Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes

作者：Xiufeng Yang, Guangshuai Liu, Qi Wang, Xiaodong Gao, Tian Xia, Chao Zhao, Huashan Dou, Honghai Zhang · 发表于：Ecology and Evolution · 年份：2021 · DOI：10.1002/ece3.8071 · 被引用次数：8 · 研究领域：Adipose Tissue and Metabolism、Peroxisome Proliferator-Activated Receptors、RNA Research and Splicing

Abstract The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA‐seq to obtain a comprehensive dataset, and performed selection analysis and sequence‐level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity ( CFI and LRRFIP1 ), protein synthesis ( GOLGA4 , CEP19 and SLC35A2 ), and DNA damage repair ( MDC1 ). Further functional enrichment analyses demonstrated that two positively selected genes ( ACO1 and ACAD10 ) were involved in metabolic process (GO:0008152, p ‐value = .032), representing a significant enrichment. Sequence anal...