Evolutionary origin of genomic structural variations in domestic yaks

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 19, 2023

Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not distinguished previously. We constructed a graph-genome for 47 genomes 7 cross-fertile bovine species. This allowed detection 57,432 high-resolution structural (SVs) within across the species, which were genotyped in 386 individuals. evolutionary origins diverse SVs domestic yaks phylogenetic analyses. further identified 334 genes overlapping with that bore potential signals selection from wild yaks, plus an additional 686 introgressed cattle. Nearly 90% Introgression SV spanning KIT gene triggered breeding white yaks. validated significant association selected stratified expression, contributes phenotypic variations. Our results highlight different contribute diversity

Язык: Английский

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Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Ноя. 28, 2023

Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across wide range of agro-ecosystems, from extremely hot semiarid regions humid tropical regions. However, their adaptive genetic changes following dispersal into East Asia the Indian subcontinent have remained poorly documented. Here, we characterize global diversity using high-quality whole-genome sequencing data 354 indicine cattle 57 breeds/populations, including major phylogeographic groups worldwide. We reveal probable migration was along coastal route rather than inland routes and detected introgression other bovine species. Genomic carrying morphology-, immune-, heat-tolerance-related genes underwent divergent selection according Asian agro-ecologies. identify distinct sets loci that contain promising candidate variants for adaptation semi-arid ecosystems. Our results indicate rapid successful environments promoted by localized banteng and/or gaur. findings provide insights history environmental cattle.

Язык: Английский

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Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Сен. 18, 2023

Abstract Background Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds East Asia taurine indicine origins that have evolved adapt cold hot environments, respectively. However, few studies investigated SVs Asian their roles adaptation, little is known about adaptively introgressed cattle. Results In this study, we examine the climate adaptation these two lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison assemblies along with 18 obtained long-read sequencing data provides a catalog 123,898 nonredundant SVs. Several detected from long reads exons genes associated epidermal differentiation, skin barrier, bovine tuberculosis resistance. Functional investigations show 108-bp exonic insertion SPN may affect uptake Mycobacterium macrophages, which might contribute low susceptibility tuberculosis. Genotyping 373 whole 39 identifies 2610 differentiated “north–south” gradient China overlap 862 related enriched pathways adaptation. We identify 1457 Chinese indicine-stratified possibly originate banteng frequent Conclusions Our findings highlight unique contribution disease

Язык: Английский

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Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Сен. 6, 2022

Abstract Wild yak ( Bos mutus ) and domestic grunniens are adapted to high altitude environment have ecological, economic, cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, genetic cellular bases underlying adaptations of extreme conditions remains elusive. In present study, we assembled two chromosome-level genomes, one each for wild yak, screened structural variants (SVs) through long-read data taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 carrying special type SVs were differentially expressed in lungs cattle yak. We then constructed first single-cell gene expression atlas lung tissues identified a yak-specific endothelial cell subtype. By integrating transcriptome data, cells highest proportion marker lungs. Furthermore, pathways which related medial thickness formation elastic fibers These findings provide new insights into high-altitude adaptation important implications understanding physiological pathological responses large mammals humans hypoxia.

Язык: Английский

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Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau

Science Advances, Год журнала: 2023, Номер 9(50)

Опубликована: Дек. 13, 2023

Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about history.

Язык: Английский

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Global dispersal and adaptive evolution of domestic cattle: a genomic perspective

Stress Biology, Год журнала: 2023, Номер 3(1)

Опубликована: Апрель 18, 2023

Abstract Domestic cattle have spread across the globe and inhabit variable unpredictable environments. They been exposed to a plethora of selective pressures adapted variety local ecological management conditions, including UV exposure, diseases, stall-feeding systems. These resulted in unique important phenotypic genetic differences among modern breeds/populations. Ongoing efforts sequence genomes commercial breeds/populations, along with growing availability ancient bovid DNA data, significantly advanced our understanding genomic architecture, recent evolution complex traits, common adaptation cattle. Here, we review origin domestic illustrate environmental adaptations

Язык: Английский

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Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference

Molecular Biology and Evolution, Год журнала: 2022, Номер 39(7)

Опубликована: Июль 1, 2022

Abstract Genetic recombination plays a critical role in the emergence of pathogens with phenotypes such as drug resistance, virulence, and host adaptation. Here, we tested hypothesis that between sympatric ancestral populations leads to divergent variants zoonotic parasite Cryptosporidium parvum modified ranges. Comparative genomic analyses 101 isolates have identified seven subpopulations isolated by distance. They appear be descendants two populations, IIa northwestern Europe IId from southwestern Asia. Sympatric areas both subtypes subsequent selective sweeps led new mosaic genomes preference. Subtelomeric genes could involved adaptive selection subpopulations, while copy number variations encoding invasion-associated proteins are potentially associated These observations reveal origins C. suggest pathogen import through modern animal farming might promote

Язык: Английский

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Profiling the immune epigenome across global cattle breeds

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Май 22, 2023

Abstract Background Understanding the variation between well and poorly adapted cattle breeds to local environments pathogens is essential for breeding with improved climate disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences breeds, at epigenetic chromatin levels remains characterized. Here, we generate, sequence analyse over 150 libraries base-pair resolution explore dynamics of DNA methylation accessibility bovine immune system across three distinct lineages. Results We find extensive divergence taurine indicine cell types, which linked two sub-species. The unique type profiles enable deconvolution complex cellular mixtures using digital cytometry approaches. Finally, show sub-categories CpG islands based on their that discriminate classes distal gene proximal discrete transcriptional states. Conclusions Our study provides a comprehensive resource methylation, RNA expression diverse populations. findings have important implications, from understanding how editing consequently regulatory backgrounds, may impacts designing effective epigenome-wide association studies in non-European breeds.

Язык: Английский

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Whole‐genome resequencing uncovers diversity and selective sweep in Kazakh cattle

Animal Genetics, Год журнала: 2024, Номер 55(3), С. 377 - 386

Опубликована: Апрель 1, 2024

Abstract The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk meat production, use as draft animals. They an excellent original breed that could be enhanced by breeding hybrid improvement. However, genomic diversity signature selection underlying germplasm characteristics require further elucidation. Herein, we evaluated 26 genomes comparison with 103 seven other breeds from regions around world to assess genetic variability. We revealed relatively low linkage disequilibrium at large SNP distances was strongly correlated largest effective population size among cattle. Using structural analysis, next demonstrated a taurine lineage restricted Bos indicus introgression Notably, identified putative selected genes associated resistance disease body within Together, our findings shed light on evolutionary history profile cattle, well offering indispensable resources for resource conservation crossbreeding program implementation.

Язык: Английский

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The Genomic Legacy of Aurochs hybridization in ancient and modern Iberian Cattle

Опубликована: Янв. 7, 2025

Cattle have been a valuable economic resource and cultural icon since prehistory. From the initial expansion of domestic cattle into Europe during Neolithic period, taurine ( Bos taurus ) their wild ancestor, aurochs B. primigenius ), had overlapping ranges, leading to ample opportunities for mating (whether intended by farmers or not). We performed bioarchaeological analysis 24 remains from Iberia dating Mesolithic Roman period. The archaeogenomic dataset allows us investigate extent domestic-wild hybridization over time, providing insight species’ behavior human hunting management practices aligning changes with genomic transitions in archaeological record. Our results show frequent Chalcolithic, likely reflecting mix herding relatively unmanaged herds, mostly male female involved hybridization. This is supported isotopic evidence consistent ecological niche sharing, only few possibly being managed. proportion ancestry constant about 4000 years ago, probably due herd selection against first generation hybrids, coinciding other transitions. level (∽20%) continues modern western European breeds including Spanish Lidia breed which bred its aggressiveness fighting ability, but does not display elevated levels ancestry. study takes glance at impact actions introgression establishment as one most important species today.

Язык: Английский

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