Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes

Yeyu Chen; Ya Liu; Quan Gong; Jiansheng Lai; Mingjiang Song; Jun Du; Xiaochuan Deng

doi:10.7717/peerj.5389

Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes

PeerJ. 2018 Jul 27:6:e5389. doi: 10.7717/peerj.5389. eCollection 2018.

Authors

Yeyu Chen^#¹, Ya Liu^#¹, Quan Gong¹, Jiansheng Lai¹, Mingjiang Song¹, Jun Du¹, Xiaochuan Deng¹

Affiliation

¹ The Sichuan Academy of Agricultural Sciences, The Fishery Institute, Chengdu, China.

^# Contributed equally.

Abstract

Background: Acipenser dabryanus, an endemic Chinese species, has been listed as a first-class protected animal in China. Sturgeons are among the oldest and most primitive group of existing fish in the world and occupy a special place in the evolutionary history of fish. Thus, a study of the reproduction and sex differentiation of sturgeon will be of great value for fish as well as the whole vertebrate group.

Methods: In this study, we conducted comparative analysis of the testes and ovaries transcriptomes of A. dabryanus to screen for sex-differentiation and sexual development-related genes.

Results: The transcriptome sequencing of six cDNA libraries generated 265 million clean reads, encompassing 79 Gb of sequences. The N50 and mean length of the identified 91,375 unigenes were 1,718 and 989 bp, respectively. A total of 6,306, 9,961, 13,170, 15,484, and 23,588 unigenes were annotated in the clusters of orthologous groups, gene ontology categories, Kyoto Encyclopedia of Genes and Genomes Pathway, euKaryotic orthologous groups, and NCBI non-redundant protein databases, respectively. A total of 5,396 differentially expressed genes were found between the two sexes, with 1,938 predicted to be up-regulated in ovaries and 3,458 in testes. A total of 73 candidate genes known to be involved in sex differentiation and sexual development were searched in the transcriptome of A. dabryanus of which 52 showed significant similarity. We highlighted six genes that are differentially expressed between the two sexes and may play important roles in sex differentiation and gonad maintenance. In addition, 24,271 simple sequence repeats (SSRs) and 550,519 single-nucleotide polymorphisms (SNPs) were detected.

Discussion: This work represents the first transcriptome study comparing the ovary and testis in A. dabryanus. The putative differentially expressed genes between the gonads provide an important source of information for further study of the sex-differentiation related genes and the sex-differentiation mechanism in sturgeons. The SSRs or SNPs identified in this study will be helpful in the discovery of sex-related markers in A. dabryanus.

Keywords: Acipenser dabryanus; Differentially expressed genes; Ovary; Sex-related genes; Testis; Transcriptome.

Grants and funding

This work was supported by grants from the Project of Screening of Sex-related Genes and Makers for Acipenser dabryanus Based on Transcriptome Sequencing (2018JY0636), Project of Screening of Sex-linked Markers and Sex Determination Gene for Acipenser dabryanus Based on Transcriptome Sequencing Technology (No. 2017QNJJ-013), the Project of Provincial 13th Five Years’ Animal Breeding of Sichuan Province (No. 2016NYZ0047) and the Development of Microsatellite Derived from Acipenser dabryanus and Its Application in Paternity Test (No. 2017QNJJ-012). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.