Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

Cheng, Qimin; Li, Yuanfeng; Wang, Yahui; Ping, Jie; Lu, Yiming; Zhou, Gangqiao

doi:10.1101/2020.12.01.401174

Cited by 13 publications

(20 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The number of variants rapidly decreases with length, consistent with the reports in humans using long-read sequencing [5, 6, 27]. We observed noticeable peaks at 150 bp corresponding to SINES, 1,350 bp and 1,600 bp corresponding to LTR, as well as 7,750 bp corresponding to LINES (Fig 2A).…”

Section: Resultssupporting

confidence: 89%

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Gong

Zhang

et al. 2021

Preprint

View full text Add to dashboard Cite

Structural variations (SVs) are a major contributor of genetic diversity and phenotypic variations, however their prevalence and functions in domestic animals are largely unexplored. Here, we assembled 26 haplotype-resolved genome assemblies from 13 genetically diverse sheep breeds using PacBio HiFi sequencing. We then constructed an ovine graph pan-genome and demonstrated its advantage in discovering 142,593 biallelic SVs (Insertions and deletions), 7,028 divergent alleles and 13,419 multiallelic variations with high accuracy and sensitivity. To link the SVs to genotypes, we genotyped the SVs in 687 resequenced individuals of domestic and wild sheep using a graph-based approach and identified numerous population-stratified variants, of which expression-associated SVs were detected by integrating RNA-seq data. Taking the varying sheep tail morphology as example, we located a putative causative insertion in HOXB13 gene responsible for the long tail and reported multiple large SVs associated with the fat tail. Beyond generating a benchmark resource for ovine structural variants, our study also highlighted that the population genetics analysis based on graph pan-genome rather than reference genome will greatly benefit the animal genetic research.

show abstract

Section: Resultssupporting

confidence: 89%

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Gong

Zhang

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…2d ). A total of 75.4% of the SVs contained repeat sequences or interspersed elements (Supplementary Data 6 ), similar to the percentage of 78.3% detected in the Chinese Tibetan and Han populations 28 . This was consistent with the knowledge that SVs tend to occur in segments with more repetitive sequences 1 .…”

Section: Resultssupporting

confidence: 70%

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

Jiang

et al. 2021

Nat Commun

View full text Add to dashboard Cite

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.

show abstract

“…S6E. Thus, a further whole-genome sequencing project based on geographically different Sherpa people with larger sample size and single-molecule real-time sequencing technology should be conducted focused on Sherpa people in the next step, as the genetic findings in Tibetans [53].…”

Section: Finer-scale Population Demographic History and Natural Selec...mentioning

confidence: 99%

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Wang

Tang

et al. 2022

Forensic Science International: Genetics

View full text Add to dashboard Cite

Characterization of Structural Variation in Tibetans Reveals New Evidence of High-altitude Adaptation and Introgression

Cited by 13 publications

References 63 publications

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

The first sheep graph-based pan-genome reveals the spectrum of structural variations and their effects on tail phenotypes

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Contact Info

Product

Resources

About