TY - JOUR
T1 - Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies
AU - Wang, Shaolin
AU - Peatman, Eric
AU - Abernathy, Jason
AU - Waldbieser, Geoff
AU - Lindquist, Erika
AU - Richardson, Paul
AU - Lucas, Susan
AU - Wang, Mei
AU - Li, Ping
AU - Thimmapuram, Jyothi
AU - Liu, Lei
AU - Vullaganti, Deepika
AU - Kucuktas, Huseyin
AU - Murdock, Christopher
AU - Small, Brian C.
AU - Wilson, Melanie
AU - Liu, Hong
AU - Jiang, Yanliang
AU - Lee, Yoona
AU - Chen, Fei
AU - Lu, Jianguo
AU - Wang, Wenqi
AU - Xu, Peng
AU - Somridhivej, Benjaporn
AU - Baoprasertkul, Puttharat
AU - Quilang, Jonas
AU - Sha, Zhenxia
AU - Bao, Baolong
AU - Wang, Yaping
AU - Wang, Qun
AU - Takano, Tomokazu
AU - Nandi, Samiran
AU - Liu, Shikai
AU - Wong, Lilian
AU - Kaltenboeck, Ludmilla
AU - Quiniou, Sylvie
AU - Bengten, Eva
AU - Miller, Norman
AU - Trant, John
AU - Rokhsar, Daniel
AU - Liu, Zhanjiang
N1 - Copyright:
Copyright 2010 Elsevier B.V., All rights reserved.
PY - 2010/1/22
Y1 - 2010/1/22
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=77349083472&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77349083472&partnerID=8YFLogxK
U2 - 10.1186/gb-2010-11-1-r8
DO - 10.1186/gb-2010-11-1-r8
M3 - Article
C2 - 20096101
AN - SCOPUS:77349083472
VL - 11
JO - Genome Biology
JF - Genome Biology
SN - 1465-6914
IS - 1
M1 - r8
ER -