Yang Xiufeng, Liu Guangshuai, Wang Qi, Gao Xiaodong, Xia Tian, Zhao Chao, Dou Huashan, Zhang Honghai
College of Life Science Qufu Normal University Qufu China.
Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China.
Ecol Evol. 2021 Aug 30;11(19):13475-13486. doi: 10.1002/ece3.8071. eCollection 2021 Oct.
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 ( and ), protein synthesis (, and ), and DNA damage repair (). Further functional enrichment analyses demonstrated that two positively selected genes ( and ) were involved in metabolic process (GO:0008152, -value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the , and genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.
银狐和蓝狐是具有重要经济价值的毛皮动物，分别由人类从它们的野生同类北极狐和赤狐驯化而来。养殖狐与野生狐表现出明显差异，包括生理、体型、能量代谢和免疫方面的差异。然而，这些差异背后的分子机制目前尚不清楚。在本研究中，我们为每种养殖狐的多个混合组织构建了转录组文库，利用RNA测序获得了一个全面的数据集，并对直系同源基因进行了选择分析和序列水平分析，以鉴定可能受人类驯化影响的基因。分别获得了超过1.533亿、2.480亿、8160万和6580万条clean reads，并分别组装成118577、401520、79900和186988个单基因，AF、BF、RF和SF的平均长度范围分别为521至667 bp。选择压力分析表明，在两组（AF与BF以及RF与SF）中分别鉴定出11个和14个正选择基因。其中一些基因与天然免疫（和）、蛋白质合成（、和）以及DNA损伤修复（）相关。进一步的功能富集分析表明，两个正选择基因（和）参与代谢过程（GO:0008152，-值 = 0.032），具有显著富集。对两组共有的117个直系同源基因的序列分析表明，、和基因可能在养殖狐中受到人工选择影响，其突变位点位于大多数哺乳动物中高度保守的序列内。我们的结果为未来狐及其他养殖动物的遗传研究和辅助育种改进提供了有价值的转录组资源。
