A Comprehensive Transcriptome Provides Candidate Genes for Sex Determination/Differentiation and SSR/SNP Markers in Yellow Catfish

Abstract

Sex dimorphic growth pattern has significant theory and application implications in fish. Recently, a Y-and Xspecific allele marker-assisted sex control technique has been developed for mass production of all-male population in yellow catfish (Pelteobagrus fulvidraco), but the genetic information for sex determination and sex control breeding has remained unclear. Here, we attempted to provide the first insight into a comprehensive transcriptome covering multiple tissues from XX females, XY males, and YY super-males of yellow catfish by using 454 GS-FLX platform, for a better assembly and gene coverage. A total of 1,202,933 high quality reads (about 540 Mbp) were obtained and assembled into 28,297 contigs and 141,951 singletons. BLASTX searches against the NCBI non-redundant protein database (nr) led a total of 52,564 unique sequences including 18,748 contigs and 33,816 singletons to match 25,669 known or predicted unique proteins. All of them with annotated function were categorized by gene ontology (GO) analysis, and 712 were assigned to reproduction and reproductive process. Some potential genes relevant to reproductive system including steroid hormone biosynthesis and GnRH (gonadotropin-releasing hormone) signaling pathway were further identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis; and at least 21 sex determination and differentiation-related genes, such as Dmrt1, Sox9a/b, Cyp19b, WT1, and AMH were identified and characterized. Additionally, a total of 82,794 simple sequence repeats (SSRs), 26,450 single nucleotide polymorphisms (SNPs), and 4,145 insertions and deletions (INDELs) were revealed from the transcriptome data. Therefore, the current transcriptome resources highlight further studies on sex-control breeding in yellow catfish and will benefit future studies on reproduction and sex determination in teleost fish.

Identification of Sex-Specific Markers Reveals Male Heterogametic Sex Determination in Pseudobagrus ussuriensis

“…In this study, we developed three pairs of sex-specific primers and used them to efficiently identify genetic sex in P. ussuriensis. Of course, the currently screened sex-specific markers and the surrounding regions should be significant for identifying sex determination gene or sex-related genes in this fish species, and some identified techniques, such as BAC library screening (Li et al 2014a, b) and comprehensive transcriptome analysis (Zhang et al 2014a, b;Chen et al 2015), will be useful for this purpose.…”

Sex differences in the expression of GH/IGF axis genes underlie sexual size dimorphism in the yellow catfish (Pelteobagrus fulvidraco)

“…Yellow catfish males grow much faster than the females. Therefore, we cloned the GH/IGF axis genes, GH, IGF-1, and IGF-2, from the transcriptome of yellow catfish (Chen et al, 2015) and characterized their different expressions in males and females.…”

A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata)

“…454 sequencing of liver and white skeletal muscle cDNA normalised libraries from S. aurata juveniles submitted to starvation or feeding on five selected diets allowed us to generate transcriptomes for liver, skeletal muscle and a hybrid transcriptome integrating data from both tissues. The number of isotigs (19,530), contigs (23,956) and average isotig and contig length (1330 bp and 901 bp, respectively) of the hybrid transcriptome indicates that effective data assemblies were carried out compared to values reported for other fish species of interest in aquaculture [44]. In contrast to previous studies, prior to 454 pyrosequencing we constructed normalised libraries using tissue samples from long-term starved fish and fish fed five diets differing in macronutrient composition to allow maximal representation of transcripts abundance and diversity in regard to dietary condition.…”