doi:10.1093/gbe/evaa060

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata.

210 single-copy orthogroups from 37 tunicates + 10 outgroups. Questions the annotation (gene name) of the Hox genes in Oikopleura.

Kocot KM, Tassia MG, Halanych KM, Swalla BJ.

Mol Phylogenet Evol. 2018 Apr;121:166-173. doi:10.1016/j.ympev.2018.01.005

Phylogenomics offers resolution of major tunicate relationships.

A matrix of 798 genes totaling 254,865 amino acid positions places appendicularians as the sister group to all other tunicates.

Ganot P, Thompson EM.

Patterning through differential endoreduplication in epithelial organogenesis of the chordate, Oikopleura dioica.

Dev Biol. 2002 Dec 1;252(1):59-71. doi:10.1006/dbio.2002.0834

In the epithelial cells, “endoreduplication begins before tailshift and stops during gamete differentiation.” “Endocycles are asynchronous within a given field of oikoplastic cells, but the replication pattern is bilaterally symmetrical.” “In mature animals, final ploidy levels ranged from a low of 34 C in chain of pearl nuclei to 1300 C in giant Eisen nuclei.” Cells with higher ploidy had shorter gap phases.

Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA.

A genome database for a Japanese population of the larvacean Oikopleura dioica.

Dev Growth Differ. 2020 Jul 16. doi:10.1111/dgd.12689

The OSKA2016 genome.

Masunaga A, Liu AW, Tan Y, Scott A, Luscombe NM.

J Vis Exp. 2020 Jun 16;(160). doi:10.3791/61279

Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica.

OISTs culture protocol.

Russell R. Hopcroft, John C. Roff

Journal of Plankton Research, Volume 17, Issue 2, February 1995, Pages 205–220, https://doi.org/10.1093/plankt/17.2.205

Zooplankton growth rates: extraordinary production by the larvacean Oikopleura dioica in tropical waters

Generation time of ~1 day for O. dioica in Jamaica at 29°C.

Vorobev A, Dupouy M, Carradec Q, Delmont TO, Annamalé A, Wincker P, Pelletier E.

Genome Res. 2020 Apr;30(4):647-659. doi:10.1101/gr.253070.119

Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.

Metagenomics-based transcriptomes (MGTs): metatranscriptomic-based unigenes of the MATOU-v1 catalog detected by metagenomic reads mapping in at least three different Tara Oceans samples and displaying no more than 90% of their total genomic occurrence signal in a single sample, grouped based on the covariation of their genomic abundance across the samples, with a minimum of 500 unigenes per group. Oikopleuridae detected (Figure 1).

Seo HC, Edvardsen RB, Maeland AD, Bjordal M, Jensen MF, Hansen A, Flaat M, Weissenbach J, Lehrach H, Wincker P, Reinhardt R, Chourrout D.

Nature. 2004 Sep 2;431(7004):67-71. doi:10.1038/nature02709

Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica.

No BAC clone was found with more than one Hox gene.

Katija K, Troni G, Daniels J, Lance K, Sherlock RE, Sherman AD, Robison BH.

Nature. 2020 Jun 3. doi:10.1038/s41586-020-2345-2

Revealing Enigmatic Mucus Structures in the Deep Sea Using DeepPIV

Laser sheet imaging and 3D modeling of the inner house of Bathochordaeus larvaceans.

Calatayud S, Garcia-Risco M, Rojas NS, Espinosa-Sánchez L, Artime S, Palacios Ò, Cañestro C, Albalat R.

Metallomics. 2018 Nov 14;10(11):1585-1594. doi: 10.1039/c8mt00177d.

Metallothioneins of the urochordate Oikopleura dioica have Cys-rich tandem repeats, large size and cadmium-binding preference.

Found with “low-restrictive tblastn searches using C. robusta and H. curvata MTs as well as Cephalochordate and Vertebrate MTs as query sequences”.

Patry WL, Bubel M, Hansen C, Knowles T.

PeerJ. 2020;8:e8938. Published 2020 Apr 7. doi:10.7717/peerj.8938

Diffusion Tubes: A Method for the Mass Culture of Ctenophores and Other Pelagic Marine Invertebrates

Also tested on Oikopleura dioica.

Kienle N, Kloepper TH, Fasshauer D.

BMC Evol Biol. 2016 Oct 18;16(1):215.

Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell.

Also reports the loss of peroxisomal genes in Oikopleura.

Žárský V, Tachezy J.

Biol Direct. 2015 Dec 23;10:74. doi:10.1186/s13062-015-0101-6

Evolutionary loss of peroxisomes--not limited to parasites.

Loss of peroxisomes in O. dioica. Speculates that the advantage might be “rendering the organisms resistant to xenobiotics that become activated in the peroxisomal lumen in response to frequent redox reactions”.

Fenaux R. and G. Gorsky

Rapp. Comm. int. Mer Medit., 29, 9 (1985).

Nouvelle technique d'élevage des appendiculaires

ciesm.org/online/archives/abstracts/pdf/29/ART_0358.pdf

Helicoidal paddle to stir the culture.

Paffenhöfer, G.

The cultivation of an appendicularian through numerous generations.

Mar. Biol. 22, 183–185 (1973). https://doi.org/10.1007/BF00391782

O. dioica fed with “flagellates Isochrysis galbana (4 µm width) and Monochrysis lutheri (4 µm width), and the diatom Cyclotella nana (Thalassiosira pseudonana) which had a width of 5 µm”

Anna V. Savelieva (2019)

Invertebrate Reproduction & Development, 63:2, 100-110, DOI: 10.1080/07924259.2018.1561529

An electron microscopic study of early gonadogenesis in the hermaphroditic appendicularian Oikopleura gracilis (Tunicata, Oikopleuridae)

to_read

Nucleic Acids Res. 2015 Apr 20;43(7):3701-11. doi:10.1093/nar/gkv169

Henriet S, Sumic S, Doufoundou-Guilengui C, Jensen MF, Grandmougin C, Fal K, Thompson E, Volff JN, Chourrout D.

Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline.

“In several Tor elements, env expression is driven by an internal promoter and not by the 5′LTR.” “Using human HEK293T cells, [...] Env was associated with cell membranes during subcellular fractionation.” “Some Tor elements are active and have recently integrated copies in Oikopleura germline DNA.” “Comparison of Argonaute protein sequences in the Oikopleura genome identified a single Piwi, sharing diagnostic residues with fly and vertebrate Piwi.” ”Our results show that expression of Tor in somatic tissues was located in proximity to germ cells. Tor RNA seemed mostly absent from germ cells themselves.”

Djurhuus A, Closek CJ, Kelly RP, Pitz KJ, Michisaki RP, Starks HA, Walz KR, Andruszkiewicz EA, Olesin E, Hubbard K, Montes E, Otis D, Muller-Karger FE, Chavez FP, Boehm AB, Breitbart M.

Nat Commun. 2020 Jan 14;11(1):254. doi: 10.1038/s41467-019-14105-1.

Environmental DNA reveals seasonal shifts and potential interactions in a marine community.

Found Oikopleura 18S sequences in MiSeq run SRR8473276.

PLoS Genet. 2019 Feb 8;15(2):e1007943. doi:10.1371/journal.pgen.1007943

Berry TE, Saunders BJ, Coghlan ML, Stat M, Jarman S, Richardson AJ, Davies CH, Berry O, Harvey ES, Bunce M.

Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events.

Oikopleura detected in the 18S data.

Mol Biol Evol. 2004 Nov;21(11):2022-33 doi:10.1093/molbev/msh207

Volff JN, Lehrach H, Reinhardt R, Chourrout D.

Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica.

Primary paper for Odin (Oikopleura dioicanon-LTR) and Tor (Ty3/gypsy Oikopleura retrotransposon) elements.

TBlastN search for reverse-transcriptases suggests “extinction, or at least strong copy number reduction, of major clades of non-LTR retrotransposons”. “About 80 Odin reverse transcriptase sequences were detected by TBlastN analysis in the 41 Mb genome assembly of O. dioica using a 335 amino acid reverse transcriptase sequence as a query (we can not exclude that some nonoverlapping short hits might belong to a same partially sequenced element). About 30% of Odin endonuclease and reverse transcriptase-encoding sequences were corrupted by stop or frameshift mutations, suggesting that an important proportion of Odin elements is not functional. The degree of nucleotide sequence identity between Odin elements ranged from less than 60% up to 90%.”

“About 180 Tor reverse transcriptase sequences were detected in the 41 Mb genome assembly (about 50 sequences for Tor2, Tor3, and Tor4, but only two for Tor1; the remaining sequences were too short to be classified unambiguously). The degree of nucleotide identity inside of the Tor2, Tor3, and Tor4 families ranged from less than 60% up to 98–99% (the two Tor1 elements showed 70% nucleotide identity). On average, open reading frame–corrupting mutations were observed each 7.5 kb, 2.8 kb, and 16 kb for Tor2, Tor3, and Tor4, respectively.” “The Tor4b family might have acquired its env-like gene from a paramyxovirus.”

“Among other groups of LTR retrotransposons, only DIRS1-like elements were found in Oikopleura.” “About 70 reverse transcriptase sequences from DIRS1-related elements were detected in the 41 Mb genome assembly, with degrees of nucleotide identity ranging from less than 60% up to 90%. DIRS1-related elements were apparently absent from the sea squirt genome and would therefore represent the only type of autonomous retroelement lost in C. intestinalis but present in O. dioica.”

“Penelope-like retroelements were detected in the genome of both O. dioica and C. intestinalis. [...] Complete elements with an apparently intact unique open reading frame encoding a reverse transcriptase and a C-terminal YIG endonuclease were identified, suggesting recent activity. This was confirmed by the presence of very similar elements presenting 98–99% nucleotide identity. However, the high divergence between some copies (less than 60% nucleotide identity) showed the diversity and ancient origin of the group [...]. About 60 reverse transcriptase sequences were detected in the 41 Mb genome assembly.”

Pichon J, Luscombe NM, Plessy C.

F1000Res. 2019 Dec 10;8:2072. doi:10.12688/f1000research.21551.1

Widespread use of the "ascidian" mitochondrial genetic code in tunicates.

NCBI's table 13 is to be used for O. dioica. However, for longicauda and *chordaeus, the code might differ.

Inoue J, Nakashima K, Satoh N.

Genes (Basel). 2019 Apr 10;10(4). pii: E294. doi:10.3390/genes10040294

ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes.

A second GH6 gene (with no CesA domain) was found in Tunicates.

Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P.

Nucleic Acids Res. 2020 Jan 8;48(D1):D668-D675. doi:10.1093/nar/gkz955

ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.

First release of ANISEED with O. dioica in.

Onuma TA, Hayashi M, Gyoja F, Kishi K, Wang K, Nishida H.

Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4188-4198. doi:10.1073/pnas.1916858117

A chordate species lacking Nodal utilizes calcium oscillation and Bmp for left-right patterning.

“Descendant cells of the L- and R-cells were distributed asymmetrically throughout the organism, even in most morphologically symmetric organs.” “L- and R-cells in the two-cell embryo show stereotyped asymmetries in their cell fates; this is in contrast to ascidian and vertebrate embryos.” “Both oral glands [...] were L-descendants. In contrast, the subchordal cells, [...] were R-descendants. The oral gland and subchordal cells have been proposed to share an ontogenic origin, because only larvacean species with an oral gland have subchordal cells. However, our results suggest that these two cells had a different origin.” “Bmp.a expression was detected in 40% of the R-cells, but none of the L-cells.” “Ca2+ oscillation is required for Bmp.a expression.”

Frey K, Pucker B.

Cells. 2020 Feb 18;9(2). pii: E458. doi:10.3390/cells9020458

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites.

A bioinformatics screen confirms the increased use of GA/AG splicing in Oikopleura dioica and the copepod Eurytemora affinis, out of 489 animal species. In both cases, an extended consensus was found: AG|GAA/AG (vertical bar is end of exon).

Wada H, Satoh N.

Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1801-4 doi:10.1073/pnas.91.5.1801

Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA.

Source for the 18S sequence D14360 (Oikopleura sp, provenance not described). Primer sequences: 5'-CTGGTTGATCCTGCCAG-3' and 5'-CACCTACGGA(AT)ACCTTG-3'

Pedro Freitas de Carvalho; Sérgio Luiz Costa Bonecker

Braz. arch. biol. technol. vol.53 no.1 Curitiba Jan./Feb. 2010

Seasonal and spatial variability of appendicularian density and taxonomic composition in the Caravelas Estuary (Northeastern Brazil) and adjacent coastal area

“O. dioica was the most frequent and abundant species in all the samples.”

Galt, C.P., Sykes, P.F.

Mar. Biol. 77, 155–159 (1983). doi:10.1007/BF00396313

Sites of bioluminescence in the appendicularians Oikopleura dioica and O. labradoriensis (Urochordata: Larvacea).

Light is produced by the granular inclusions.

Øvrebø JI, Campsteijn C, Kourtesis I, Hausen H, Raasholm M, Thompson EM.

Cell Cycle. 2015;14(6):880-93. doi:10.1080/15384101.2015.1006000

Functional specialization of chordate CDK1 paralogs during oogenic meiosis.

”Differential spatiotemporal dynamics of the odCDK1a, d and e paralogs and the meiotic polo-like kinase 1 (Plk1) and aurora kinase determine the subset of meiotic nuclei in prophase I arrest that will seed growing oocytes and complete meiosis. Whereas we find odCDK1e to be non-essential, knockdown of the odCDK1a paralog resulted in the spawning of non-viable oocytes of reduced size. Knockdown of odCDK1d also resulted in the spawning of non-viable oocytes. In this case, the oocytes were of normal size, but were unable to extrude polar bodies upon exposure to sperm, because they were unable to resume meiosis from prophase I arrest, a classical function of the sole CDK1 during meiosis in other organisms.“

Ganot P, Moosmann-Schulmeister A, Thompson EM.

Dev Biol. 2008 Dec 15;324(2):266-76. doi:10.1016/j.ydbio.2008.09.016

Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura.

H3S28p signal grows becomes highest only in the subset of H2S10p-labeled oocytes that become selected for maturation. MAPK inhibition has a similar effect to microtubule destabilisation.

Atsuo Nishino, and Masaaki Morisawa

ZOOLOGICAL SCIENCE 15: 723–727 (1998) doi:10.2108/zsj.15.723

Rapid Oocyte Growth and Artificial Fertilization of the Larvaceans Oikopleura dioica and Oikopleura longicauda

Oikopleura (dioica and longicauda) sampled from Moroiso bay, Misaki, Miura peninsula and cultivated at 18 °C. In O. dioica, the first polar body is visible 5 min after fertilisation and the second polar body 15 min after fertilisation. O. longicauda individuals can self-fertilise. F. pellucida could not be in vitro fertilised with the same method.

Ganot P, Bouquet JM, Kallesøe T, Thompson EM.

Dev Biol. 2007 Feb 15;302(2):591-600 doi:10.1016/j.ydbio.2006.10.021

The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production.

The coenocyst is a syncytium containing nurse nuclei and meiotic nuclei surrounded by their cytoplasms and connected by ring channels. Figure 1p of spawned oocytes in cortical metaphase I shows 3 DNA masses. Germline-specific expression of Vasa.

Barham EG.

Science. 1979 Sep 14;205(4411):1129-31 doi:10.1126/science.205.4411.1129

Giant larvacean houses: observations from deep submersibles.

Abundances as high as one per cubic meter reported at depth of 25 to 50 m in pelagic waters near the western middle American coast.

Galt, Charles P.

Fishery Bulletin 1979, 77(2), pp514–9

First records of a giant pelagic tunicate, Bathochordaeus charon (Urochordata, Larvacea), from the eastern Pacific Ocean, with notes on its biology

https://www.st.nmfs.noaa.gov/spo/FishBull/77-2/772toc.html

https://www.st.nmfs.noaa.gov/spo/FishBull/77-2/galt.pdf

Specimens collected at 500 m depth in Isaacs-Kidd midwater trawls (California).

Syst Biol. 2000 Mar;49(1):52-64 doi:10.1080/10635150050207384

Swalla BJ, Cameron CB, Corley LS, Garey JR.

Urochordates are monophyletic within the deuterostomes.

Places appendicularians as sister to all other tunicates, but notes that long branches raise uncertaincies.

J Mol Evol. 2008 Dec;67(6):594-607. doi:10.1007/s00239-008-9149-6

Marz M, Kirsten T, Stadler PF.

Evolution of spliceosomal snRNA genes in metazoan animals.

”The snRNAs of the minor spliceosome were in most cases single-copy genes.” The minor spliceosome was not found in Oikopleura dioica, but it was found in Ciona. “SnRNA locations are not syntenically conserved, i.e., snRNA behave like mobile elements in their genomic context.”

Curr Biol. 2019 Oct 7;29(19):3193-3199.e4. doi:10.1016/j.cub.2019.07.092

Henriet S, Colom Sanmartí B, Sumic S, Chourrout D.

Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis.

In Fritillaria borealis, most ancestral GT/AG canonical introns were lost. New AG/AR introns with non-canonical splice sites were created by the insertion of MITEs (miniature inverted-repeat transposable elements) after TA sites. Splicing of non-canonical introns can be inhibited with Pladienolide B. Non-canonical introns of F. bor and O. dioica genes can not be spliced in HEK293T cells, but canonical introns can. In ~90% of lariats from F. bor or O. dio, the branchpoint is an A. Distance to 3′ splice site is similar in both species. A single U2 spliceosome was found in F. bor.

Mol Biol Evol. 2012 Feb;29(2):487-502. doi:10.1093/molbev/msr136

Campsteijn C, Ovrebø JI, Karlsen BO, Thompson EM.

Expansion of cyclin D and CDK1 paralogs in Oikopleura dioica, a chordate employing diverse cell cycle variants.

to_read

Capitanio FL, Daponte MC and Esnal GB.

Antarctic Science 15 (4): 476–482 (2003) doi:10.1017/S0954102003001585

The classification of Antarctic appendicularians: the Oikopleura gaussica group

Proposes that O. gaussica, O. valdiviae, O. drygalskii, and O. weddelli actually form a single species. It has oral gland cells, and a variable (8~14) number of subchordal cells, on the right (ventral) side of the tail.

Robert Fenaux

Journal of the Marine Biological Association of the United Kingdom. Volume 73, Issue 3, August 1993, pp. 635-646

A new genus of midwater appendicularian: Mesoikopleura with four species

Sampled at 700-900 m depth. No buccal glands. Trunk sizes 740~1400 µm. Tail sizes of 7200~8750 µm. Either numerous small amphicordal cells on both sides of the tail (M. enterospira, M. youngbluthi) or seven (4+3) fusiform amphicordal celss (gyroceanis). Splits Oikopleurinae into two groups according to the presence or absence of buccal lips: Alabiata and Labiata.

Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A.

Dev Suppl. 1994:125-33.

Gene duplications and the origins of vertebrate development.

Attempt to clone Hox genes with degenerate primers only yielded one clone.

Flood, P. R.

MEPS 71:291-295

Yellow-stained oikopleurid appendicularians are caused by bacterial parasitism

Rod-shaped (0.6 or 0.4 µm-wide) bacteria observed by transmission and electron microscopy in O. dioica and O. vanhoeffeni

Guillermo Aravena & Sergio Palma

Rev. chil. hist. nat. v.75 n.2 Santiago jun. 2002

Taxonomic identification of appendicularians collected in the epipelagic waters off northern Chile (Tunicata, Appendicularia)

O. dioica and many other appendicularians found near northern Chile. Detailed taxonomical descriptions.

Riki Sato, Yuji Tanaka, Takashi Ishimaru

Journal of Plankton Research, Volume 23, Issue 4, April 2001, Pages 415–423, doi:10.1093/plankt/23.4.415

House Production by Oikopleura dioica (Tunicata, Appendicularia) Under Laboratory Conditions

Generation time of Tôkyô bay's O. dioica: 6 days at 15°C, 4 days at 20°C and 3 days at 25°C. Fed with I. galbana and Tetraselmis sp. Individuals produced ~50 houses in their life. Higher temperature increases house production (from ~0.5 / h at 15°C to ~ 0.8 / h at 25 °C. Artificial clogging with the diatom Ditylum increased house renewal..

La couche öikoplastique de l'Appendiculaire Oïkopleura albicans (Leuckart) (Tunicata)

Morph. Tiere (1971) 69: 184. https://doi.org/10.1007/BF00280746

Fenaux, R. Z.

À lire

Charles P. Galt, Matthew S. Grober and Paul F. Sykes

The Biological Bulletin 168, no. 1 (February 1985): 125-134.

Taxonomic correlates of bioluminescence among appendicularians (urochordata: larvacea)

Bioluminescence stimulated by agitation. Field-collected houses of species that lack oral glands also sometimes emit light, possibly because of bioluminescent dinoflagellates. O. dioica has oral glands and bioluminescent rudiment inclusions. Neither O. longicauda nor Bathochordaeus charon have oral glands and bioluminescence. O. dioica not as abundant as other oiks in the Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature = 30 °C; night dives).

Choy CA, Robison BH, Gagne TO, Erwin B, Firl E, Halden RU, Hamilton JA, Katija K, Lisin SE, Rolsky C, S Van Houtan K.

Sci Rep. 2019 Jun 6;9(1):7843. doi: 10.1038/s41598-019-44117-2.

The vertical distribution and biological transport of marine microplastics across the epipelagic and mesopelagic water column.

“The number of microplastic particles contained within a [Bathochordaeus] sinker ranged from 3 to 17 (mean 10.7 microplastic particles ± 5.3 particles standard deviation).”

Robison BH, Reisenbichler KR, Sherlock RE.

Science. 2005 Jun 10;308(5728):1609-11 doi:10.1126/science.1109104

Giant larvacean houses: rapid carbon transport to the deep sea floor.

Bathochordaeus species may produce one house per day. Sinking houses are an important contribution to the carbon flux to the sea floor.

María Delia Viñas, Rubén Mario Negri, Georgina Daniela Cepeda, Daniel Hernández, Ricardo Silva, María Cristina Daponte & Fabiana Lía Capitanio

Marine Biology Research, 2013 Vol. 9, No. 4, 371—382, http://dx.doi.org/10.1080/17451000.2012.745003

Seasonal succession of zooplankton in coastal waters of the Argentine Sea (Southwest Atlantic Ocean): prevalence of classical or microbial food webs

O. dioica found all year near Mar del Plata in 2000—1, where it was most abundant in summer.

Russell R. Hopcroft, John C. Roff

Journal of Plankton Research, Volume 20, Issue 3, 1998, Pages 557–569, doi:10.1093/plankt/20.3.557

Production of tropical larvaceans in Kingston Harbour, Jamaica: are we ignoring an important secondary producer?

O. longicauda was usually more abundant than O. dioica.

伊藤,栄樹/飯塚,昭二 (Itoh, Hideki / Iizuka, Shoji)

大村湾における動物プランクトンに関する研究―II 輪虫類,枝角類,矢虫類,尾虫類および底生生物幼生の季節的出現

Studies on the Zooplankton in Omura Bay―II Seasonal Occurrences of Rotatoria, Cladocera, Sagittoidea, Appendiculata and Benthos Larvae

長崎大学水産学部研究報告, v.49, pp.1-10; 1980

[[!handle 10069/30542 desc="O. dioica found in the Omura (Nagasaki) bay."]]

Nakamura, Y.

Hydrobiologia (1998) 385: 183. doi:10.1023/A:1003531812536

Blooms of tunicates Oikopleura spp. and Dolioletta gegenbauri in the Seto Inland Sea, Japan, during summer

O. dioica was dominant in a first bloom, but O. longicauda dominated the second one. Population decrease between the blooms might have been caused by predation by anchovy larvae.

Russell R.Hopcroft and Bruce H.Robison

Journal of Plankton Research, Volume 21, Issue 10, 1 October 1999, Pages 1923–1937, doi:10.1093/plankt/21.10.1923

A new mesopelagic larvacean, Mesochordaeus erythrocephalus, sp. nov., from Monterey Bay, with a description of its filtering house

House is ~30cm ø; ~2 tail beats per s. Heavily pigmented digestive tract. “Although we are inclined to ally this genus most closely to Bathochordaeus, we note several features that raise questions with regard to its placement within the subfamily Bathochordaeinae (represented only by the genus Bathochordaeus) as opposed to the Oikopleurinae.”

Ayla J. Doubleday, Russell R. Hopcroft

Journal of Plankton Research, Volume 37, Issue 1, January/February 2015, Pages 134–150

Interannual patterns during spring and late summer of larvaceans and pteropods in the coastal Gulf of Alaska, and their relationship to pink salmon survival

“Across seasons, O. labradoriensis and F. borealis abundance were negatively related to temperature.” “O. dioica occurred in highest abundance during late summer relative to spring. During this time, O. dioica abundance was positively related to temperature and chlorophyll-a, but negatively related to salinity, and had a maximum abundance at nearshore stations.” “When season and year were pooled, the 150-µm net collected 34% of the abundance that the 53-µm net collected for Oikopleura spp., 34% of the abundance for Fritillaria spp. and 30% of the abundance for L. helicina. If we assume, time-of-day has no impact on the distribution of either group (i.e. no diel vertical migrations), then the 505-µm net captures 10% of the 53-µm net.” “The 505-µm mesh nets indicate that Oikopleura spp. had highest abundance at the surface”

Proc Natl Acad Sci U S A. 2008 May 20;105(20):7229-34. doi:10.1073/pnas.0710196105

Stach T, Winter J, Bouquet JM, Chourrout D, Schnabel R.

Embryology of a planktonic tunicate reveals traces of sessility.

“Clonal organization of the tissues is essentially invariant among individuals”

Dev Biol. 2019 Jun 1;450(1):9-22. doi:10.1016/j.ydbio.2019.03.006

Mikhaleva Y, Tolstenkov O, Glover JC.

Gap junction-dependent coordination of intercellular calcium signalling in the developing appendicularian tunicate Oikopleura dioica.

Calcium waves observed with GCaMP6. Each wave is preceded by a “minipeak”. Two connexins (CxA and CxB) are expressed during embyogenesis. ”Knockdown of both CxA and CxB mRNA severely disrupts Ca2+ wave propagation and thereby also synchronization.“

P. V. Bhavanarayana, P. N. Ganapati

Proceedings of the Indian Academy of Sciences - Section B (1972) 75: 1.

Distribution of pelagic tunicates in the western part of the Bay of Bengal

O. dioica reported in the bay of Bengal.

Tokioka, Takasi

Seto Mar. Biol. Lab., 1960, 3, 130–221.

Studies on the distribution of appendicularians and some thaliaceans of the North Pacific, with some morphological notes.

Multiple records of O. dioica in the North Pacific.

Cell Cycle. 2019 Jul 15:1-20. doi:10.1080/15384101.2019.1634954

Feng H, Raasholm M, Moosmann A, Campsteijn C, Thompson EM.

Switching of INCENP paralogs controls transitions in mitotic chromosomal passenger complex functions.

Components of the constitutive centromere-associated network (CCAN) at the inner kinetochore seem to be missing in the genome. H3T3p and H3S28p mark inner centromeric regions (single spots) and H3T11p mark outer centromeric regions (pairs of spots). Fluorescent microscopy pictures supporting a 2 × 3 karyotype.

PLoS One. 2014 Apr 2;9(4):e93787. doi:10.1371/journal.pone.0093787

Subramaniam G, Campsteijn C, Thompson EM.

Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry.

Growth arrest (GA) discovered by culturing animals in crowded conditions, but can also be striggered by reduction of food intake before D4. After that, starvation reduces the number of gametes produced instead of inducing GA. In GA, cell cycle stops in both the somatic and germ lines. GA can also be induced by the TOR inhibitor CCI-779. Animals in GA can survice up to ~18 days at 15°C.

LI Kaizhi, YIN Jianqiang, HUANG Liangmin, LIAN Shumin and ZHANG Jianlin

Acta Oceanol. Sin. (2012) 31: 135. https://doi.org/10.1007/s13131-012-0243-7 Oikopleura

Distribution patterns of appendicularians and copepods and their relationship on the northwest continental shelf of South China Sea during summer

The most frequent appendicularians in northern south China sea were O. longicauda and O. rufescens, before O. dioica.

Shih-Hui Hsiao, Samba Kâ Tien-Hsi Fang and Jiang-Shiou Hwang

Hydrobiologia (2011) 666:317–330

Zooplankton assemblages as indicators of seasonal changes in water masses in the boundary waters between the East China Sea and the Taiwan Strait

High abundance (>30%) of appendicularians in spring 2005 in the low-temperature, high-salinity surface waters of North-East coastal Taiwan stations. (Temperatures were low in comparison with autumn, but high in comparison with the other stations in spring.

Samba Kâ and Jiang-Shiou Hwang

Zoological Studies 50(2): 155-163 (2011)

Mesozooplankton Distribution and Composition on the Northeastern Coast of Taiwan during Autumn: Effects of the Kuroshio Current and Hydrothermal Vents

2 stations in coastal Northern Taiwan and 5 near Kueishan island and its vent(s) were sampled in Sept 2009. In average, O. ruf > O. dio > O. lon but this varies by station. Statio 7 (close to a vent) is a diversity hotspot.

http://zoolstud. sinica. edu. tw/Journals/50.2/155. pdf

Franco, P., Chen, H. & Liu, G. J.

J. Ocean Univ. China (2014) 13: 782. https://doi.org/10.1007/s11802-014-2376-0

Distribution and abundance of pelagic tunicates in the North Yellow Sea

O. dioica and O. longicauda found throurought the 2006-2007 sampling year in the Yellow sea. Abundance peaked in spring and was minimal in winter, where water temperature could be lower than 10 °C.

Pietro Franco, HongJu Chen, Jiang Shiou Hwang.

Zoological Studies 55: 28 (2016). doi:10.6620/ZS.2016.55-28

Taxonomic Composition and Seasonal Distribution Changes of Pelagic Tunicates in the Waters Off Nuclear Power Plants in Northern Taiwan in Relation to Environmental Conditions.

O. dioica found in North-East taiwanese cosatal waters in 2014-2015, most abundant in summer and always the most abundant appendicularian. No impact of the power plants was found.

P. Franco, H.-U. Dahms, W.-T. Lo & J.-S. Hwang

Journal of Natural History, 2017, 51:15-16, 917-936, DOI:10.1080/00222933.2017.1293180

Pelagic tunicates in the China Seas

O. dioica is found coastal areas all around Taiwan and was most abundant in 6/7 sampling sites.

Paolo Burighel, Carlo Brena, Gian Bruno Martinucci, Francesca Cima

Invertebrate Biology, 120: 278-293. doi:10.1111/j.1744-7410.2001.tb00038.x

Gut ultrastructure of the appendicularian Oikopleura dioica (Tunicata)

“We propose the following hypothesis for food processing in the alimentary canal. Absorption of material digested by the enzymes of the gastric band begins in the left lobe of the stomach. In the globular cells, endocytosis of macromolecules may occur, followed by intracellular digestion. Absorption continues in the right lobe of the stomach, where the ciliated microvillar cells store material in the form of lipid droplets. In the stomach, food is wrapped in a peritrophic membrane secreted by the epithelium, and fecal pellets form in the vertical intestine. These pellets advance through the intestine, while absorption continues in the ciliated microvillar and rectal globular cells; proteins are stored in the rectum. The gut epithelium might also be involved in ion and liquid transport for absorption and/or osmoregulation of internal fluid.”

Histone variant innovation in a rapidly evolving chordate lineage.

BMC Evol Biol. 2011 Jul 15;11:208. doi: 10.1186/1471-2148-11-208.

Moosmann A, Campsteijn C, Jansen PW, Nasrallah C, Raasholm M, Stunnenberg HG, Thompson EM.

“47 histone genes (6 H4, 10 H3, 15 H2A, 11 H2B and 5 H1 genes) encoding 31 different histone proteins (2 H4, 6 H3, 11 H2A, 7 H2B and 5 H1) were identified.” “There is no H2AX homolog in O. dioica.” (H2AX is implicated in DNA repair). CenH3 is present.

Kimura S, Ohshima C, Hirose E, Nishikawa J, Itoh T.

Protoplasma. 2001;216(1-2):71-4.

Cellulose in the house of the appendicularian Oikopleura rufescens.

Electron diffraction analysis found highly crystalline cellulose Iβ.

Spada F, Chioda M, Thompson EM.

J Cell Biochem. 2005 Aug 1;95(5):885-901. doi:10.1002/jcb.20416

Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles.

Knobs are also seem to be in H4K20me2. In endocycling cells, H4K20me2 tends to be stronger in BrdU-negative (short pulse) cells. CldU/IdU staining confirms that H4K20me2 decreases during the S phase of endocycling cells. In mitotically cycling cells, BrdU-low cells tended to be H4K20me2-weak. Strong H3S28p and H3S10p staining (M phase markers) correlated with strong H4K20me2 staining. In NIH3T3 cells, H4K20me2 peaks at M phase and then decreases from G1 to G2. H4K16Ac stainings were not reproducible across antibodies.

Chromosome Res. 2005;13(1):57-72 doi:10.1007/s10577-005-6845-6

Spada F, Vincent M, Thompson EM.

Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin.

“Knobs” of heterochromatin, prominently visible in endocycling nuclei, are mildly enriched for H3K9me2 and H42K20me2 and 5mC, enriched for H3K4me4, highly enriched for H3K9me3 and depleted in H4K8Ac and H3K4me2 and elongating RNA Polymerase II. “Inhibition of polII transcription in NIH3T3 cells does not diminish global levels of H3 Me3K4 and results in increased H3 Me3K4 labelling in pericentromeric chromatin.”

Biol Cell. 2007 May;99(5):273-87 doi:10.1042/BC20060124

Spada F, Koch J, Sadoni N, Mitchell N, Ganot P, De Boni U, Zink D, Thompson EM.

Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura.

“[In endocycling cells,] simultaneous staining of DNA, RNA and membranes showed [...] deep invaginations of the nuclear envelope.” “O. dioica endocycling nuclei showed no polytenization or in loco gene amplification.” “An oikosin 6 probe [indicated] a family of related genes at multiple loci. Oikosin 4 and 6 were physically linked in a number of BAC clones.” “[Antibodies against splicing factors] failed to detect speckles in O. dioica endocycling nuclei and no interchromatin cluster granules were observed in the TEM images, suggesting these nuclei lack prominent splicing-factor domains.”

Ganot P, Kallesøe T, Thompson EM.

Dev Biol. 2007 Feb 15;302(2):577-90 doi:10.1016/j.ydbio.2006.10.022

The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura.

In early meiotic nuclei, telomeres and nuclear pore complexes ”cluster in non-overlapping regions of the nuclear envelope”. During some stages of oocyte maturation, the telomeres of the endocycling nurse cells “clustered at the nuclear periphery, in a compartment with no detectable elongating RNA polymerase II”. Colchicine treatment induced early oocyte differenciation. Used rabbit polyclonal anti-histone H3 phospho-serine 10 (H3S10P) from Upstate, cat. num. 06-570.

Chromosome Res. 2007;15(2):189-201. doi:10.1007/s10577-006-1112-z

Schulmeister A, Schmid M, Thompson EM.

Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica.

Telomeric FISH stainings with a (TTAGGG)n probe. H3.3S31 is phosphorylated during mitosis and meiosis, and not in endocycling cells. “On prometaphase chromosomes [...] H3S28P was restricted to distal chromosomal regions adjacent to telomeres whereas H3.3S31P spread throughout entire chromosomes.” “[The histone 3.3 genes] contain introns, are found outside histone clusters and their transcripts are polyadenylated.”

Chioda M, Eskeland R, Thompson EM.

Mol Biol Evol. 2002 Dec;19(12):2247-60 doi:10.1093/oxfordjournals.molbev.a004048

Histone gene complement, variant expression, and mRNA processing in a urochordate Oikopleura dioica that undergoes extensive polyploidization.

“Densitometric analyses of Southern blots yielded estimates of 9–11 H4 genes, 11–14 H3 genes, 15–19 H2A genes, 18–20 H2B genes, and 4–7 H1 genes.” “The quintet cluster consisted of a central H1 gene flanked by divergently transcribed H3-H4 and H2A-H2B pairs, an organization found in other organisms such as humans. The quintet cluster is extremely compact, covering only 3.5 kb.” “Both visual inspection and PRATT analysis (Jonassen 1997 ) of the sequences 3′ to the conserved stem-loop revealed no consensus 3′ purine-rich histone downstream element (HDE) that interacts with U7 snRNA in the processing of histone mRNAs. In fact, no consensus sequence or pattern motif of any kind was discovered 3′ of the stem-loop in O. dioica histone gene sequences.”

Coppola U, Ristoratore F, Albalat R, D'Aniello S.

Cell Mol Life Sci. 2019 Apr 26. doi:10.1007/s00018-019-03103-7

The evolutionary landscape of the Rab family in chordates.

“O. dioica lineage showed 11 additional losses, Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, Rasef, EFcab4/Rab44 and RabX1. This species has, therefore, lost almost the 50% of the Rab toolkit, being the metazoan species with the smallest number of Rab subfamilies described so far.” “We detected [...] 5 independent duplications in O. dioica (Rab5/17, Rab6, Rab7, Rab10, Rab35).” O. dioica lost the Rab-EF chimeras Rasef and EFcab4/44, but kept Rab46.

Dev Biol. 2018 Sep 11. pii: S0012-1606(17)30888-6. doi:10.1016/j.ydbio.2018.09.003

Almazán A, Ferrández-Roldán A, Albalat R, Cañestro C.

Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates.

7 actins: 4 muscular that have the same common ancestor with all muscular actins from other species, and 3 cytoplasmic ones.

Bassham S and Postlethwait J.

Dev Biol. 2000 Apr 15;220(2):322-32 DOI:10.1006/dbio.2000.9647

Brachyury (T) expression in embryos of a larvacean urochordate, Oikopleura dioica, and the ancestral role of T.

O. dioica contains a single ortholog of Brachyury (T, TBXT). Early expression appears restricted to notochord precursors. Later, subchordal cells, and even later, hindgut cells also express TBXT. Translated cDNA sequence was deposited under accession number AAG22592.

King, K.R., Hollibaugh, J.T. & Azam, F.

Mar. Biol. (1980) 56: 49–57. doi:10.1007/BF00390593

Predator-prey interactions between the larvacean Oikopleura dioica and bacterioplankton in enclosed water columns

“Apparently, O. dioica has minimal influence on the population dynamics of the free-living bacteria, although bacteria may form a substantial portion of the larvacean's diet.”

Sakiko Orui Sakaguchi, Tetsuro Ikuta, Gen Ogawa, Kodai Yamane, Naonobu Shiga, Hiroshi Kitazato, Katsunori Fujikura, Kiyotaka Takishita.

Fish Sci (2017) 83: 757. https://doi.org/10.1007/s12562-017-1106-0

Morphological identity of a taxonomically unassigned cytochrome c oxidase subunit I sequence from stomach contents of juvenile chum salmon determined using polymerase chain reaction

Finds that the COI sequence AY116609 and the 18S sequence AB013014 are probably mis-labled.

PLoS One. 2017 Apr 14;12(4):e0175851. doi:10.1371/journal.pone.0175851

Algueró-Muñiz M, Alvarez-Fernandez S, Thor P, Bach LT, Esposito M, Horn HG, Ecker U, Langer JAF, Taucher J, Malzahn AM, Riebesell U, Boersma M.

Ocean acidification effects on mesozooplankton community development: Results from a long-term mesocosm experiment.

Concludes that “the Gullmar Fjord mesozooplankton community structure is not expected to change much under realistic end-of-century OA [ocean acidification] scenarios as used here”. Data submitted to PANGEA includes Oikopleura abundance. https://doi.pangaea.de/10.1594/PANGAEA.871233

Sherlock RE, Walz KR, Schlining KL, Robison BH.

Mar Biol. 2017;164(1):20. doi:10.1007/s00227-016-3046-0

Morphology, ecology, and molecular biology of a new species of giant larvacean in the eastern North Pacific: Bathochordaeus mcnutti sp. nov.

B. mcnutti are 3–10 cm long. Their tails have a blue outline. Gravid individuals descend as low as 800 m, but spawning is thought to happen above 100 m. The CO1 gene is ~12% different between B. mcnutti and B. strygius.

Endy Spriet

1997, Master thesis, the University of Bergen.

Studies on the house building epithelium of Oikopleurid appendicularia (Tunicata): Early differentiation and description of the adult pattern of oikoplast cells

High-resolution pictures of nuclear stains of O.labradoriensis, O. vanhoeffeni, O. dioica, O. villafrancae and O. albicans.

Naville M, Henriet S, Warren I, Sumic S, Reeve M, Volff JN, Chourrout D.

Curr Biol. 2019 Mar 2. pii: S0960-9822(19)30139-3. doi:10.1016/j.cub.2019.01.080

Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements.

Larger genomes found in larger species. No evidence for genome duplication. Transposable element density correlated with genome size. SINEs (short interspersed nuclear elements) and MITEs (miniature inverted transposable elements) account for most of the TE expansion. Ancestor is likely to have had a small genome.

Kaj Holmberg and Ragnar Olsson

Vidensk. Meddr. dansk naturh. Foren. (1984) 145:43—52 (no DOI found)

The origin of Reissner's fibre in an appendicularian, Oikopleura dioica

The Reissner's fiber in O. dioica is produced by a single ”fibrogen” cell. Electron microsocopy of this cell show a large perikaryon, cisternas, and a single cilium, which is inserted in the central canal.

Berná L and Alvarez-Valin F.

Mar Genomics. 2015 Dec;24 Pt 1:47-54. doi:10.1016/j.margen.2015.07.007

Evolutionary volatile Cysteines and protein disorder in the fast evolving tunicate Oikopleura dioica.

O. dioica proteins are shorter and proportionally less disordered than in other chordates. Correlation between presence of cysteines (thought to be stabilising) and disorder is lower in O. dioica. Cysteines in ordered domains are also less conserved in O dioica compared to other chordates.

Olsson R.

(1993). Book chapter in Oksche A., Rodríguez E.M., Fernández-Llebrez P. (eds) The Subcommissural Organ. Springer, Berlin, Heidelberg. pp 33—39

Reissner’s Fiber Mechanisms: Some Common Denominators.

Figure 2 panel 6 schematises Oikopleura's fibrogen cell.

Neuroscience. 1999 Jan;88(2):655-64 doi:10.1016/S0306-4522(98)00252-8

Gobron S, Creveaux I, Meiniel R, Didier R, Dastugue B, Meiniel A.

SCO-spondin is evolutionarily conserved in the central nervous system of the chordate phylum.

A Southern blot suggests the presence of a gene encoding a SCO-spondin in Oikopleura.

Berná L, D'Onofrio G, Alvarez-Valin F.

Mol Phylogenet Evol. 2012 Feb;62(2):708-17. doi:10.1016/j.ympev.2011.11.013

Peculiar patterns of amino acid substitution and conservation in the fast evolving tunicate Oikopleura dioica.

Faster evolution for regulatory genes. High and even mutation rates for every aminoacid suggest a relaxation of functional constraints. This is particularly surpising for cystein, which is highly conserved in other fast-evolving species such as Ciona. The frequency of C is reduced of 10% compared with Ciona.

Berná L and Alvarez-Valin F.

Genome Biol Evol. 2014 Jul 8;6(7):1724-38. doi:10.1093/gbe/evu122

Evolutionary genomics of fast evolving tunicates.

Parallel review about genome compaction in Ciona and Oikopleura.

N. Mojib, M. Thimma, M. Kumaran, R. Sougrat and X. Irigoien

Limnology and Oceanography. Volume 62, Issue 1, January 2017, Pages 299-310

Comparative metatranscriptomics reveals decline of a neustonic planktonic population

Decrease of appendicularians and copeopds during a Trichodesmium in the Red sea in 2012.

Kiyotaka Hidaka

Plankton and Benthos Research 2008 Volume 3 Issue 3 Pages 152-164

Species composition and horizontal distribution of the appendicularian community in waters adjacent to the Kuroshio in winter–early spring

In 1972, 1976, 1977, 1978, 1982 or 1986, O. dioica was rare but relatively more abuntant in slope waters, which are colder (~15—17°C) as opposed to oceanic area Kuroshio (18.5–20.0°C) or subtropical waters (similar temperatures as Kuroshio).

Journal of Experimental Marine Biology and Ecology Volume 189, Issues 1–2, 28 June 1995, Pages 1-11

Shin-ichi Uye and Seiko Ichino

Seasonal variations in abundance, size composition, biomass and production rate of Oikopleura dioica (Fol) (Tunicata: Appendicularia) in a temperate eutrophic inlet

Reproduction all year (mature stages detected in winter). Trunk length higher in winter than in summer.

Nakashima K, Yamada L, Satou Y, Azuma J, Satoh N.

Dev Genes Evol. 2004 Feb;214(2):81-8.

The evolutionary origin of animal cellulose synthase.

The cellulose synthase genes in Tunicates are thought to be of actinobacterial origin, because the tunicate CesA gene contains two domains with similarity with a cellulose synthase and a cellulase of the glycoside hydrolase (GH)-6 family, and these genes are often found in proximity in actinobacteria.

Wang K, Omotezako T, Kishi K, Nishida H, Onuma TA.

Dev Genes Evol. 2015 Jun;225(3):149-59. doi:10.1007/s00427-015-0502-7

Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.

Only one splice leader was found and it was identical to the one reported by Ganot. “Samples were prepared from cohorts of a single pair.” “The transcript sequences showed a high degree of variability between the Japanese and Norwegian O. dioica populations. The average degrees of nucleotide and amino acid sequence conservation were 91.0 and 94.8 %, respectively.” “In the present analysis, the SL was observed in 40.8 % of mRNA species. It showed preferential linkage to adenine at the 5′ ends of the downstream exons. Intriguingly, the trans-splicing occurs more frequently in eggs than in larvae.” “Among the 12,311 assembled transcripts, 63 and 99 % were detected in eggs and larvae, respectively. Thus, the mRNAs of most of genes are present at the developing larval stage. In this quick developer, it is most probable that residual maternal mRNAs are still preserved in 8 hpf larvae.” “The raw data were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (SRP accession number: SRP050571, run accession numbers are SRR1693762, SRR1693765, SRR1693766, and SRR1693767) and Gene Expression Omnibus (GEO accession: GSE64421).”

Castellanos I.A., Morales-Ramírez Á., Suárez-Morales E.

In: Wehrtmann I.S., Cortés J. (eds) Marine Biodiversity of Costa Rica, Central America. Monographiae Biologicae, vol 86. Springer, Dordrecht

Appendicularians (Urochordata)

O. dioica not reported in Costa Rica, but presence considered plausible.

Mol Ecol. 2014 Jun;23(11):2740-56. doi:10.1111/mec.12781

Mojib N, Amad M, Thimma M, Aldanondo N, Kumaran M, Irigoien X.

Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia.

Mass spectrometry shows that astaxanthin is the main carotenoid pigment in O. dioica. β‐carotene is probably taken from the food chain. Two cytochrome P450 β‐carotene hydroxylase genes were identified (CBY21750 and CBY13480) and may be involved in the conversion to astaxanthin. Three carotenoid‐binding proteins from the lipocalin family were found in the genome, and may be implicated in providing blue color by binding to astaxanthin.

Curr Biol. 2005 Jan 11;15(1):R12-3 doi:10.1016/j.cub.2004.12.010

Edvardsen RB, Seo HC, Jensen MF, Mialon A, Mikhaleva J, Bjordal M, Cartry J, Reinhardt R, Weissenbach J, Wincker P, Chourrout D.

Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica.

O. dioica has 83 homeobox genes. Lost groups of genes do not fully overlap between O. dioica and C. intestinalis, suggesting a larger common core in the ancestral tunicate.

Janice Lawrence, Joachim Töpper, Elżbieta Petelenz‐Kurdziel, Gunnar Bratbak, Aud Larsen, Eric Thompson, Christofer Troedsson and Jessica Louise Ray

Limnol. Oceanogr. 63, 2018, S244–S253

Viruses on the menu: The appendicularian Oikopleura dioica efficiently removes viruses from seawater

O. dioica can filter, ingest and defecate the Emiliania huxleyi virus, but it is yet unclear if it is digested.

Proc Biol Sci. 2018 May 16;285(1878). pii: 20180056. doi:10.1098/rspb.2018.0056

Conley KR, Lombard F, Sutherland KR.

Mammoth grazers on the ocean's minuteness: a review of selective feeding using mucous meshes.

Review on marine filter feeders.

Sci Adv. 2017 Aug 16;3(8):e1700715. doi:10.1126/sciadv.1700715

Katija K, Choy CA, Sherlock RE, Sherman AD, Robison BH.

From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea.

B. stygius fed with microplastic particles.

Sci Adv. 2017 May 3;3(5):e1602374. doi:10.1126/sciadv.1602374

Katija K, Sherlock RE, Sherman AD, Robison BH.

New technology reveals the role of giant larvaceans in oceanic carbon cycling.

DeepPIV, particule image velocimetry in the deep see using laser sheet illumination. B. stygius and mcnutti specimens with tail lenght ranging between 2.2 and 2.9 cm can filter between 22 and 76 liters per hour.

Sci Rep. 2018 Jun 14;8(1):9106. doi:10.1038/s41598-018-27509-8

López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J.

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity.

28% of the RNA reads in the oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian. rRNA sequences with no known homologs suggest a new group of tunicates, “MAME 1”. However, given very long branches in the phylogenetic tree, this finding needs to be confirmed.

Commun Biol. 2018 Aug 24;1:121. doi:10.1038/s42003-018-0127-2

Torres-Águila NP, Martí-Solans J, Ferrández-Roldán A, Almazán A, Roncalli V, D'Aniello S, Romano G, Palumbo A, Albalat R, Cañestro C.

Diatom bloom-derived biotoxins cause aberrant development and gene expression in the appendicularian chordate Oikopleura dioica

Polyunsaturated aldehydes released by diatoms impair the development of O. dioica by delaying the onset of expression of developmental genes. Cell proliferation is not affected and “defensome” genes such as Aldh genes or Gclm (Glutamate-cysteine ligase modifier) are induced by the toxins. Chaetoceros calcitrans, a diatom used as food when culturing O. dioica, is also shown to have a toxic effect.

Dhugal Lindsay, Mitsuko Umetsu, Mary Grossmann, Hiroshi Miyake, Hiroyuki Yamamoto

Subseafloor Biosphere Linked to Hydrothermal Systems pp 639-666, 08 November 2014

The Gelatinous Macroplankton Community at the Hatoma Knoll Hydrothermal Vent

Oikopeuridae found in the deep sea. One Bathochordaeus had a ~2m-big house.

R. E. Sherlock, K. R. Walz and B. H. Robison

Marine Biodiversity Records 2016 9:79 doi:10.1186/s41200-016-0075-9

The first definitive record of the giant larvacean, Bathochordaeus charon, since its original description in 1900 and a range extension to the northeast Pacific Ocean

“In over two decades of exploring the mesopelagic waters of Monterey Bay, CA, remarkably few Bathochordaeus charon (n = 15) were observed, while thousands of B. stygius have been encountered.” Accession number for 18S rRNA: KT881545

P. R. Flood

Marine Biology October 1991, Volume 111, Issue 1, pp 95–111

Architecture of, and water circulation and flow rate in, the house of the planktonic tunicate Oikopleura labradoriensis.

Estimates that 35 ml of water are filtered each hour.

Dev Biol. 2014 Nov 15;395(2):299-306. doi:10.1016/j.ydbio.2014.09.006

Kishi K, Onuma TA, Nishida H

Long-distance cell migration during larval development in the appendicularian, Oikopleura dioica.

The oral gland precursor is a syncytium with 4 nuclei that migrates anteriorly. The two differentiated oral gland cells have two nuclei each, as demonstrated by a co-staining of nuclei (H2B-mCherry) and cell membrane (PH-YF). The endodermal strand is the strand of 16 cells that lie in a single line. The endodermal cells strand migrate from the tail to the trunk and give rise to the posterior part of the digestive tract (rectum), but not the anus. Removal of the trunk suggests that it is not necessary for initiation of the migration. The subchordal cell precursors migrate along the right side of the notochord in the space that has been filled with endodermal strand cells. Amputation experiments indicate that the posterior portion of the tail is required for posterior migration of subchordal cell precursors.

Acta Zoologica Volume 72, Issue 4 December 1991, Pages 251-256

G. Fredriksson and R. Olsson

The Subchordal Cells of Oikopleura dioica and O. albicans (Appendicularia, Chordata)

The subchordal cells display considerable variability of ultrastructure, which might be explained by the alternation between highly exocytic and highly endocytic stages. O. dioica has two subchordal cells; O. albicans has “a multitude of quite small subchordal cells” with “essentially the same cytology”.

Niimura Y.

Genome Biol Evol. 2009 Apr 30;1:34-44. doi:10.1093/gbe/evp003

On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species.

No ORs found in Oikopleura or Ciona

Christofer Troedsson, Jean-Marie Bouquet, Dag L. Aksnes and Eric M. Thompson

Mar Ecol Prog Ser Vol. 243: 83–91, 2002 Published November 13

Resource allocation between somatic growth and reproductive output in the pelagic chordate Oikopleura dioica allows opportunistic response to nutritional variation.

Defines four phases of development that transition with inflating the first house, growing the reproductive organ, and spawning. In phase 3, an increasing number of eggs is produced when available food increases, but the length of the phase and the size of the eggs stays comparable between standard and 1/6 food amounts. Generation time was 132 ± 13 h (5.5 d) at 20 °C and 159 ± 20 h (6.9 d) at 15 °C.

Onuma TA, Isobe M, Nishida H.

Cell Tissue Res. 2017 Feb;367(2):213-227. doi:10.1007/s00441-016-2524-5

Internal and external morphology of adults of the appendicularian, Oikopleura dioica: an SEM study.

A good reminder that there are also a few neural and subchordal cells in the tail.

Nakashima K, Nishino A, Hirose E.

Naturwissenschaften. 2011 Aug;98(8):661-9. doi:10.1007/s00114-011-0815-y

Forming a tough shell via an intracellular matrix and cellular junctions in the tail epidermis of Oikopleura dioica (Chordata: Tunicata: Appendicularia).

In larvae, the tail is enclosed in the larval enveloppe. In adults, the tail fins are made of single triangular epithelial cells attached with tight junctions to the other epitheilal cells covering the tail on the left and right sides. The muscle cells are attached to the epithelial cells via a basal membrane. Up and down the notochord, a sinus separates the muscle cells of each side. In the muscle cells, mitochondria are packed on the exterior side and muscle fibers are on the interior side.

Keats R. Conley Brad J. Gemmell Jean‐Marie Bouquet Eric M. Thompson and Kelly R. Sutherland

Limnol. Oceanogr. 63, 2018, 927–938

A self‐cleaning biological filter: How appendicularians mechanically control particle adhesion and removal.

Smaller particles adhere more than larger ones.

Fenaux R

Zoomorphology October 1986, Volume 106, Issue 4, pp 224–231

The house of Oikopleura dioica (Tunicata, Appendicularia): Structure and functions

“In our cultures, the tails beat slowly when the suspended particles were numerous and rapidly when they were few.”

Deng W, Henriet S, Chourrout D.

Curr Biol. 2018 Sep 27. pii: S0960-9822(18)31132-1. doi:10.1016/j.cub.2018.08.048

Prevalence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway.

In circularisation assays, the ratio between end-joining and homologous recombination is similar in O. dioica compared with other eukaryotes. Nevertheless, end-joining is more likely to concatenate than to circularise linear plasmids. The presence of microhomologies trigger microdeletions, consistend with the absence of the “classical” end-joining pathway. These microdeletions are much more frequent than in other organisms. Comparisons between Norvegian and Japanese strains suggest that the microdeletions could be part of the mechansism driving the compaction of O. dioica's genome.

José Luis Acuña and Markus Kiefer.

Limnology and Oceanography Volume 45, Issue 3, Pages 608–18, 26 April 2000

Functional response of the appendicularian Oikopleura dioica.

“Particles cleared from suspension by O. dioica are ingested and transformed into fast‐sinking fecal pellets at low FC, while they are mainly accumulated into slow to fast‐sinking filter houses at high FC”. Food used in this study: Isochrysis galbana (5.5 µm in size), Tetraselmis suecica (9.5 µm), and Chlorella sp. (3.5 µm).

Journal of Plankton Research, Volume 2, Issue 2, 1 April 1980, Pages 145–167 doi:10.1093/plankt/2.2.145

R. Fenaux S. Dallot

Répartition des Appendiculaires au large des côtes de Californie

Distributions of appendicularian species can be sorted according to the presence or absence of O. dioica (other species tend to co-occur by clusters). O. dioica tends to co-occur with F. Tenella. O. longicauda is the most abundant. The total amount of appendicularians is higher where O. dioica is found.

Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D.

Dev Biol. 2018 Sep 11. pii: S0012-1606(18)30157-X. doi:10.1016/j.ydbio.2018.09.006

Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors.

The tandem-duplicated propA and probB genes participate to the development of the house secreting epitelium and control (directly or indirectly) oik41a.

Nucleic Acids Res. 2013 Jan;41(Database issue):D845-53. doi:10.1093/nar/gks1159

Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni H, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM, Manak JR.

OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.

Tiling array expression data for 12 developmental stages.

Ecology Vol. 3, No. 1 (Jan., 1922), pp. 55-64

Christine E. Essenberg

The Seasonal Distribution of the Appendicularia in the Region of San Diego, California

Higher abundances of O. dioica in cool temperatures during winter.

Development. 2010 May;137(9):1483-92. doi:10.1242/dev.044503

Sagane Y, Zech K, Bouquet JM, Schmid M, Bal U, Thompson EM.

Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans.

O. dioica has two cellulose synthase genes (Od-CesA1 and Od-CesA2).

Cell Mol Life Sci. 2011 May;68(9):1623-31. doi:10.1007/s00018-010-0556-7

Nakashima K, Nishino A, Horikawa Y, Hirose E, Sugiyama J, Satoh N.

The crystalline phase of cellulose changes under developmental control in a marine chordate.

O. dioica has two cellulose synthase genes (Od-CesA1 and Od-CesA2) that are 68 % similar.

Inoue J, Satoh N.

Mol Biol Evol. 2018 Apr 1;35(4):914-924. doi:10.1093/molbev/msy002

Deuterostome Genomics: Lineage-Specific Protein Expansions That Enabled Chordate Muscle Evolution.

Duplication of some muscle genes in the stem Oikopleura lineage, perhaps reflecting the importance of tail movement during larval and adult stages.

Proc Natl Acad Sci U S A. 2018 Jul 30. pii: 201806614. doi:10.1073/pnas.1806614115

Lynagh T, Mikhaleva Y, Colding JM, Glover JC, Pless SA.

Acid-sensing ion channels emerged over 600 Mya and are conserved throughout the deuterostomes.

O. dioica, like other deuterostomes, has acid-sensing ion channels (ASICs). They are expressed in the nervous system.

Nat Rev Genet. 2007 Dec;8(12):932-42 doi:10.1038/nrg2226

Cañestro C, Yokoi H, Postlethwait JH.

Evolutionary developmental biology and genomics.

O. dioica only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.

Cell Cycle. 2018 Jul 4. doi:10.1080/15384101.2018.1486167

Feng H & Thompson EM

Specialization of CDK1 and Cyclin B paralog functions in a coenocystic mode of oogenic meiosis.

O. dioica has multiple CDK1 and Cyclin B paralogs.

Science. 2010 Dec 3;330(6009):1381-5. doi:10.1126/science.1194167

Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D.

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

Link to Supplementary Material.

1,260 scaffolds (70.4 Mb), 395 Kb N50, 15,152 ESTs clusters in the reference assembly, excluding 4,196 the allelic scaffolds (45 Mb, 21.8 Kb N50).

Colombera D. & Fenaux R.

Italian Journal of Zoology, 1973, 40:3-4, 347-353

Chromosome form and number in the larvacea

“In 10 anaphase plates (fig. 10) a chromosome number of 16 was regularly found. I n another five anaphase plates, presumably because of chromosome losses during the squashing, a lower number mas found.

These chromosomes are exceedingly small, without morphologically differentiated structures. They are rod-shape, with a sharp bend in a medial or submedial position ; of the two arms individuated by the bend, one is often thinner than the other.

As is often the result of squashing, the direction of tlie chromosome movement is clearly altered for some chromosomes. Since none of the chromosomes appears to be homologous we consider such chromosomes to be meiotic and in consequence we mould assign a haploid number of eight to 0. dioica, with the reservation that the above mentioned plates might be mitotic in which case the true haploid number would be four.”

Reports 16 chromosomes in meiotic cells (8 haploid chromosomes).

Wilhelm Friedrich Körner

Zeitschrift für Morphologie und Ökologie der Tiere Vol. 41, No. 1 (20.Mai 1952), pp. 1-53

Untersuchungen über die Gehäusebildung bei Appendicularien (Oikopleura dioica Fol)

Figure legends:

Abb. 18. Oikopleura dioica Fol. Anaphase aus dem Ektoderm der Larve. Maßstab 10 µ.

Abb. 19a u. b. Oikopleura dioica Fol. a Äquatorialplatte aus einer Spermiocyte I. Ordnung. Nach Karmin-Essigsäurepräparaten. b Oogenetische Meiose mit 3 Chromosomentetraden. Maßstab 10 µ.

Reports 3 haploid chromosomes in sperm and oocytes, one beign longer than the others. Also reports an observation of 7 chromosomes in a somatic mitotic cell. “Die zur Untersuchung benutzten Tiere stammten ausschließlich aus dem Wattenmeer der Deutschen Bucht.” (all animals were collected from the Wadden sea)

T. Aida

The journal of the College of Science, Imperial University of Tokyo, Japan (東京帝國大學紀要. 理科) 23 pp. 1-25 , 1907-12-23

NCID:AA0069577 Reports that the most common appendicularian in Japan are O. longitudica, O. dioica and O. fusiformis. They are “found almost in all seasons and in every part of the coast”. Nevertheless, “even the most common species O. longitudica can not be taken at all times throughout the year”.

Martí-Solans J, Belyaeva OV, Torres-Aguila NP, Kedishvili NY, Albalat R, Cañestro C.

Mol Biol Evol. 2016 Sep;33(9):2401-16. doi:10.1093/molbev/msw118

Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate.

Some genes are lost (Aldh1a, Cyp26, Rdh10, Rdh16, and Bco1) and others show signs of neofunctionalisation (RdhE2, Aldh8a1). “O. dioica did not contain atRA at concentrations that were likely to play any role in developmental or physiological processes.”

Zoolog Sci. 2010 Feb;27(2):128-33. doi:10.2108/zsj.27.128.

Oikopleura dioica alcohol dehydrogenase class 3 provides new insights into the evolution of retinoic acid synthesis in chordates.

Cañestro C, Albalat R, Postlethwait JH.

Adh3 is the only MDR-Adh in the Oikopleura genome. It strictly conserves the eight residues that constitute the signature of all Adh3 and other residues as well, therefore probably metabolising the same types of substrates as in other species. (Adh3 is the ancestral MDR-Adh genes in vertebrates; Adh1, 2 and 4 show signs of neofunctionalisation).

Navratilova P, Danks GB, Long A, Butcher S, Manak JR, Thompson EM.

Epigenetics Chromatin. 2017 Jan 17;10:3. doi:10.1186/s13072-016-0110-4

Sex-specific chromatin landscapes in an ultra-compact chordate genome.

Chromatin domains usually smaller than 7 nucleosomes. 5-methylcytosine detected by immunoprecipitation and microarray analysis (MeDIP-chip).

Delsuc F, Brinkmann H, Chourrout D, Philippe H.

Nature. 2006 Feb 23;439(7079):965-8.

Tunicates and not cephalochordates are the closest living relatives of vertebrates.

Phylogenetic study of 146 genes in 28 species places tunicates next to vertebrates (together forming the “Olfactores” clade proposed earlier by others), and suggests that cephalochordates may be closer to echinoderms, questionning the monophyly of chordates. This was refuted by Bourlat et al. in 2006. Oikopleura is basal to other tunicates (and was not included in Bourlat et al).

Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJ, Delsuc F.

BMC Evol Biol. 2009 Aug 5;9:187. doi:10.1186/1471-2148-9-187

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.

Phylogenetic tree built with 18S rRNA sequences from 110 species including 4 Oikopleuridae places Oikopleuridae as sister group of Stolidobranchia. Nevertheless, it might be an artefact of AT-richness or long-branch attraction. Many other articles on the topic are cited in this paper.

Delsuc F, Philippe H, Tsagkogeorga G, Simion P, Tilak MK, Turon X, López-Legentil S, Piette J, Lemaire P, Douzery EJP.

BMC Biol. 2018 Apr 13;16(1):39. doi:10.1186/s12915-018-0499-2

A phylogenomic framework and timescale for comparative studies of tunicates.

Phylogenetic tree based on 258 orthologous proteins from 63 species shows Oikopleura as a sister group of all other tunicates, with a split 447 ± 20 Mya ago. A long-branch attraction artefact can nevertheless not be excluded.

J Mol Evol. 2004 Oct;59(4):448-57 doi:10.1007/s00239-004-2636-5

Edvardsen RB, Lerat E, Maeland AD, Flåt M, Tewari R, Jensen MF, Lehrach H, Reinhardt R, Seo HC, Chourrout D.

Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica.

Study on housekeeping genes suggests that “Most Oikopleura introns occupy nonconserved positions and probably originate from numerous late intron gains or sliding of ancient introns”. Conservation within paralogs suggest possible gene conversion events.

Olsen LC, Kourtesis I, Busengdal H, Jensen MF, Hausen H, Chourrout D.

BMC Dev Biol. 2018 Feb 27;18(1):4. doi:10.1186/s12861-018-0165-5

Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica.

Localised pumilio (pum1) and vasa (vas4) RNAs. Prior hatching, pum1 is found outside the embryo!

Omotezako T, Matsuo M, Onuma TA, Nishida H

Sci Rep. 2017 Mar 10;7:44226. doi:10.1038/srep44226

DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica.

A clone library was prepared by subtracting male to female cDNAs. Clones were screened by pools of 5 and then resolved individually. Identifies genes related to cell structure and adhesion.

Danks GB, Navratilova P, Lenhard B, Thompson EM

BMC Genomics. 2018 Feb 26;19(1):164. doi:10.1186/s12864-018-4504-5

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.

“369/502 (73.5%) of genes that are specifically expressed in the testis are associated with a TCTAGA promoter element, compared to 100/906 (11.0%) that are specific to the ovary and 7/275 (2.5%) that are specific to the trunk.” “Strong association of gene body DNA methylation with TATA-dependent promoters in O. dioica.” “Maternal promoters in O. dioica were located on the X-chromosome more frequently than expected.”

Danks GB, Raasholm M, Campsteijn C, Long AM, Manak JR, Lenhard B, Thompson EM.

Mol Biol Evol. 2015 Mar;32(3):585-99. doi:10.1093/molbev/msu336

Trans-Splicing and Operons in Metazoans: Translational Control in Maternally Regulated Development and Recovery from Growth Arrest.

“39% of annotated gene models are trans-spliced with the SL.” “42% of SL transcripts are monocistronic; in these cases SL trans-splicing has a function other than resolving polycistronic mRNA.” “A second wave of gene activation peaked at the metamorphic tailshift stage where 2,578 genes were switched on for the first time. Here, 80% of genes were non-trans-spliced nonoperon genes, only 4% were SL-trans-spliced operon genes, and 10% were SL-trans-spliced monocistronic genes.” “A Switch from Predominantly Trans-Spliced to Predominantly Non-trans-Spliced Transcripts Occurs at the Maternal to Zygotic Transition” Parallel study in O. dioica, C. elegans and C. intestinalis suggests that “trans-splicing itself, rather than the organization of genes into operons, is the common factor for maternal mRNA in these metazoans”. The TOP motif of ribosomal protein genes is provided by the SL in O. dioica. “We find that SL-trans-spliced mRNAs are enriched in the ovary and oocytes.”

Cañestro C, Bassham S, Postlethwait J.

Dev Biol. 2005 Sep 15;285(2):298-315 doi:10.1016/j.ydbio.2005.06.039

Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain.

The Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain. 3 otx paralogs. No expression of pax2/5/8 in the gap between otxa + otxb and hox1.

PLoS One. 2012;7(7):e40172. doi:10.1371/journal.pone.0040172

Hosp J, Sagane Y, Danks G, Thompson EM.

The evolving proteome of a complex extracellular matrix, the Oikopleura house.

“Almost half of the oikosin complement exhibit no known domain structures or other similarities to known proteins, suggesting de novo appearance in the appendicularian lineage. Known domains are implicated in cellulose binding, protein-protein interactions or sPLA2 activity. Production of the latter is concentrated in epithelial regions associated with construction of the fcf, suggesting a possible role of this structure in innate immune defence.” “The genomic organization of oikosin loci appears incompatible with common enhancers or locus control regions exerting [...] a coordinate regulatory role.”

PLoS One. 2018 Jan 3;13(1):e0190625. doi:10.1371/journal.pone.0190625

Bouquet JM, Troedsson C, Novac A, Reeve M, Lechtenbörger AK, Massart W, Skaar KS, Aasjord A, Dupont S, Thompson EM.

Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions.

Fertilty increases with acidity (tested values: 7.6, 8.0, 8.4), and generation time decreases with temperature (tested values: 12.0, 14.2, 14.5 and 17.2). Survival decreases at higher pH and temperature values. The gamete quality is not reduced. In mesocosms, the increase of temperature of +3°C at pH 7.6 resulted in 2.5- and 5-fold increases in abundance.

BMC Genomics. 2012 Feb 2;13:55. doi:10.1186/1471-2164-13-55

Yadetie F, Butcher S, Førde HE, Campsteijn C, Bouquet JM, Karlsen OA, Denoeud F, Metpally R, Thompson EM, Manak JR, Goksøyr A, Chourrout D.

Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics.

“Oikopleura appears to have the smallest CYP complement of sequenced animal genomes and has no detectable CYP1 family genes. AhR, which is the transcriptional regulator of CYP1 family genes in vertebrates, is also undetectable in Oikopleura. Thus, the AhR signaling pathway may not exist in Oikopleura. Components of the Nrf2 signaling pathway appear to be conserved in Oikopleura.”

Science. 2001 Dec 21;294(5551):2506 doi:10.1126/science.294.5551.2506

Seo HC, Kube M, Edvardsen RB, Jensen MF, Beck A, Spriet E, Gorsky G, Thompson EM, Lehrach H, Reinhardt R, Chourrout D.

Miniature genome in the marine chordate Oikopleura dioica.

Genome size estimated to 72 ± 13 Mb by DNA contents and comparison to Ciona. A large-scale shotgun sequencing of 128,386 short reads lead to a lower-bound estimate of 65 Mb and 15,000 genes.

Ganot P, Kallesøe T, Reinhardt R, Chourrout D, Thompson EM.

Mol Cell Biol. 2004 Sep;24(17):7795-805. doi:10.1128/MCB.24.17.7795-7805.2004

Spliced-Leader RNA trans Splicing in a Chordate, Oikopleura dioica, with a Compact Genome.

5′ splice leader (SL) found in 90/158 ESTs containing a start codon. The SL RNA is found downstream of the 5S RNA in at least 40 occurences, and aproximately 2/3 of all the 5S rRNA genes. Its sequence is ACTCATCCCATTTTTGAGTCCGATTTCGATTGTCTAACAG. O. doica is the first chordate where gene operons have been described. Intercistronic regions are very short (<30 nt). “In comparing 52 distinct trans-splice acceptor sites to 605 cis-splice acceptor sites, the same consensus sequence, `TTT(C/T/A)AG`, was observed at both intron and intercistronic region 3′ ends. A notable difference from cis splicing was that most exons trans spliced to the leader (133 of 145) started with an adenosine, whereas the start of cis-spliced exons did not show any nucleotide preference.” In the cycD operon, only the last gene (cycD) has a `AAUAAA` polyadenylation signal.