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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetics, Physiology, and Health Research to Improve Catfish Production

Location: Warmwater Aquaculture Research Unit

Title: Assembly of 500,000 Inter-Specific Catfish Expressed Sequence Tags and Large Scale Gene-Associated Marker Development for Whole Genome Association Studies

Authors
item Wang, S -
item Peatman, E -
item Abernathy, J -
item Waldbieser, Geoffrey
item Lindquist, E -
item Richardson, P -
item Murdock, Christopher
item Small, Brian
item Quiniou, Sylvie
item Liu, Z -

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 22, 2010
Publication Date: January 22, 2010
Citation: Wang, S., Peatman, E., Abernathy, J., Waldbieser, G.C., Lindquist, E., Richardson, P., Murdock, C.A., Small, B.C., Quiniou, S., 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:R8.

Interpretive Summary: A large scale, collaboration between seven institutions led to the production of more than 400,000 total (111,578 unique) DNA sequences derived from active genes in channel and blue catfish. This is among the largest collections of expressed sequences for any fish species. The sequence data will be useful for examining global levels of gene expression in catfish tissues in response to genetic or environmental changes. A large number of single nucleotide polymorphisms were identified within and between each species, and these polymorphisms will be useful for marking and associating genomic regions that are involved in the control of important production traits. The expressed sequences will also support and inform the reference genome sequencing project for channel and blue catfish that is now underway.

Technical Abstract: 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. 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. 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.

Last Modified: 4/19/2014
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