Research Article: De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens

Date Published: February 3, 2017

Publisher: Public Library of Science

Author(s): Yan-He Li, Han-Ping Wang, Hong Yao, Paul O’Bryant, Dean Rapp, Liang Guo, Eman A. Waly, Christoph Englert.

http://doi.org/10.1371/journal.pone.0171187

Abstract

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.

Partial Text

Yellow perch, Perca flavescens, natively distributes from central Canada, east and southeast through the Great Lakes—St. Lawrence and the upper Mississippi basins and on the Atlantic slope from Maine to Georgia [1]. It is a vital recreational and commercial species in Chesapeake Bay and the Great Lakes [2]. Yellow perch females outgrow males starting from 8–11 cm in total length and also have dominant and subordinated females [3]. Yellow perch have an XY sex-determination system [4]. Uniquely, yellow perch female have only one ovary and spawn egg ribbons (all the eggs in a ribbon-like bag). Also sex-reversed pseudo-males develop a single gonad [4]. Male skewed sex ratios have been observed in experimental and natural populations (Wang et al. unpublished data). Thus, yellow perch doubtlessly attracted much attention for its value as the material of studying mechanism of sexual dimorphism, sex determination, and sexual selection.

A total of 211,976 contigs were obtained and 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified from assembled contigs. No female- and pseudo-male-biased genes were found being involved in any pathways. Male-biased genes were found being involved in 29 pathways, of which neuroactive ligand receptor interaction was highly involved. Pyruvate kinase was highly expressed in muscle. 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. Further experiments would be needed to test the roles of the enzyme pathways involved and the gene expression profiles associated with those pathways.

 

Source:

http://doi.org/10.1371/journal.pone.0171187

 

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