De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens.
Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing. A total of 212,180 contigs were obtained, ranging from 127 to 64,876 bp, and N50 of 1,066 bp. The assembly RNA-Seq contigs (≥200bp) were then used for subsequent analyses, including annotation, pathway analysis, and microsatellites discovery. No female- and pseudo-male-biased genes were involved in any pathways while male-biased genes were involved in 29 pathways, and neuroactive ligand receptor interaction and enzyme of trypsin (enzyme code, EC: 3.4.21.4) was highly involved. Pyruvate kinase (enzyme code, EC: 2.7.1.40), which plays important roles in cell proliferation, was highly expressed in muscles. In addition, a total of 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified. This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.|College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, PRC.
Yan-He
YH
Li
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Han-Ping
HP
Wang
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Hong
H
Yao
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Paul
P
O'Bryant
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Dean
D
Rapp
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Liang
L
Guo
Fish Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, Ohio, United States of America.
Eman A
EA
Waly
D000818:Animals; D049109:Cell Proliferation / Q000235:genetics / Q000502:physiology; D005260:Female; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010471:Perches / Q000235:genetics* / Q000502:physiology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D012727:Sex Characteristics; D019849:Sex Determination Processes / Q000235:genetics