Pangenome graphs and their applications in biodiversity genomics

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Язык: Английский

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Landmarks in the history of selective sweeps

Animal Genetics, Год журнала: 2023, Номер 54(6), С. 667 - 688

Опубликована: Сен. 14, 2023

Abstract Half a century ago, seminal article on the hitchhiking effect by Smith and Haigh inaugurated concept of selection signature. Selective sweeps are characterised rapid spread an advantageous genetic variant through population hence play important role in shaping evolution research diversity. The process which beneficial allele arises becomes fixed population, leading to increase frequency other linked alleles, is known as or draft. Kimura's neutral theory complementary, with ‘null model’ positive ‘signal’. Both widely accepted evolution, especially genomics enabling precise measurements. Significant advances genomic technologies, such next‐generation sequencing, high‐density SNP arrays powerful bioinformatics tools, have made it possible systematically investigate signatures variety species. Although history relatively recent, progress has been last two decades, owing increasing availability large‐scale data development computational methods. In this review, we embark journey selective sweeps, ranging from early theoretical work recent empirical studies that utilise data.

Язык: Английский

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Deciphering climate resilience in Indian cattle breeds by selection signature analyses

Tropical Animal Health and Production, Год журнала: 2024, Номер 56(2)

Опубликована: Янв. 17, 2024

Язык: Английский

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Comprehensive selection signature analyses in dairy cattle exploiting purebred and crossbred genomic data

Mammalian Genome, Год журнала: 2023, Номер 34(4), С. 615 - 631

Опубликована: Окт. 16, 2023

Язык: Английский

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The complete mitochondrial genome of the ‘Extinct in the Wild’ Spix’s Macaw (Cyanopsitta spixii)

Journal of Ornithology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

Язык: Английский

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Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype

Marine Biotechnology, Год журнала: 2025, Номер 27(1)

Опубликована: Фев. 1, 2025

Abstract Selective breeding is a powerful tool for improving aquaculture production. A well-managed program essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, diversity in broodstock must be restored by introducing individuals from external populations. However, this reduce the accumulated gains selective breeding. introduction of with superior phenotypes will allow restoration without sacrificing these gains. study, we demonstrated possibility using selectively bred (SB) randomly (RB) population coho salmon ( Oncorhynchus kisutch ). Forty males growth were selected RB genomic crossed 127 collected females SB population, producing newly (NB) population. Genetic assessed statistics effective number alleles, allele richness, observed heterozygosity 11 microsatellite markers, was higher NB than RB. Additionally, fork length body weight compared among three after 12 months post-fertilization common tanks. The least-squares means similar between (164.9 mm 57.9 g) (161.1 53.7 g), while both significantly greater (150.4 43.0 g). Our results highlight effectiveness genome-assisted gene flow restoring compromising gain growth.

Язык: Английский

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Mitogenomic insights into the population structure and demographic history of zig-zag eels (Mastacembelus armatus) in southern China

Aquaculture Reports, Год журнала: 2025, Номер 42, С. 102748 - 102748

Опубликована: Март 19, 2025

Язык: Английский

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A Comprehensive Review: Molecular and Genealogical Methods for Preserving the Genetic Diversity of Pigs

Applied Sciences, Год журнала: 2025, Номер 15(6), С. 3394 - 3394

Опубликована: Март 20, 2025

Anthropogenic activities and rapidly increasing climate change have led to a significant loss of genetic diversity in domestic animals. Genealogical data traditionally been used monitor diversity. However, due dependency on pedigree completeness errors that can occur genealogical records, inaccurate estimation population parameters, such as the inbreeding coefficient or effective size, might occur. To reduce possible errors, it is necessary combine with molecular data. An integrated approach using leads optimization breeding programs while controlling within Molecular techniques single nucleotide polymorphism (SNP) genotyping, whole-genome sequencing (WGS), genome-wide association studies (GWASs) enable detailed understanding breed-specific profiles their use conservation programs. In addition, methods structural variation (SV) analysis pangenome epigenomic profiling provide more comprehensive insight into The particular importance for an autochthonous breed its resilience unfavorable climatic conditions, specific productive traits, disease resistance. A combined helps maintain sustainable agricultural systems under evolving environmental challenges.

Язык: Английский

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Complete Mitochondrial Genome of Two Amathusiini Species (Lepidoideae: Nymphalidae: Satyrinae): Characterization, Comparative Analyses, and Phylogenetic Implications

Genes, Год журнала: 2025, Номер 16(4), С. 447 - 447

Опубликована: Апрель 12, 2025

Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized systematics of Satyrinae. Notably, Amathusiini exhibits particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. Methods: We employed high-throughput sequencing assemble complete species, Discophora sondaica Aemona amathusia. Our study revealed novel insights through comparative genomics, which encompassed all available genomes. Additionally, we conducted reconstruction using maximum likelihood Bayesian inference approaches, utilizing most extensive dataset Results: closed, circular measure 15,333 bp for D. 15,423 A. amathusia, maintaining ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, an AT-rich control region. Comparative analyses 71 strong conservation across multiple parameters: nucleotide composition (AT content range: 77.9–81.8%), codon usage bias (ENC = 30.83–37.55), tRNA secondary structures, region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), atp8 exhibiting highest rate 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies nodal support: ((Satyrini + Melanitini) (Amathusiini Elymniini) Zetherini), confirming sister relationship between Elymniini. Within Satyrini, five subtribes formed monophyletic groups: Ypthimina, Erebiina, Maniolina, Satyrina, Melanargiina, arranged as ((Ypthimina (Erebiina Maniolina)) (Satyrina Melanargiina)). Mycalesina, Lethina, Parargina comprised well-supported clade (BS 100%; PP though internal required further resolution due Lethina’s polyphyly. Conclusions: This provides into genomic evolution while elucidating efficacy mitogenomic data resolving deep this ecologically significant subfamily. findings establish genome baselines systematic research underscore essential pathways refining subtribal-level taxonomy integrative approaches.

Язык: Английский

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Genome-wide comparative analysis of variability and population structure between autochthonous Turkish chicken breeds and commercial hybrid lines

Poultry Science, Год журнала: 2025, Номер unknown, С. 105193 - 105193

Опубликована: Апрель 1, 2025

Язык: Английский

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