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

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Abstract

Sex dimorphic growth pattern has significant theory and application implications in fish. Recently, a Y- and X-specific 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.

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Acknowledgments

This work was supported by grants to Jie Mei from the Fundamental Research Funds for the Central Universities (2013PY068, 52902–0900202496, 52204–12018) and the National Natural Science Foundation of China (31301931), and to Jian-Fang Gui from the special Fund for Agro-scientific Research in the Public Interest from the Ministry of Agriculture of China (2009030406), the National Key Basic Research Program (2010CB126301). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China

    Xin Chen, Jie Mei, Junjie Wu, Jing Jing, Wenge Ma, Jin Zhang, Weimin Wang & Jian-Fang Gui

  2. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan, 430072, China

    Cheng Dan & Jian-Fang Gui

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  1. Xin Chen
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  2. Jie Mei
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  3. Junjie Wu
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  4. Jing Jing
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  5. Wenge Ma
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  6. Jin Zhang
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  7. Cheng Dan
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  9. Jian-Fang Gui
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Correspondence to Jie Mei or Jian-Fang Gui.

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Figure S1

Length distribution of Open reading frame (ORF) from all contigs of the transcriptome. (GIF 7 kb)

(TIFF 422 kb)

Table S1

Summary of BLAST nr result for all unique sequences in the transcriptome. (XLSX 1404 kb)

Table S2

List of all the reproduction and reproductive process related genes found in GO analysis of the yellow catfish transcriptome. (XLSX 107 kb)

Table S3

KEGG pathways discovered in the unigenes, contigs and singletons of yellow catfish transcriptome (XLSX 790 kb)

Table S4

The primer sequences for real-time PCR study. (DOCX 17 kb)

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Chen, X., Mei, J., Wu, J. et al. A Comprehensive Transcriptome Provides Candidate Genes for Sex Determination/Differentiation and SSR/SNP Markers in Yellow Catfish. Mar Biotechnol 17, 190–198 (2015). https://doi.org/10.1007/s10126-014-9607-7

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