Ren X, Li R, Wei X, Bi Y, Ho VWS, Ding Q, Xu Z, Zhang Z, Hsieh CL, Young A, Zeng J, Liu X, Zhao Z.

Nucleic Acids Res. 2018 Feb 16;46(3):1295-1307. doi:10.1093/nar/gkx1277

Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni.

”the coding sequences of [the] one-to-one orthologs exhibited only around a 90% identity, and most of [the] introns and intergenic regions were not alignable” “we produced [15,157] one-to-one orthologous gene pairs between C. briggsae and C. nigoni.” “we extracted all of the best hits between the two genomes that were >1 kb in size [and] observed over 400 interchromosomal translocations” “[we produced] produce homozygous viable introgressions representing ∼28% of the C. briggsae genome” “We observed a significantly higher [alignment score] in recombination sites than in genomic background” “Nearly half of the reduced genome in C. briggsae could be explained by its lost repeats relative to the C. nigoni genome. These differences in genome size and repeat content are expected to create gaps in the sequence alignment or make the syntenic sequences not alignable.”

Tandonnet S, Koutsovoulos GD, Adams S, Cloarec D, Parihar M, Blaxter ML, Pires-daSilva A.

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis.

G3 (Bethesda). 2019 Apr 9;9(4):1211-1230. doi: 10.1534/g3.119.0011

Nigon elements

Stevens L, Félix MA, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M.

Evol Lett. 2019 Apr 2;3(2):217-236. doi:10.1002/evl3.110

Comparative genomics of 10 new Caenorhabditis species.

“Phylogenetic relationships of 32 Caenorhabditis species”

Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJM, Baugh LR, Andersen EC.

Genome Biol Evol. 2022 Apr 10;14(4):evac042. doi:10.1093/gbe/evac042

Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.

“the genomes of C. elegans and C. briggsae are more highly rearranged than their outcrossing sister species, C. inopinata and C. nigoni (17.1% of neighboring genes are rearranged in the selfers compared with 15.0% in the outcrossers)”

Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA.

Commun Biol. 2020 Nov 9;3(1):656. doi:10.1038/s42003-020-01377-3

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.

“80% of 7,361 one-to-one orthologous genes are shared on syntenic chromosomes between [H. contortus and C. elegans]” “The distance between ortholog pairs [...] is correlated up to ~100 kbp [...], but is largely lost above 100 kbp ”

Gonzalez de la Rosa PM, Thomson M, Trivedi U, Tracey A, Tandonnet S, Blaxter M.

G3 (Bethesda). 2021 Jan 18;11(1):jkaa020. doi:10.1093/g3journal/jkaa020

A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes.

“subtelomeric extensions rang[ing] from 4 to 133 kb” present in germ line but absent in somatic cells.

Sun S, Shinya R, Dayi M, Yoshida A, Sternberg PW, Kikuchi T.

Microbiol Resour Announc. 2020 Oct 22;9(43):e01000-20. doi:10.1128/MRA.01000-20

Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1.

70 Mb genome, 6 chromosomes, enriched for repeats at the arms ends. Hi-C contact map shows strong interaction between all the central regions of the chromosomes.

Hinman AW, Yeh HY, Roelens B, Yamaya K, Woglar A, Bourbon HG, Chi P, Villeneuve AM.

Proc Natl Acad Sci U S A. 2021 Aug 17;118(33):e2109306118. doi:10.1073/pnas.2109306118

_Caenorhabditis elegans+ DSB-3 reveals conservation and divergence among protein complexes promoting meiotic double-strand breaks.

DSB-3, likely homologue of Mei4, interacts with DSB-1 and DSB-2 (likely homologues of Rec114). Together, they are interdependent for localisation to meiotic nuclei and promoting formation of crossovers. Yeast two-hybrid experiments that DSB-3 binds SPO-11 via DSB-1.

Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P.

Nat Biotechnol. 2008 Aug;26(8):909-15. doi:10.1038/nbt.1482

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

“One remarkable feature is that most of the genome is composed of pairs of homologous segments that may denote former diverged alleles. This suggests that M. incognita is evolving without sex toward effective haploidy through the Meselson effect.”

Woodruff GC, Johnson E, Phillips PC.

BMC Evol Biol. 2019 Mar 11;19(1):74. doi:10.1186/s12862-019-1388-1

A large close relative of C. elegans is slow-developing but not long-lived.

“C. inopinata females were longer-lived than wild-type C. elegans hermaphrodites at 25°C, with a median total lifespan that was four days higher [...] However, C. inopinata females were only marginally longer lived than C. elegans (fog-2) pseudo-females.”

Evol Lett. 2018 Jul 16;2(4):427-441. doi:10.1002/evl3.67

Woodruff GC, Willis JH, Phillips PC.

Dramatic evolution of body length due to postembryonic changes in cell size in a newly discovered close relative of Caenorhabditis elegans

“This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells.”

Nat Commun. 2018 Aug 10;9(1):3216. doi:10.1038/s41467-018-05712-5

Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D, Tsuyama K, Maeda Y, Namai S, Kumagai R, Tracey A, Holroyd N, Doyle SR, Woodruff GC, Murase K, Kitazume H, Chai C, Akagi A, Panda O, Ke HM, Schroeder FC, Wang J, Berriman M, Sternberg PW, Sugimoto A, Kikuchi T.

Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

123-Mb genome assembled into six chromosomes. Divergence time between C. elegans and C. inopinata estimated to about 10.5 Mya (142.73 million generations ago, assuming a generation time of 30 days). Proliferation of transposons and other repetitive elements (LTR, LINE, and Tc1/mariner). “The C. inopinata genome contains 641 LTR retrotransposon elements, 104 of which contain full protein domains (intact LTRs) In comparison, C. elegans and C. briggsae have 62 and 128 LTR retrotransposon elements, respectively, with 10 intact LTRs found in each.” “The most common type of repetitive sequence in the C. inopinata genome is the TcMar transposase Tc1 family [...] comprising 8.85% of the genome, compared with 1.31% and 3.04% of the C. elegans and C. briggsae genomes, respectively”. “Gene collinearity is largely conserved despite frequent intra chromosomal rearrangements.” “Higher synonymous substitution rates (dS) in autosomal arm regions than in the centre regions for C. elegans and C. inopinata one-to-one orthologues.” “Notably, C. inopinata has highly conserved gene synteny and orthology of essential genes with C. elegans and C. briggsae, but differs substantially in morphology and ecology. We hypothesise that activation of transposable elements possibly due to de-silencing through an altered small RNA pathway could be a driving force of rapid diversification of C. inopinata from other Caenorhabditis species.”

Woodruff GC, Phillips PC.

BMC Ecol. 2018 Aug 21;18(1):26. doi: 10.1186/s12898-018-0182-z.

Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps.

C. inopinata is travelling from fig to fig on Ceratosolen pollinating fig wasps. It appears to be very specialised in both the fig species and the wasp species.

Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC.

Curr Biol. 2017 Oct 9;27(19):2928-2939.e6. doi:10.1016/j.cub.2017.08.038

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.

“By comparing divergence rates with those of Caenorhabditis, we estimate that the asexual clade originated ca. 18 mya”. “We obtained a genome assembly of 158 Mb with an N50 of 124 kb”. “the haploid size [...] is ~88 Mb”. “~4% average difference between [heterozygous] alleles.” “Genomic regions in D. pachys have generally maintained the same chro- mosomal identity since diverging from Caenorhabditis”. “ we used macro- synteny with C. elegans to infer an ancestral chromosome iden- tity (ACD) for each D. pachys scaffold.” “We identified specific patterns of rearrangements consistent with an order of ACD fusions.” “The data [of reciprocal reaggangements between ACDs] thus allow us to propose that four ancestral chromosomes became fused in the order I-X-III-II” “Telomeres are either absent from the D. pachys genome or are highly divergent from the ancestral telomeric sequence.” “The combined absence of telomere sequences and mainte- nance proteins suggests a connection between chromosome fusion and loss of telomeres”. “84% of homozygous regions localize to ACDs I and X, which are neighbors in the inferred chromosomal fusion”. ”The reductional division during meiosis I is skipped; the two chromosomes condense but do not pair or synapse.” “The phenotype of C. elegans rec-8 mutants is reminiscent of the modified meiosis in D. pachys. [...] rec-8 is one of the conserved meiosis genes that was not detected in the D. pachys and D. coronatus genomes”

Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR.

Nat Commun. 2019 Nov 21;10(1):5268. doi:10.1038/s41467-019-13245-8

The genome of a subterrestrial nematode reveals adaptations to heat

“61.4 Mb comprising 880 scaffolds with N50 of 313 kb, though 90% of the sequence is encoded on just 193 scaffolds. ~95% complete according to BUSCO and CEGMA.”

Nat Genet. 2014 Jul;46(7):693-700. doi:10.1038/ng.3010

Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M.

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

Clustering scaffolds on the number of shared orthologs they have with scaffolds of a related species' genome identifies three chromosomes.