Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing

Rui Ruan; Tong Feng; Ying Li; Huamei Yue; Huan Ye; Hao Du; Qingyou Liu; Jue Ruan; Chuangju Li; Qiwei Wei

doi:10.1016/j.ygeno.2021.11.012

Screening and identification of female-specific DNA sequences in octaploid sturgeon using comparative genomics with high-throughput sequencing

Genomics. 2021 Nov;113(6):4237-4244. doi: 10.1016/j.ygeno.2021.11.012. Epub 2021 Nov 14.

Authors

Rui Ruan¹, Tong Feng², Ying Li¹, Huamei Yue¹, Huan Ye¹, Hao Du¹, Qingyou Liu³, Jue Ruan⁴, Chuangju Li⁵, Qiwei Wei⁶

Affiliations

¹ Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
² Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
³ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China.
⁴ Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China. Electronic address: ruanjue@caas.cn.
⁵ Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. Electronic address: lcj@yfi.ac.cn.
⁶ Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China. Electronic address: weiqw@yfi.ac.cn.

PMID: 34785350
DOI: 10.1016/j.ygeno.2021.11.012

Abstract

In this study, six candidate female-specific DNA sequences of octaploid Amur sturgeon (Acipenser schrenckii) were identified using comparative genomic approaches with high-throughput sequencing data. Their specificity was confirmed by traditional PCR. Two of these sex-specific sequences were also validated as female-specific in other eight sturgeon species and two hybrid sturgeons. The identified female-specific DNA fragments suggest that the family Acipenseridae has a ZZ/ZW sex-determining system. However, one of the two DNA sequences has been deleted in some sturgeons such as Sterlet sturgeon (Acipenser ruthenus), Beluga (Huso huso) and Kaluga (H. dauricus). The difference of sex-specific sequences among sturgeons indicates that there are different sex-specific regions among species of sturgeon. This study not only provided the sex-specific DNA sequences for management, conservation and studies of sex-determination mechanisms in sturgeons, but also confirmed the capability of the workflow to identify sex-specific DNA sequences in the polyploid species with complex genomes.

Keywords: Acipenseridae; Comparative genomics; Complex genome; K-mers; Sex-specific DNA fragments.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Female
Fishes* / genetics
Genome*
Genomics
High-Throughput Nucleotide Sequencing