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
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 obtained 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 annotation results showed that 25 887, 21 822, and 10 008 Unigenes were annotated into three GO classifications: biological process, cellular component, and molecular function. Three thousand thirty transcription factors were predicted, and 22 560 microsatellites were obtained. Differential expression analysis showed 3 216 differentially expressed genes between females and males, of which 1 796 were significantly 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 enrichment analysis showed that Epstein-Barr virus infection, complement and coagulation cascades, and protein 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 Fibrinogen, including Fga, Fgb, and Fgg. The gene expression of female and male R. ocellatus had an apparent sex bias. This study's results supplemented the transcriptomic information of R. ocellatus and revealed 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.