Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation

Shijun Xiao; Zhenbo Mou; Dingding Fan; He Zhou; Ming Zou; Yu Zou; Chaowei Zhou; Ruibin Yang; Jiaqi Liu; Shilin Zhu; Yajuan Li; Yanchao Liu; Fei Liu; Wanliang Wang; Benhe Zeng; Hong Li; Di Wang; Haiping Liu

doi:10.1016/j.isci.2020.101497

Genome of Tetraploid Fish Schizothorax o'connori Provides Insights into Early Re-diploidization and High-Altitude Adaptation

iScience. 2020 Aug 22;23(9):101497. doi: 10.1016/j.isci.2020.101497. eCollection 2020 Sep 25.

Authors

Shijun Xiao^{1

2

3}, Zhenbo Mou¹, Dingding Fan⁴, He Zhou⁵, Ming Zou², Yu Zou², Chaowei Zhou^{1

6}, Ruibin Yang⁴, Jiaqi Liu², Shilin Zhu², Yajuan Li⁵, Yanchao Liu¹, Fei Liu¹, Wanliang Wang¹, Benhe Zeng¹, Hong Li⁷, Di Wang⁷, Haiping Liu¹

Affiliations

¹ Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.
² Department of Computer Science, Wuhan University of Technology, Wuhan, China.
³ College of Plant Protection, Jilin Agriculture University, Changchun, Jilin, China.
⁴ College of Fisheries, Huazhong Agricultural University, Wuhan, China.
⁵ College of Fisheries and Life Science, Dalian Ocean University, Dalian, China.
⁶ Department of Aquaculture, College of Animal Science, Southwest University, Chongqing, China.
⁷ Novogene Bioinformatics Institute, Beijing, China.

Abstract

Whole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). Here, we present a genome for Schizothorax o'connori, a QTP endemic fish and showed the species as a young tetraploid with a recent WGD later than ∼1.23 mya. We exhibited that massive insertions between duplicated genomes caused by transposon bursts could induce mutagenesis in adjacent sequences and alter the expression of neighboring genes, representing an early re-diploidization process in a polyploid genome after WGD. Meanwhile, we found that many genes involved in DNA repair and folate transport/metabolism experienced natural selection and might contribute to the environmental adaptation of this species. Therefore, the S. o'connori genome could serve as a young tetraploid model for investigations of early re-diploidization in polyploid genomes and offers an invaluable genetic resource for environmental adaptation studies of the endemic fish of the QTP.

Keywords: Biological Sciences; Evolutionary Biology; Genomics; Transcriptomics.