Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis). (3rd November 2020)

• Record Type: Journal Article
• Authors: Liang, Dong; Zhao, Pengju; Si, Jingfang; Fang, Lingzhao; Pairo-Castineira, Erola; Hu, Xiaoxiang; Xu, Qing; Hou, Yali; Gong, Yu; Liang, Zhengwen; Tian, Bing; Mao, Huaming; Yindee, Marnoch; Faruque, Md Omar; Kongvongxay, Siton; Khamphoumee, Souksamlane; Liu, George E; Wu, Dong-Dong; Barker, James Stuart F; Han, Jianlin; Zhang, Yi
• Editors: Wilson, Melissa
• Is Part Of: Molecular biology and evolution. Volume 38:Number 3(2021)
• Page Start: 1122
• Page End: 1136
• Publication Date: 2020-11-03
• Subjects: white coat color -- water buffalo -- ASIP gene -- LINE-1 -- transposon -- convergent evolution; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msaa279
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2, 809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo ( Bubalus bubalis ). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.