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Marine Biotechnology

, Volume 17, Issue 2, pp 190–198 | Cite as

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

  • Xin Chen
  • Jie MeiEmail author
  • Junjie Wu
  • Jing Jing
  • Wenge Ma
  • Jin Zhang
  • Cheng Dan
  • Weimin Wang
  • Jian-Fang GuiEmail author
Original Article

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.

Keywords

Yellow catfish Transcriptome Sex determination/differentiation All-male fish Super-male fish SSR/SNP 

Notes

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.

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

10126_2014_9607_Fig8_ESM.gif (8 kb)
Figure S1

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

10126_2014_9607_MOESM1_ESM.tif (422 kb)
(TIFF 422 kb)
10126_2014_9607_MOESM2_ESM.xlsx (1.4 mb)
Table S1 Summary of BLAST nr result for all unique sequences in the transcriptome. (XLSX 1404 kb)
10126_2014_9607_MOESM3_ESM.xlsx (107 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)
10126_2014_9607_MOESM4_ESM.xlsx (790 kb)
Table S3 KEGG pathways discovered in the unigenes, contigs and singletons of yellow catfish transcriptome (XLSX 790 kb)
10126_2014_9607_MOESM5_ESM.docx (18 kb)
Table S4 The primer sequences for real-time PCR study. (DOCX 17 kb)

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Xin Chen
    • 1
  • Jie Mei
    • 1
    Email author
  • Junjie Wu
    • 1
  • Jing Jing
    • 1
  • Wenge Ma
    • 1
  • Jin Zhang
    • 1
  • Cheng Dan
    • 2
  • Weimin Wang
    • 1
  • Jian-Fang Gui
    • 1
    • 2
    Email author
  1. 1.College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
  2. 2.State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesUniversity of the Chinese Academy of SciencesWuhanChina

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