Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

Shaolin Wang, Eric Peatman, Jason Abernathy, Geoff Waldbieser, Erika Lindquist, Paul Richardson, Susan Lucas, Mei Wang, Ping Li, Jyothi Thimmapuram, Lei Liu, Deepika Vullaganti, Huseyin Kucuktas, Christopher Murdock, Brian C. Small, Melanie Wilson, Hong Liu, Yanliang Jiang, Yoona Lee, Fei ChenJianguo Lu, Wenqi Wang, Peng Xu, Benjaporn Somridhivej, Puttharat Baoprasertkul, Jonas Quilang, Zhenxia Sha, Baolong Bao, Yaping Wang, Qun Wang, Tomokazu Takano, Samiran Nandi, Shikai Liu, Lilian Wong, Ludmilla Kaltenboeck, Sylvie Quiniou, Eva Bengten, Norman Miller, John Trant, Daniel Rokhsar, Zhanjiang Liu

Research output: Contribution to journalArticle

74 Scopus citations

Abstract

Background: Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results: A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (I. furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least 4 sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions: This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra- specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

Original languageEnglish (US)
Article numberr8
JournalGenome biology
Volume11
Issue number1
DOIs
StatePublished - Jan 22 2010

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    Wang, S., Peatman, E., Abernathy, J., Waldbieser, G., Lindquist, E., Richardson, P., Lucas, S., Wang, M., Li, P., Thimmapuram, J., Liu, L., Vullaganti, D., Kucuktas, H., Murdock, C., Small, B. C., Wilson, M., Liu, H., Jiang, Y., Lee, Y., ... Liu, Z. (2010). Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome biology, 11(1), [r8]. https://doi.org/10.1186/gb-2010-11-1-r8