Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers

Abstract

Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers. Physiol Genomics 46: 798 -807, 2014. First published September 2, 2014; doi:10.1152/physiolgenomics.00088.2014.-Yellow catfish (Pelteobagrus fulvidraco) has been recognized as a vital freshwater aquaculture species in East and Southeast Asia. In addition to its commercial interest, it is also attracted much attention because of its value in studying sex-determination mechanisms. A comprehensive gonadal transcriptome analysis is believed to provide a resource for genome annotation, candidate gene identification, and molecular marker development. Herein, we performed a de novo assembly of yellow catfish gonad transcriptome by high-throughput Illumina sequencing. A total of 82,123 contigs were obtained, ranging from 351 to 21,268 bp, and N50 of 2,329 bp. Unigenes of 21,869 in total were identified. Of these, 229 and 1,188 genes were found to be specifically expressed in XY gonad tissue for 1 yr and 2 yr old yellow catfish, respectively; correspondingly, 51 and 40 genes were identified in XX gonad tissue at those two stages. Gene ontology and KEGG analysis were conducted and classified all contigs into different categories. A large number of unigenes involved in sex determination were identified, as well as microsatellites and SNP variants. The expression patterns of sex-related genes were then validated by quantitative real-time PCR (qRT-PCR) suggesting the high reliability of RNA-Seq results. In this study, the transcriptome of yellow catfish gonad was first sequenced, assembled, and characterized; it provides a valuable genomic resource for better understanding of yellow catfish sex determination as well as development of molecular markers, thereby assisting in the production of monosex yellow catfish for aquaculture. sex-related; gene expression; transcriptome sequencing YELLOW CATFISH (Pelteobagrus fulvidraco) has been recognized as a vital freshwater aquaculture species in East and Southeast Asia. In addition to its commercial interest, it has also attracted much attention because of its value in the study of dimorphism and sex-determination mechanisms. Genetically, yellow catfish harbors an XX/XY system (38). The sexual growth dimorphism favors males in this species; males of yellow catfish can be up to 30 -50% larger than female siblings under the same breeding condition in the first year, and one to two times larger than females in the second year (38). Thus, knowing the underpinnings of sex determination and sex dimorphism would help develop methods to achieve monosex consisting production (9) to meet the increasing demand of the aquaculture market.The gonad is the primary organ presenting morphological signs of sexual dimorphism. It has bipotential fates to form either ovary or testis depending on a sex determination cue in many fish species; the development of gonad is referred as sex differentiation. Gene expression between sexes has a great portion of difference in gonad...

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…The GO analysis in this research was similar to the testes transcriptome analysis for the channel catfish by Sun et al, [52] and the yellow catfish by Lu et al, [53]. Four of the top five GO terms in the biological process category for the channel catfish (cellular process, metabolic process, biological regulation, and response to stimulus) and the top four GO terms for the yellow catfish (cellular process, singleorganism process, metabolic process, and biological regulation) matched the top five GO terms in this study [52,53].…”

“…The binding, catalytic activity, transporter activity, and molecular transducer GO terms were represented within the top five GO terms of the molecular function category for all three testis transcriptome studies. For the cellular componentcategory, four of the top five GO terms for the channel catfish (cell, organelle, macromolecular complex, and extracellular region) and four of the top five GO terms for the yellow catfish (cell, organelle, membrane, and macromolecular complex) matched the top five GO terms in this study [52,53]. The cell, organelle, and macromolecular complex GO terms were observed within the top five GO terms in all three testis studies.…”

“…Four of the top five GO terms in the biological process category for the channel catfish (cellular process, metabolic process, biological regulation, and response to stimulus) and the top four GO terms for the yellow catfish (cellular process, singleorganism process, metabolic process, and biological regulation) matched the top five GO terms in this study [52,53]. Within all three testis studies, the cellular process, metabolic process, and biological regulation GO terms were observed as being with in the top four contributors for the biological category.…”

“…Within all three testis studies, the cellular process, metabolic process, and biological regulation GO terms were observed as being with in the top four contributors for the biological category. For the molecular function category, four of the top five GO terms for the channel catfish (binding, catalytic activity, molecular transducer activity, and transporter activity) and four of the top five GO terms for the yellow catfish (binding, catalytic activity, transporter activity, and molecular transducer activity) matched the top four GO terms in this study [52,53]. The binding, catalytic activity, transporter activity, and molecular transducer GO terms were represented within the top five GO terms of the molecular function category for all three testis transcriptome studies.…”

Identification of neomales in South American catfish Rhamdia quelen on the basis of the sex ratio in the progeny

“…These genes have been identified in a few species (Matsuda et al, 2002;Kamiya et al, 2012;Yano et al, 2012) and have been used as chromosomal markers to distinguish pairs of sex chromosomes (Okutsu et al, 2015). In addition, functional genomic studies (transcriptomics) currently applied to fish have identified genes that are complementary to those considered essential for sex determination (Zhang et al, 2011;Yano et al, 2012;Sun et al, 2013;Tao et al, 2013;Lu et al, 2014).…”