Study on a sex bias in gene expression of Rhodeus ocellatus based on RNA-seq

LIU Kai; FENG Xiaoyu; WU Yanqin; XIE Nan; CHU Tianjiang

doi:10.13984/j.cnki.cn37-1141.2024.05.011

Abstract：Understanding the sex bias of gene expression is helpful to understand the dimorphism of sex-related phenotypes,and it is also a significant field in the study of gene-phenotype interactions.To fill the genetic data gap and reveal sex bias in gene expression,RNA-seq of the muscle of Rhodeus ocellatus was carried out for the first time.Three females and three males were collected,respectively,and the muscle tissue was dissected from the fish.The exfoliated tissue was ground in liquid nitrogen,and total RNA was extracted.Then sequences through the Illumina HiSeq sequencing platform,and differential expression gene analyses were performed.The results showed that the Clean Data of 6.39 GB and 6.70 GB were obtained from the female and male R.ocellatus,respectively,and 46 194 Unigenes were ob-tained after assembly,with 59.68 Mb and an average sequence length of 1 354.67 bp.24 754 Unigenes were annotated by comparing the databases,accounting for 53.59％of all Unigenes.GO functional an-notation results showed that 25 887,21 822,and 10 008 Unigenes were annotated into three GO classi-fications:biological process,cellular component,and molecular function.Three thousand thirty tran-scription factors were predicted,and 22 560 microsatellites were obtained.Differential expression anal-ysis showed 3 216 differentially expressed genes between females and males,of which 1 796 were sig-nificantly up-regulated and 1 420 were significantly down-regulated in males.GO enrichment analysis showed that gene expression differences between males and females were mainly concentrated on GO terms such as hydrolase activity,transporter activity,and extracellular region.KEGG pathway enrich-ment analysis showed that Epstein-Barr virus infection,complement and coagulation cascades,and pro-tein digestion and absorption pathway were the three pathways with the most enriched differential genes.Protein-protein interaction network analysis showed that there were two major protein-protein interaction networks between female and male individuals.One consists of Proteasome Endopeptidase Complex,including PSMD1,Psmd3,Psmd5,and other related genes;the other consists of Fibrino-gen,including Fga,Fgb,and Fgg.The gene expression of female and male R.ocellatus had an appar-ent sex bias.This study's results supplemented the transcriptomic information of R.ocellatus and re-vealed the sex bias of gene expression in R.ocellatus,and provided data support for further research on the sex bias of gene expression and phenotype interactions.