Evolutionary origin of genomic structural variations in domestic yaks

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 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

Language: Английский

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Genomics-based taxonomy to clarify cannabis classification

Genome, Journal Year: 2023, Volume and Issue: 66(8), P. 202 - 211

Published: May 10, 2023

In the 18th century, Carolus Linnaeus created a formalized system of classification living organisms based on their anatomic relationships, which we know as taxonomic nomenclature. Historically, genus Cannabis has been described three ways under this system: sativa by C. in 1753, indica J.B. Lamarck 1785, and ruderalis D.E. Janischewsky 1924, with these classifications having derived from physical, morphological, chemical, geographical data. Today, confusing taxonomy led to an ongoing debate about whether consists single species or multiple distinct subspecies. Recently, genome sequencing bioinformatics have provided greater resolution assignments at level. As result, some previously discussed frameworks brought into question. The aim review is provide historical context for confusion surrounding highlight recent research genomics-based taxonomical approaches clarify question taxonomy. We suggest that latest evidence shifts away previous framework points towards consisting highly diverse monotypic species.

Language: Английский

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Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(2), P. 339 - 351

Published: Jan. 9, 2024

Language: Английский

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Subfamily evolution analysis using nuclear and chloroplast data from the same reads

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp data with nuclear DNA information offers more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing to construct genome-based trees and phylogenetic using Read2Tree, cost-efficient method extracting conserved gene sequences from data, focusing on Aurantioideae subfamily, which includes Citrus relatives. resulting were consistent existing derived high-throughput sequencing, diverged trees. To elucidate underlying complex processes causing discordances, implemented an integrative workflow that utilized multiple alignments of each generated by conjunction other phylogenomic methods. Our analysis revealed incomplete lineage sorting predominantly drives while introgression ancient also contribute topological discrepancies within certain clades. This study underscores cost-effectiveness both analyses understanding relationships.

Language: Английский

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Analysis of the distribution pattern of the ectomycorrhizal fungus Cenococcum geophilum under climate change using the optimized MaxEnt model

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(9)

Published: Sept. 1, 2023

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Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

animal, Journal Year: 2024, Volume and Issue: 18(6), P. 101147 - 101147

Published: March 28, 2024

Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed south China's tropical island province Hainan, possess distinctive traits such hair, moderate growth rate, good meat quality, small body size. However, they exhibit exceptional resilience to rough feeding conditions, high-quality meat, show remarkable resistance stress heat. In this study, we resequenced whole genome goats study economic basis these leveraged whole-genome sequencing data from 33 analyze single nucleotide polymorphism(SNP) density, Runs homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) selection characteristics. Our findings revealed that harbor substantial degree variation, with total 23 608 983 polymorphisms (SNPs) identified. ROHs identified 53 710 segments, predominantly composed short fragments, inbreeding events mainly occurring in ancient ancestors, estimates based on ROH typically values ranging 0.107 0.186. This primarily attributed significant declines over recent generations. Moreover, 921 candidate genes within intersection region iHS. Several are associated immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 LEPR), quality (ACOX1, SSTR1, CAMK2B, PPP2CA PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 CDK19), (TLR2, IFI44, ENPP1, STK3 NFATC1). The presence may be adaptation local climate conditions. insights gained provide valuable references solid foundation preservation, breeding, utilization resources.

Language: Английский

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RAD-seq data for Engelhardia roxburghiana provides insights into the palaeobiogeography of Hainan Island and its relationship to mainland China since the late Eocene

Palaeogeography Palaeoclimatology Palaeoecology, Journal Year: 2024, Volume and Issue: 651, P. 112392 - 112392

Published: July 24, 2024

Language: Английский

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Evolutionary divergence on the Qinghai-Tibet Plateau: How life-history traits shape the diversity of plateau zokor and pika populations

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

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Environmental and climatic drivers of phenotypic evolution and distribution changes in a widely distributed subfamily of subterranean mammals

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 878, P. 163177 - 163177

Published: March 30, 2023

Language: Английский

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Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot

Horticulture Research, Journal Year: 2024, Volume and Issue: 11(4)

Published: April 1, 2024

, an extremely rare population of apricots, originated in warm South-East China and is excellent material for genetic breeding. However, most apricots two related species (

Language: Английский

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