Bibliographie à la volée.

2Ome 3′ UTR 3′ end 454 5′ UTR 5mC 7SK 8-oxo-G 96-wells AI ANI Alu BCR Bioconductor Biotechnology Brenner C33a CAGE CDR3 COVID-19 CRISPR CaSki ChIP Ciona CpG Crick DGT DNA DNAi DNAse I DNase-hypersensitivity DTT Dictyostelium Drosophila EBV ENCODE ES EcoP15I EpiSC Fluidigm FoxP3 Fritillaria Fucci H2AX H3K27ac H3K27me3 H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K4me4 H3K9ac H3K9me2 H3K9me3 H3S10p H3S28p H3S31p H3T3p H42K20me2 H4K16Ac H4K20me2 H4K8Ac HDAC HIV HPV HeLa Helicos HepG2 LAST LNA LPA LTR MHC MRI OIST OSC Oikopleura Okinawa Olf-1 Oxford plot PCR PEG PETM PLA PRDM9 Parkinson’s disease QTL RACE RNA RNA-inheritance RNA-protein RNA-seq RNA polymerase RNAse R RNP granules RT-PCR RdRP SAGE SARS-CoV-2 SNP SRA STRT Sanger SiHa TATA-box TCR TFBS Taq Trizol UTR adenylylation adipocyte agarose ageing alignment allelic expression amplification analysis annotation antibody antisense application aptamer arabidopsis archaea artefact assembly auto immunity automation bHLH bacteria barcode bat beads benchmark betaine bias bidirectional bioRxiv biochemistry biotin bistable blood brain buffer cDNA calcium cancer cap capture catecholaminergic cell-cell interaction cell conversion cell culture cell cycle cell line cell type cellulose centromere cephalochordate cephalopod cerebellum chicken chimeric transcript chimpanzee chromatin chromosome chromothripsis circuit circular RNA click climate clock cloning clustering comparison compartment complex-loci copy number coral cytometry cytoplasm damage database degradation demethylase dendrite detection development diagnostic differentiation dog dosage droplet drug drug delivery dsRNA eDNA eQTL editing education electrophoresis elongation embryo embryoid body emulsion endosymbiosis enhancer environment enzyme epicentre epigenetic evolution exon painting exonuclease exosome experiment design expression factory fingerprint fish fixation floor-plate flow cytometry fluorescence format fractionation frog function fusion transcript genetics genome germ line global warming graft granule growth guanylation hair hairpin haplotype heart heavy chain hemichordate heterodimer heterogeneity high-throughput histone historical human hybridisation iPS imaging immune-system immunity immunoglobulin imprinting in vivo infection information inhibition inosine integration intellectual-property intron isoform isothermal journal club karyotype knock-out labelling lamin lariat laser-capture library ligase lineage lipid live liver localisation locus boundary loop lymphocyte lysis m6A mC mRNA machine learning manganese mangrove mass spectroscopy maternal mechanical force mechanism medaka meiosis metabolism methanol method methylation miRNA microarray microfluidic microplastic microscopy missing-method mitochondrion model modification modified base monkey mosquito motif mouse muller element multiplex muscle mutation mycoplasma nanoCAGE nanopore natural selection nematode network neurogenin neuron nick noise nomenclature non-coding non-polyadenylated non coding normalisation not read nuclear body nucleolus nucleosome nucleotides nucleus occupancy ocean acidification ocular-dominance olfaction oligo-capping oligonucleotides open data open science operon organoid outreach pH paired-end pangenome parasite parvalbumin patent peak peroxydase pharmacology pheromones phosphatase phylogeny physiology piRNA pig plankton plant plasticity policy polony poly-A polymerase polyploid polysome population population transcriptomics post translational modification power law primase prion privacy product profile program prokaryote promoter promotome protein proteome proteomics publishing purification purkinje pyrophosphatase qPCR radioisotope random priming rat recombination recycle regulation repair repeat repeats repertoire replication repression reprogramming reticulocyte reverse-transcription reverse transcription review ribosome ribozyme richness robot sRNA scale-free screen selection selex sequence sequence tag sequence tags sequencing sex siRNA silencing single cell single chain single gene single molecule single strand size small RNA small samples snoRNA software somatic mutation sorting speciation spike splicing ssbp statistics stem cell storage structure subgenome superfamily supergene synapse synteny synthetic systems biology tRNA tag tags taxonomy telomere temperature template switching termination theory therapy thermo-enhancement thymus to read trans-splicing transcript transcript count transcription transcription factor transcriptome translation translatome transolcation transport transposase transposon trehalose triple helix tunicate turnover ultraconserved ultrasound unicellular unnatural base vaccine vanadium variants virus visual cortex yeast zebrafish α chain αβ chains β chain γH2AX μORF

Chantzi N, Georgakopoulos-Soares I.

The repertoire of short tandem repeats across the tree of life.

Genome Biol. 2025 Dec 12;26(1):425. doi:10.1186/s13059-025-03893-z

“The average STR density was 1.51 STR bp per kB” “Plasmodium falciparum shows the highest STR genomic density (109 bp/kB)” “19,645 viruses and 5 bacteria lacked STRs altogether” “the bacterial kingdom Fusobacteriati is depleted of STRs” “for prokaryotic genomes, we notice that one bp repeat unit STRs are highly depleted. Notably, trinucleotide and hexanucleotide tandem repeats are also enriched in most prokaryotic phyla” “bacterial and archaeal genomes are, on average, not more repetitive than expected by chance in contrast to eukaryotic and viral genomes.”

Shuai Li, Mengtan Liu, Aiyong Wan, Zhiqiang Xu, Shiwei Wang, Yi Liang, Zengxia Zhao & Guangtao Zhang

Limited growth and recruitment of Oikopleura dioica (Tunicata: Appendicularia) in the Jiaozhou Bay, China

J. Ocean. Limnol. (2025). doi: 10.1007/s00343-025-503

_O. dioica was mostly found from June to December 2011. Salinity varied between ~31 and ~28, and temperature between ~25 and ~5. Chlorophyl peaked in both winter and summer, but cyanobacteria only peaked in summer. Wild animals never reached the size of lab animals during the whole year.

Kim Y, Tanner HM, Rosenthal JJC, Brangwynne CP

STAR Protoc. 2025 Sep 19;6(3):103994. doi:10.1016/j.xpro.2025.103994

Protocol for the isolation, culture, and transfection of squid primary cells

Fibroblast-like cells migrate out of optic lobe, eye or gill explants after trypsin digestion, and can be transfected, but no cell division was observed. Insulin-transferrin-selenium (ITS-G), FGF and EGF are present in the cell culture medium.

Oleg Tolstenkov, Rodolfo da Silva Mazzarini Baldinotti, Sissel Norland, Anne Elin Aasjord, Daniel Chourrout, Marios Chatzigeorgiou

bioRxiv 2025.12.03.692109; doi: 10.64898/2025.12.03.692109

Behavioral ontogeny in a pelagic tunicate reveals the deep origins of chordate behavioral developmental plasticity

“We built a behavioral atlas of the planktonic tunicate Oikopleura dioica across its life cyclefrom larval to adult stages using high-throughput tracking and unsupervised analysis.”

Marc Fabregà-Torrus, Alfonso Ferrández-Roldán, Gaspar Sánchez-Serna, Beatriz Iralde Cárdenas, Cristian Cañestro

bioRxiv 2025.12.09.693291; doi: 10.64898/2025.12.09.693291

Evolution of Tunicate lifestyles shaped by Myosin heavy chain gene duplications, losses, and the diversification of tail muscle cell identities in Oikopleura dioica

O. dioica lost the jaw/body wall myosin heavy chain and amplified the paraxial ones.

Gaspar Sánchez-Serna, Paula Bujosa, Alfonso Ferrández-Roldán, Marc Fabregá-Torrus, Ana Alonso-Bartolomé, Laura Reyner-Laplana, Nuria P. Torres-Águila, Cristian Cañestro

bioRxiv 2025.12.09.693154; doi: 10.64898/2025.12.09.693154

Downstream effects of the “Less, but More” Fgf signaling in Oikopleura dioica: Fgf receptor expansion and RTK pathway simplification

Like in ascidians, the classical Ras protein is lost but was probably substituted by other related Ras proteins

Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A.

Cell. 2018 Nov 29;175(6):1533-1545.e20. doi:10.1016/j.cell.2018.10.023

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.

Survey of 45 metabolic traits over 400 million years of yeast evolutionary history suggests that lineages evolved by gene loss from a generalist ancestor. “We estimate the origin of the subphylum between 317 and 523 (95% credibility interval; posterior mean date: 404) million years ago (mya); the origin of the CUG-Ser1 clade, which contains the major opportunistic pathogen C. albicans, between 178 and 248 (210) mya, the origin of the whole-genome duplication (WGD) clade between 82 and 105 (93) mya, and the divergence of S. cerevisiae and C. albicans from their sister species (Saccharomyces paradoxus and Candida dubliniensis) between 4.0 and 5.8 (4.9) mya and 5.0 and 14.0 (8.7) mya, respectively”

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Edwards SV, Fang B, Khost D, Kolyfetis GE, Cheek RG, DeRaad DA, Chen N, Fitzpatrick JW, McCormack JE, Funk WC, Ghalambor CK, Garrison E, Guarracino A, Li H, Sackton TB.

Science. 2025 Dec 11;390(6778):eadw1931. doi:10.1126/science.adw1931

Multispecies pangenomes reveal a pervasive influence of population size on structural variation.

“We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes”

Gosselin S, Fullmer MS, Feng Y, Gogarten JP.

Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support.

Syst Biol. 2022 Feb 10;71(2):396-409. doi:10.1093/sysbio/syab060

“The distance (abbreviated Total Average Nucleotide Identity, or tANI) was calculated by using the formula: tANI -ln(AFANI). The natural log added to this calculation counteracts saturation for low AFANI values” Mostly tested on bacteria but also briefly on primates and yeasts

Liu S, Shi C, Chen C, Tan Y, Tian Y, Macqueen DJ, Li Q.

Cell Rep. 2025 May 27;44(5):115697. doi:10.1016/j.celrep.2025.115697

Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves.

“contiguous shell/core gene block[s …] consisted of singletons (80.4% in B. belcheri, 74.9% in B. floridae) or contained fewer than 5 genes (99.0% in B. belcheri, 99.1% in B. floridae).” “in the B. belcheri reference genome [and] 20 of the analysed resequenced samples [we found] the integrated genome of a herpes-like virus spanning 149,856 bp in length. […] Overall, BelcheriHV-1 was 24 × less impacted by nucleotide variations than the B. belcheri genome, with an average of one SNP per 5,958 nt, vs one SNP per 174 nt, respectively.” “[the dispensable genes] found in hemizygosity in only one of the two parental genotypes […] were absent in 40% of the offspring (expected 50%) and those found in hemizygosity in both parental genomes […] were absent in 19% of the offspring (expected 25%).”

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