Biochemistry (Moscow), Journal Year: 2023, Volume and Issue: 88(12-13), P. 2007 - 2022
Published: Dec. 1, 2023
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
140
Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)
Published: Feb. 15, 2024
Abstract Mammals exhibit different rates of cancer, with long-lived species generally showing greater resistance. Although bats have been suggested to be resistant cancer due their longevity, this has yet systematically examined. Here, we investigate resistance across seven bat by activating oncogenic genes in primary cells. Both vitro and vivo experiments suggest that Myotis pilosus (MPI) is particularly cancer. The transcriptomic functional analyses reveal the downregulation three ( HIF1A , COPS5 RPS3 ) largely contributes MPI. Further, identify loss a potential enhancer containing binding site upstream MPI, resulting . These findings not only provide direct experimental evidence for but also offer insights into natural mechanisms mammals.
Language: Английский
Citations
14
Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown
Published: Feb. 7, 2025
Language: Английский
Citations
0
Mobile DNA, Journal Year: 2025, Volume and Issue: 16(1)
Published: April 16, 2025
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: March 14, 2024
ABSTRACT Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector Lyme borreliosis and tick-borne encephalitis in Western Eurasia. ticks have large repetitive genomes that not yet well characterized. Here we generate two high-quality I . genome assemblies, haploid sizes approximately 2.15 Gbp. We find transposable elements comprise at least 69% I. genomes, amongst highest proportions found animals. highly diverse novel, so constructed repeat library for using our scapularis , another major borreliosis. To understand impact on compared their accumulation sister species. these species to be drivers evolution ticks. assemblies will valuable resources biological insights into this important ectoparasite. Our findings highlight further research required.
Language: Английский
Citations
3
PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e17651 - e17651
Published: July 8, 2024
Background Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data bat species hinder insights into their processes, particularly within the Myotis genus of Vespertilionidae family. In Mexico, 15 exist, with three— M. vivesi , findleyi planiceps —being endemic conservation concern. Methods We obtained samples analysis. Each three DNA was extracted, sequenced, assembled. The scaffolding carried out utilizing yumanensis genome via a genome-referenced approach ntJoin program. GapCloser employed fill gaps. Repeat elements were characterized, gene prediction done ab initio homology methods MAKER pipeline. Functional annotation involved InterproScan, BLASTp, KEGG. Non-coding RNAs annotated INFERNAL, tRNAscan-SE. Orthologous genes clustered using Orthofinder, phylogenomic tree reconstructed IQ-TREE. Results present assemblies these Illumina NovaSeq 6000, each exceeding 2.0 Gb, over 90% representing single-copy according BUSCO analyses. Transposable elements, including LINEs SINEs, constitute 30% genome. Helitrons, consistent Vespertilionids, identified. Values around 20,000 from derived correlation specific functions. Comparative analysis orthologs among eight revealed 20,820 groups, 4,789 being single copy orthogroups. RNA annotated. Phylogenomic supported chiropterans’ relationships. These resources contribute significantly understanding evolution, diversification patterns, aiding efforts endangered species.
Language: Английский
Citations
2
Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)
Published: Aug. 7, 2024
Abstract Convergence offers an opportunity to explore what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present emergent model system study convergent in nature a mammalian group, the bat genus Myotis. Three foraging strategies—gleaning, trawling, aerial hawking, each characterized by different sets of phenotypic features—have evolved independently multiple times biogeographic regions isolation for millions years. To investigate basis convergence functional changes linked ecomorphological convergence, sequenced annotated 17 new genomes screened 16,426 genes positive selection associations between relative evolutionary rates strategies across 30 species representing all Myotis ecomorphs geographic as well among sister groups. We identify that describe both phylogenetic trends. infer colonization environments may have first required hearing sensory perception, followed fecundity development, metabolism carbohydrates, heme degradation. These prey acquisition digestion match Our findings also suggest repeated does not always involve same but rather with molecular functions such developmental cellular processes.
Language: Английский
Citations
1
Journal of Heredity, Journal Year: 2023, Volume and Issue: 115(2), P. 203 - 211
Published: Dec. 13, 2023
Abstract Townsend’s big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North America. Considered of conservation concern throughout much its range, protection efforts would greatly benefit from understanding patterns population structure, genetic diversity, local adaptation. To facilitate such research, we present the first de novo genome assembly C. townsendii as part California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads Omni-C chromatin-proximity sequencing technologies were used to produce assembly, consistent with standard CCGP reference protocol. This comprises 391 scaffolds spanning 2.1 Gb, represented by scaffold N50 174.6 Mb, contig 23.4 benchmarking universal single-copy ortholog (BUSCO) completeness score 96.6%. high-quality will be key tool for informed management this vulnerable across range.
Language: Английский
Citations
2
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 16, 2024
Abstract Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost machinery necessary transposition and rely on closely related autonomous critical proteins. We studied two mathematical models regulation, one assuming that both tranposons their non-autonomous relatives operate under same regulatory logic, competing resources, self-attenuate while transposons continually increase, parasitizing relatives. implemented these stochastic simulations how relationships influence populations. found only outcrossing populations evolving with Parasitic regulation resulted stable maintenance TEs. tested our model predictions Caenorhabditis genomes by annotating focal families, LINEs SINE DNA transposon Mutator . broad variation - rapid mutational decay sequences allow to transpose. Together, results suggest individual families evolve according disparate rules are relevant early, acute stages invasion.
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Dec. 23, 2023
Abstract Transposable elements (TEs) can make up more than 50% of any given vertebrate’s genome, with substantial variability in TE composition among lineages. variation is often linked to changes gene regulation, genome size, and speciation. However, the role that duplication events have played generating abrupt shifts mobilome over macroevolutionary timescales remains unclear. We investigated degree which teleost (TGD) shaped diversification trajectory ray-finned fish mobilome. integrate a new high coverage Polypterus bichir data from 100 publicly available actinopterygian genomes assess implications on evolution. Our results provide no evidence for shift following TGD event. Instead, diversity appears been by history lineage specific are not correlated commonly evoked drivers such as body water column usage, or latitude. Collectively, these perspective early suggest historic ploidy may necessarily catalyze bursts innovation.
Language: Английский
Citations
1