Some bibliography

2Ome 3′ UTR 3′ end 454 5′ UTR 5mC 7SK 8-oxo-G 96-wells AI 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 PKR 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 type cellulose centromere 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 situ 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 metabolome 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 organoid outreach pH paired-end parasite parvalbumin patent peak peroxydase pharmacology pheromones phosphatase phosphorylation 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 repertoire replication repression reprogramming reticulocyte reverse transcription review ribosome ribozyme richness robot sRNA scale-free screen selection selex 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 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

Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M.

Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera.

Nat Ecol Evol. 2024 Feb 21. doi:10.1038/s41559-024-02329-4

“We assigned 4,112 orthologues (78%) to 32 ALGs: 31 autosomes and Z, the sex chromosome. Hereafter, we refer to these ALGs as Merian elements, named after the seventeenth-century lepidopterist and botanical artist, Maria Sibylla Merian” ”Merian elements have remained intact in most species” “Lepidopteran chromosomes arising from fusions retain syntenic domains that reflect the original elements. Remarkably, this includes the M17 + M20 fusion, which occurred ~200 million years ago”

Thomas D. Lewin, Isabel Jiah-Yih Liao, Mu-En Chen, John D. D. Bishop, Peter W. H. Holland, Yi-Jyun Luo

bioRxiv 2024.02.15.580425; doi:10.1101/2024.02.15.580425

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa.

Defines a “microsynteny mixing score” as 1 minus the absolute value of the spearman correlation coefficient of the ranked positions of orthologous genes on orthologous chromosome pairs.

Jia SL, Zhang M, Liu GL, Chi ZM, Chi Z.

Funct Integr Genomics. 2023 Jun 19;23(3):206. doi:10.1007/s10142-023-01127-8

Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey.

A new Aureobasidium melanogenum strain that has two subgenomes that diverged ~10 million years ago.

Genki N. Kanda, Taku Tsuzuki, Motoki Terada, Noriko Sakai, Naohiro Motozawa, Tomohiro Masuda, Mitsuhiro Nishida, Chihaya T. Watanabe, Tatsuki Higashi, Shuhei A. Horiguchi, Taku Kudo, Motohisa Kamei, Genshiro A. Sunagawa, Kenji Matsukuma, Takeshi Sakurada, Yosuke Ozawa, Masayo Takahashi, Koichi Takahashi, Tohru Natsume

Elife. 2022 Jun 28;11:e77007. doi:10.7554/eLife.77007

Robotic Search for Optimal Cell Culture in Regenerative Medicine

Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space.

Harlan Lewis and Peter H. Raven

Evolution, Volume 12, Issue 3, 1 September 1958, Pages 319–336 doi:10.1111/j.1558-5646.1958.tb02962.x

Rapid evolution in Clarkia

Frequent translocations cause bridges and circles in meiosis of hybrids.

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”

Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.

BMC Genomics. 2023 Oct 11;24(1):609. doi:10.1186/s12864-023-09718-2.

Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M.

Cutaneotrichosporon cavernicola sister species with same karyotype, ITS sequence similarity above the usual threshold for species boundaries, but scrambling of large-width regions. “If [mating infertility caused by genome rearrangement] is universal, chromosome synteny should be considered the determinant of biological species”

Stepankiw N, Yang AWH, Hughes TR.

Genome Res. 2023 Nov 9. doi:10.1101/gr.277792.123

The human genome contains over a million autonomous exons.

“∼4.2 billion paired end reads [...] mapped to ∼6 million clusters [which] encompassed ∼9% of the genome.” “Internal exons from protein-coding genes [...] had an average of 10,636 reads, [...] encompassing 32% of all reads.” “exon clusters with at least 100 reads [captured] 1,245,947 exons in total, encompassing 3.2% of the stranded genome (i.e., 6.2 Gb)“. “5.3% of all intergenic region bases [...] are part of a trapped exon [424,632], corresponding to an exon every 3311 bases on average”. “52% of GENCODE lncRNA internal exons were trapped with at least 100 reads, a figure comparable to that of mRNA internal exons (61%).” “Known alternative cassette exons displayed, on average, 2.5-fold lower inclusion rates when compared to all internal mRNA exons.” “the trapped exons are very significantly depleted from introns, but not the mRNA antisense strand, and trapped exons that are detected in introns tend to have low read counts”

bioRxiv 2023.10.30.564762; doi:10.1101/2023.10.30.564762

Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz

The brittle star genome illuminates the genetic basis of animal appendage regeneration

“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).” “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.” “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”

See all articles.