Evolution Education and Outreach, Journal Year: 2025, Volume and Issue: 18(1)
Published: April 7, 2025
Language: Английский
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half have no functional annotations Encyclopedia of DNA Elements (ENCODE) resource. Changes genes regulatory associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast imperiled biodiversity offers distinctive power identifying genetic variants function organismal phenotypes.
Language: Английский
Citations
145
Science, Journal Year: 2023, Volume and Issue: 380(6643)
Published: April 27, 2023
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal relationships exhibit relatively low rates conflict diverse datasets analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades radiated during the Cenozoic. Genomic time trees reveal accumulation cladogenic before immediately after Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance K-Pg extinction in radiation.
Language: Английский
Citations
88
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: May 14, 2023
Abstract Chromosomes are a central unit of genome organisation. One tenth all described species on Earth Lepidoptera, butterflies and moths, these generally possess 31 holocentric chromosomes. However, subset lepidopteran display dramatic variation in chromosome counts. By analysing 210 chromosomally-complete genomes, the largest analysis eukaryotic chromosomal-level reference genomes to date, we show that diverse karyotypes extant derived from 32 ancestral linkage groups, which term Merian elements. elements have remained largely intact across 250 million years evolution diversification. Against this stable background, identify eight independent lineages evaded constraint undergone extensive reorganisation - either by numerous fissions or combination fusion fission events. Outside lineages, fusions rare rarer still. Fusions tend involve small, repeat-rich and/or Z chromosome. Together, our results reveal constraints architecture Lepidoptera enable deeper understanding importance chromosomal rearrangements shaping genomes.
Language: Английский
Citations
46
Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(4), P. 777 - 790
Published: Feb. 21, 2024
Chromosomes are a central unit of genome organization. One-tenth all described species on Earth butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes show that chromosomes extant lepidopterans derived from 32 ancestral linkage groups, term Merian elements. elements have remained largely intact through 250 million years evolution diversification. Against this stable background, eight lineages undergone extensive reorganization either numerous fissions or combination fusion fission events. Outside these lineages, fusions rare rarer still. Fusions often involve small, repeat-rich sex-linked element. Our results reveal constraints architecture Lepidoptera provide deeper understanding chromosomal rearrangements eukaryotic evolution.
Language: Английский
Citations
46
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: Jan. 17, 2024
Abstract Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for western clawed frog, tropicalis , along with draft chromosome-scale sequences three distantly related emerging frog species, Eleutherodactylus coqui Engystomops pustulosus Hymenochirus boettgeri Frog chromosomes have remained remarkably stable since Mesozoic Era, limited Robertsonian (i.e., arm-preserving) translocations end-to-end fusions found among smaller chromosomes. Conservation synteny includes conservation centromere locations, marked by centromeric tandem repeats associated Cenp-a binding surrounded pericentromeric LINE/L1 elements. This work explores structure across frogs, using dense meiotic linkage map X. chromatin conformation capture (Hi-C) data all species. Abundant satellite occupy unusually long (~20 megabase) terminal regions each chromosome coincide high rates recombination. Both embryonic differentiated cells show reproducible associations telomeres, reflecting Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral from which contemporary genomes were constructed.
Language: Английский
Citations
20
Genome Research, Journal Year: 2024, Volume and Issue: unknown
Published: April 15, 2024
Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes the appendicularian tunicate Oikopleura dioica around globe reveals extreme genome scrambling caused by thousands chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate an magnitude higher than ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms sex-specific regions appear to be primary unit macrosynteny conservation. At microsyntenic level, did not operon structures, suggesting absence pressure maintain them. uncoupling with conservation O. suggests presence previously unnoticed cryptic provides new biological system challenges our previous vision speciation which similar animals always share structures.
Language: Английский
Citations
19
Science, Journal Year: 2025, Volume and Issue: 387(6737), P. 1001 - 1007
Published: Feb. 27, 2025
Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent diverse radiation with myriad morphological, ecological, behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed living on basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members all eight classes two high-quality genome assemblies monoplacophorans. Our analyses confirm proposed morphology show widespread genomic variation. flexibility likely explains both historic challenges their genomes evolutionary success.
Language: Английский
Citations
3
Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 15(11), P. a041447 - a041447
Published: Aug. 21, 2023
Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University Neuchâtel, 2000 Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 3Facultad Ciencias Exactas Químicas Naturales, Universidad N3300LQH 4Centre d'Ecologie Fonctionnelle et Evolutive, Université Montpellier, CNRS, EPHE, IRD, 34293 France 5Department Marine Sciences, Gothenburg, 405 30 Sweden 6Centre for Evolutionary 7Department Ecology Cornell University, Ithaca, New York 14853, USA 8Centre Organismal Studies, Heidelberg, 69117 Germany 9Institute Science Technology Austria (ISTA), 3400 Klosterneuburg, 10Faculty Biosciences Aquaculture, Nord 8026 Bodø, Norway 11CIBIO, Centro Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus Vairão, Universidade do Porto, 4485-661 Portugal 12BIOPOLIS Program in Genomics, Biodiversity Land Planning, Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt
Language: Английский
Citations
25
Physiological Reviews, Journal Year: 2024, Volume and Issue: 104(3), P. 1409 - 1459
Published: March 22, 2024
The collective efforts of scientists over multiple decades have led to advancements in molecular and cellular biology-based technologies including genetic engineering animal cloning that are now being harnessed enhance the suitability pig organs for xenotransplantation into humans. Using sourced from pigs with gene deletions human transgene insertions, investigators overcome formidable immunological physiological barriers pig-to-nonhuman primate (NHP) achieved prolonged xenograft survival. These studies informed design Revivicor’s (Revivicor Inc, Blacksburg, VA) genetically engineered 10 modifications (10 GE) (including inactivation 4 endogenous porcine genes insertion 6 transgenes), whose hearts kidneys been studied preclinical models brain-dead recipients. Additionally, first two clinical cases pig-to-human heart were recently performed this GE at University Maryland. Although review focuses on kidneys, organs, tissues, cell types will provide much-needed therapeutic interventions future.
Language: Английский
Citations
12
eLife, Journal Year: 2025, Volume and Issue: 13
Published: April 17, 2025
A major question in animal evolution is how genotypic and phenotypic changes are related, another when whether ancient gene order conserved living clades. Chitons, the molluscan class Polyplacophora, retain a body plan general morphology apparently little changed since Palaeozoic. We present comparative analysis of five reference quality genomes, including four de novo assemblies, covering all chiton clades, an updated phylogeny for phylum. constructed 20 linkage groups (MLGs) show that these relatively bivalve karyotypes, but chitons they subject to re-ordering, rearrangement, fusion, or partial duplication vary even between congeneric species. The largest number novel fusions most plesiomorphic clade Lepidopleurida, chitonid Liolophura japonica has genome duplication, extending occurrence large-scale within Mollusca. extreme dynamic rearrangements this stands contrast other animals, demonstrating have overcome evolutionary constraints acting on groups. conservative phenome belies rapid extensive genome.
Language: Английский
Citations
2