The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Issue 12 (4th May 2021)

• Record Type: Journal Article
• Authors: Xiao, Changyi; Li, Jingjin; Xie, Tanghui; Chen, Jianhai; Zhang, Sijia; Elaksher, Salma Hassan; Jiang, Fan; Jiang, Yaoxin; Zhang, Lu; Zhang, Wei; Xiang, Yue; Wu, Zhenyang; Zhao, Shuhong; Du, Xiaoyong
• Is Part Of: Ecology and evolution. Volume 11:Issue 12(2021)
• Page Start: 7779
• Page End: 7795
• Publication Date: 2021-05-04
• Subjects: demographic history -- goat -- phylogenetic -- RH map -- Y chromosome assembly; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.7611
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y‐linked scaffolds using existing data. A total of 11.5 Mb Y‐linked sequences were clustered into 33 scaffolds, and 187 protein‐coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole‐genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2, 000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10, 000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post‐Neolithic period. Abstract : In this paper, we first assembled goat Y chromosome into 33 scaffolds totaling 11.5 Mb, and a subset of 5.84 Mb was further ordered into an assembly with the validation of goat radiation hybrid map. Then, we identified SNPs of 96 goat samples worldwide to exploit the paternal relationships among wild bezoars and domestic goats. The paternal lineages showed a clear division of bezoars and goats into two clades, and they were independent of goat domestication. Further demographical history of paternal and maternal lineages showed evident differences, with a bottleneck effect in mtDNA around 2, 000 YBP, which may be related to the worldwide dispersal of goat in the post‐Neolithic period, implied the possibility of gender preference in goat domestication. Our research provided a new perspective of goat evolution history.