Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 22, 2025

Abstract Background East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of phenotypic diversity these remains largely unknown. Although transposable elements (TEs) been associated with variation cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap understand interactions between TEs hosts. Results Here, we describe dynamic patterns TE expression gonads during early development. Orthology inference revealed strong conservation silencing factors expansion piwil1 genes Lake Malawi likely driven by PiggyBac TEs. The expanded copies signatures positive selection retain amino acid residues essential for catalytic activity. Furthermore, cichlids express a Piwi-interacting RNA (piRNA) pathway that targets define genomic sites piRNA production find divergence closely related species, line fast evolution piRNA-producing loci. Conclusions Our findings suggest co-evolution host pathways radiations. propose has contributed diversity.

Language: Английский

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Genome-wide identification and expression profiling of the hemoglobin gene family under hypoxia stress in Sillago sihama

Comparative Biochemistry and Physiology Part D Genomics and Proteomics, Journal Year: 2025, Volume and Issue: unknown, P. 101500 - 101500

Published: March 1, 2025

Language: Английский

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The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758)

Wellcome Open Research, Journal Year: 2025, Volume and Issue: 9, P. 189 - 189

Published: April 28, 2025

We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The sequence is 669.9 megabases in span. Most of the scaffolded into 23 chromosomal pseudomolecules. Gene annotation this on Ensembl identified 23,515 protein coding genes.

Language: Английский

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 29, 2024

Abstract Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 1, 2024

Abstract East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of phenotypic diversity these remains largely unknown. Although transposable elements (TEs) been associated with variation cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns TE expression gonads during early development. Orthology inference revealed expansion piwil1 genes Lake Malawi likely driven by PiggyBac TEs. The expanded copies signatures positive selection retain amino acid residues essential for catalytic activity. Furthermore, cichlids express a Piwi-interacting RNA (piRNA) pathway that target We define genomic sites piRNA production find divergence closely related species, line fast evolution piRNA-producing loci. Our findings suggest co-evolution TEs host silencing pathways radiations. propose this has contributed to diversity.

Language: Английский

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Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 28, 2024

Abstract The evolutionary impact of structural variants, such as chromosomal inversions, is well documented, especially for their role in local adaptation high gene flow systems. However, the other genomic rearrangements like fusions, fissions, and translocations still relatively unexplored. Here we present six chromosome-level Gadid reference genomes non-migratory Atlantic cod ( Gadus morhua ) i.e., Norwegian coastal (NCC), haddock (Melanogrammus aeglefinus), burbot Lota lota ), European hake Merluccius merluccius two keystone Arctic codfishes: polar Boreogadus saida Arctogadus glacialis ). Within a comparative genomics framework, uncovered several lineage-specific resulting reduced number chromosomes compared to ancestral state cold-water adapted codfishes. identified fusions were not homologous, indicating that they originate from independent events. Additionally, partly overlapping inversions between species detected. Using smaller population dataset, degree conservation some (including breakpoint regions), suggesting these regions are under selection, potentially importance. With use genome assemblies, demonstrate how large reorganizations likely play important roles speciation processes thus, particular freezing environmental conditions. Moreover, observe massive rearrangement events can take place across short time scales.

Language: Английский

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Reference genome bias in light of species-specific chromosomal reorganization and translocations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 28, 2024

Summary Whole-genome sequencing efforts has during the past decade unveiled central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range taxa. However, employment reference genomes from distantly or even closely related species for mapping and subsequent variant calling, can lead to errors and/or biases datasets generated downstream analyses. Here, we capitalize on recently chromosome-anchored genome assemblies Arctic cod ( Arctogadus glacialis ), polar Boreogadus saida Atlantic Gadus morhua ) evaluate extent consequences bias population (approx. 15-20x coverage) both cod. Our findings demonstrate that choice impacts genetic statistics, individual depth, heterozygosity levels, cross-species comparisons nucleotide diversity (π) divergence (D XY ). Further, it became evident using more inaccurate detection characterization inversions, i.e., terms size (length) location (position), due inter-chromosomal reorganizations between species. Additionally, observe several detected species-specific inversions were split into multiple regions when mapped towards heterospecific reference. Inaccurate identification rearrangements well biased measures could potentially erroneous interpretation diversity, impede resolution adaptation, thus, impact predictions their potential respond climatic other environmental perturbations.

Language: Английский

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Long-Read De Novo Genome Assembly of Gulf toadfish Opsanus beta.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: April 5, 2024

Abstract The Gulf toadfish, Opsanus beta , within the family Batrachoididae, plays an important role ecologically and as a comparative research model. Only 4 genome assemblies are available for Batrachoids, with three being highly fragmentary not up to current assembly standards. Here we present new, de novo transcriptome toadfish using PacBio long read technology. final is among largest teleost genomes at 2.1 gigabases. This new improves significantly upon currently reference scaffold count of 62, which 23 chromosome scale, N50 98,402,768, BUSCO completeness score 97.3%. Annotation ab intio transcriptome-based methods generated 41,076 gene models. Modeling orthogroup change indicated expansion many immune associated orthogroups contraction olfactory receptor orthogroups. repetitive, ~ 70% composed simple repeats transposable elements. Satellite DNA analysis identified potential telomeric centromeric regions. improved represents valuable resource future this model organism genomics more broadly.

Language: Английский

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