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. 2010 Jan 22;11(1):R8.
doi: 10.1186/gb-2010-11-1-r8.

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

Shaolin Wang  1 , 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 Chen, Jianguo 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; Catfish Genome Consortium
Collaborators, Affiliations

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

Shaolin Wang et al. Genome Biol. .

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 (Ictalurus 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 four 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.

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Figures

Figure 1
Figure 1
Length distribution of Joint Genome Institute EST sequences.
Figure 2
Figure 2
Distribution of contig sizes.
Figure 3
Figure 3
Distribution of sequence similarity between blue catfish and channel catfish sequences.
Figure 4
Figure 4
Open reading frame (ORF) length distribution from unique sequences of the all catfish assembly.
Figure 5
Figure 5
Analysis of open reading frames (ORFs). (a) Percentage of ORFs among unique sequences from the all catfish EST assembly; (b) Percentage of ORF greater than 100 bp among unique sequences from the all catfish EST assembly; (c) Percentage of ORFs equal to or greater than 100 bp with significant BLASTX hits; (d) Percentage of ORFs smaller than 100 bp with significant BLASTX hits
Figure 6
Figure 6
Comparison of shared and unique gene identities of channel catfish and blue catfish from a total of 14,776 unique genes.
Figure 7
Figure 7
Conservation of catfish gene identities with other species. Number of catfish homologous genes identified from other species using BLASTX searches.
Figure 8
Figure 8
Categorization of four different types of SNPs from the all catfish EST assembly and examples of SNPs whose categories could not be determined. (a-d) Types of SNPs from the all catfish EST assembly that can be identified from the all catfish EST assembly. (e) Examples of SNPs whose categories could not be determined because the minor allele sequence from a given species is fewer than two.
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