Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

Yun Tuo; Wuying Chu; Jianshe Zhang; Jia Cheng; Lin Chen; Lingsheng Bao; Tiaoyi Xiao

doi:10.3389/fgene.2020.00714

Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing

Front Genet. 2020 Jul 24:11:714. doi: 10.3389/fgene.2020.00714. eCollection 2020.

Authors

Yun Tuo^{1

2}, Wuying Chu³, Jianshe Zhang³, Jia Cheng³, Lin Chen³, Lingsheng Bao³, Tiaoyi Xiao¹

Affiliations

¹ Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China.
² College of Life Science and Resources Environment, Yichun University, Yichun, China.
³ Department of Biological and Environmental Engineering, Changsha University, Changsha, China.

Abstract

Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.

Keywords: Spinibarbus caldwelli; immune genes; natural selection; orthologous unigenes; transcriptome.