Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(3), С. 519 - 535

Опубликована: Янв. 12, 2024

Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and often assumed to be causally associated with organismal innovations radiations. The 2R hypothesis suggests two WGD events (1R 2R) occurred during early vertebrate evolution. However, the timing of relative divergence gnathostomes (jawed vertebrates) cyclostomes (jawless hagfishes lampreys) unresolved whether these underlie phenotypic diversification remains elusive. Here we present inshore hagfish, Eptatretus burgeri. Through comparative analysis lamprey gnathostome genomes, reconstruct in cyclostome evolution, leveraging insights into ancestral genome. Genome-wide synteny phylogenetic analyses support scenario which 1R stem-lineage Cambrian, stem-lineage, maximally late Cambrian-earliest Ordovician, after its from cyclostomes. We find stem-cyclostomes experienced an additional independent triplication. Functional genomic morphospace demonstrate generally contribute developmental evolution similar changes regulatory both groups. appreciable morphological only but not lineage, calling question general expectation WGDs lead leaps bodyplan complexity.

Язык: Английский

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Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

Cell Genomics, Год журнала: 2025, Номер unknown, С. 100761 - 100761

Опубликована: Янв. 1, 2025

Язык: Английский

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A renaissance of microRNAs as taxonomic and phylogenetic markers in animals

Zoologica Scripta, Год журнала: 2024, Номер 53(6), С. 754 - 762

Опубликована: Июнь 21, 2024

Abstract Molecular markers for tracing animal sample origins and compositions are critical applications such as parasite detection, contamination screening, authentication. Among these, microRNAs have emerged promising candidates due to their deep conservation, near‐hierarchical evolution, stability. I here review the suitability of taxonomic also phylogenetic show how careful annotation efforts establishment curated microRNA gene database MirGeneDB tools like MirMachine revitalized research. These advancements enable accurate studies, highlighting microRNAs' potential in resolving long‐standing questions relationships extending ancient DNA environmental RNA analysis. Future research must focus on expanding complements across all Metazoa further improving methodologies.

Язык: Английский

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MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

Nucleic Acids Research, Год журнала: 2024, Номер 53(D1), С. D116 - D128

Опубликована: Ноя. 30, 2024

Abstract We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21 822 genes (5160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families, as well MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models all families, along smallRNA read data are downloadable. These enhanced annotations will allow researchers analyze properties such secondary structure features their biogenesis within robust phylogenetic context without plagued numerous false positives negatives. In light improvements, 3.0 assume responsibility naming conserved novel metazoan microRNAs. is part RNAcentral Elixir Norway publicly freely available at mirgenedb.org.

Язык: Английский

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Historical RNA expression profiles from the extinct Tasmanian tiger

Genome Research, Год журнала: 2023, Номер 33(8), С. 1299 - 1316

Опубликована: Июль 18, 2023

Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or regulation, which are only attainable at transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost historical skins extant canids, but no attempts been made so far on We extract, sequence, analyze muscle skin tissue a ∼130-year-old Tasmanian tiger ( Thylacinus cynocephalus ) desiccation room temperature museum collection. The profiles closely resemble those species, revealing specific anatomical features such as slow fibers blood infiltration. Metatranscriptomic analysis, damage, profiles, expression hotspots genome-wide further confirm thylacine origin sequences. sequences used improve protein-coding noncoding annotations, evidencing missing exonic loci location ribosomal genes while increasing number annotated microRNAs 62 325. discover thylacine-specific microRNA isoform could not confirmed without evidence. Finally, we detect traces viruses, suggesting possibility profiling viral evolution. Our results represent first successful attempt obtain an animal providing thought-to-be-lost information dynamics. These findings hold promising implications for study molecules across vast collections natural history museums well-preserved remains.

Язык: Английский

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Exploring Genome Architecture as a Source of Phylogenetic Characters for Resolving the Apulmonate Arachnid Polytomy

Опубликована: Янв. 1, 2025

Язык: Английский

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Differentially expressed miRNAs offer new perspective into cave adaptation of Astyanax mexicanus

Annals of the New York Academy of Sciences, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

Abstract Astyanax mexicanus , a species with both surface‐dwelling and multiple cave‐dwelling populations, offers unique opportunity to study repeated adaptation dark resource‐scarce environments. While previous work has identified large‐scale gene expression changes between morphs under even identical laboratory conditions, the regulatory basis of these differences remains largely unexplored. In this study, we focus on microRNAs (miRNAs) as key regulators expression. Our analysis 683 mature miRNAs, establishing first comprehensive catalog miRNAs for species. We subset differentially expressed common all studied potentially orchestrating nuanced patterns required survival in cave milieu. Furthermore, performed silico target prediction revealing possible roles developmental metabolic pathways pivotal thriving nutrient‐limited conditions. Interestingly, also observed that Molino, which is “youngest” three cavefish analyzed exhibited most abundant number among morphs. The miRNA generated, along insight into their differential across different morphs, will guide future investigations intricate world miRNA‐mediated evolution complex traits.

Язык: Английский

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A genome resource for the marine annelidPlatynereis dumerilii

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 23, 2024

The marine annelid

Язык: Английский

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Insights into early animal evolution from the genome of the xenacoelomorph worm Xenoturbella bocki

eLife, Год журнала: 2024, Номер 13

Опубликована: Авг. 7, 2024

The evolutionary origins of Bilateria remain enigmatic. One the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on view Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated Nephrozoa (protostomes deuterostomes). Genome data can provide important comparative help understand evolution biology enigmatic species better. Here, we assemble analyze genome simple, marine xenacoelomorph Xenoturbella bocki , key for our understanding early bilaterian evolution. Our highly contiguous assembly X. has size ~111 Mbp 18 chromosome-like scaffolds, with repeat content intron, exon, intergenic space comparable invertebrates. We find have similar number genes retained ancestral metazoan synteny. Key signaling pathways also largely complete most miRNAs present. Overall, conclude that complex typical bilaterians, does not reflect apparent simplicity its body plan been so sister group rest Bilateria.

Язык: Английский

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Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 4, 2024

Abstract Figure Graphical abstract During the last 800 million years of evolution animals radiated into a vast range diversity species and disparity forms lifestyles. The process involved near hierarchical increase in complexity from life with few cell types to organisms many hundreds cell-types. However, neither genome size nor number protein-coding genes can explain these differences their biological basis remains elusive. Yet, recent studies have suggested that is closely linked acquisition class protein coding gene-regulators called microRNAs. In regressive approach, investigate association between loss organismal microRNAs, we here studied Syndermata, an invertebrate group including free-living rotifers (Monogononta, Bdelloidea), epibiotic Seisonidea endoparasitic Acanthocephala. Genomic, transcriptomic morphological characterization comparisons across 25 syndermatan revealed strong correlation decreasing complexity. extends ∼85% microRNAs ∼50% BUSCO Acanthocephala, most reduced studied. Together, ∼400 ∼10 metazoan core gene losses went along one microRNA family loss. Furthermore, ∼4 families or ∼34 associated lost feature. These are first quantitative insights regulatory impact on organismic as predictable consequence parasites.

Язык: Английский

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