The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

Xiao, Changyi; Li, Jingjin; Xie, Tingting; Zhang, Sijia; Elaksher, Salma Hassan; Fan, Jun; Jiang, Yaoxin; Zhang, Lu; Zhang, Wei; Xiang, Yue; Wu, Zhenyang; Zhao, Shuhong; Du, Xiaoyong

doi:10.1002/ece3.7611

Cited by 11 publications

(9 citation statements)

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“…On the basis of WGS data, Zheng et al ( 2020) and Xiao et al (2021) reproduced the divergence of the domestic Y1 and Y2 haplogroups previously found on the basis of SNPs within or near Y-chromosomal genes (Lenstra & Econogene Consortium, 2005). Here we report a further differentiation of haplogroups, resulting in a phylogeny supported by a largely independent preliminary data set (Figure S1) and two phylogenetic algorithms.…”

Section: Discussionmentioning

confidence: 70%

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Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

et al. 2022

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By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from presentday bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene

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Section: Discussionmentioning

confidence: 70%

“…Nor does it inform us on the Y‐chromosomal variants that existed in earlier domestic goats or in their wild ancestor, the bezoar ( Capra aegagrus ; Amills et al, 2017). Whole‐genome sequencing (WGS), however, has confirmed the differentiation of the Y1 and Y2 haplogroups (Xiao et al, 2021; Zheng et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

et al. 2022

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“…1b). The two available Y chromosome assemblies of Saanen_v1 6 (CM027080.1) and ARS1 -based scaffolded contigs 29 (GCA_018357025.1) are only 9.6 Mb and 11.5 Mb in length, respectively, and were used to evaluate T2T-CHIY1.0 quality. According to the collinearity plots, the syntenic regions of ∼7 Mb between the left arms of chromosomes X and Y were not assembled in these two incomplete Y chromosome assemblies (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Wu,

Luo,

Zhang

et al. 2024

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A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing novel insights into domestication and selection in goats and related species. Here, we assembled a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), which included a Y chromosome of 20.9 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrected numerous genome-wide structural and base errors in previous assemblies and added 288.5 Mb of previously unresolved regions (PURs) and 446 newly assembled genes to the reference genome. We sequenced the genomes of five representative goat breeds for PacBio reads, and used T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 SVs (7.41%) in the PURs and 507 overlapping genes significantly enriched (Padj. < 0.05) in the keratin filament pathway. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the PURs. Also, our analyses revealed a set of novel selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

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“…Nor does it inform us on the Y-chromosomal variants that existed in earlier domestic goats or in their wild ancestor, the bezoar (Capra aegagrus; Amills et al, 2017). Whole-genome sequencing (WGS), however, has confirmed the differentiation of the Y1 and Y2 haplogroups (Xiao et al, 2021;Zheng et al, 2020).…”

Section: A Preliminary Analysis Of the Y-chromosomal Diversity Inmentioning

confidence: 99%

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Consortium

Nijman

Rosen³

et al. 2022

Preprint

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By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.

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The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 11 publications

References 135 publications

Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

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