Research article

Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue

Tae-Hun Kim¹ , Nam-Soon Kim² , Dajeong Lim³ , Kyung-Tai Lee¹ , Jung-Hwa Oh² , Hye-Sook Park¹ , Gil-Won Jang¹ , Hyung-Yong Kim¹ , Mina Jeon³ , Bong-Hwan Choi¹ , Hae-Young Lee¹ , HY Chung¹ and Heebal Kim³

¹  Division of Animal Genomics & Bioinformatics, National LivestockResearch Institute, Rural Development Administration, Omokchun-dong 564, Kwonsun-gu, Suwon, Korea

²  Laboratory of Human Genomics, Genome Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Korea

³  School of Agricultural Biotechnology, Seoul National University San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-742, Korea

author email corresponding author email

BMC Genomics 2006, 7:36doi:10.1186/1471-2164-7-36

Published:	27 February 2006

Abstract

Background

Genome research in farm animals will expand our basic knowledge of the genetic control of complex traits, and the results will be applied in the livestock industry to improve meat quality and productivity, as well as to reduce the incidence of disease. A combination of quantitative trait locus mapping and microarray analysis is a useful approach to reduce the overall effort needed to identify genes associated with quantitative traits of interest.

Results

We constructed a full-length enriched cDNA library from porcine backfat tissue. The estimated average size of the cDNA inserts was 1.7 kb, and the cDNA fullness ratio was 70%. In total, we deposited 16,110 high-quality sequences in the dbEST division of GenBank (accession numbers: DT319652-DT335761). For all the expressed sequence tags (ESTs), approximately 10.9 Mb of porcine sequence were generated with an average length of 674 bp per EST (range: 200–952 bp). Clustering and assembly of these ESTs resulted in a total of 5,008 unique sequences with 1,776 contigs (35.46%) and 3,232 singleton (65.54%) ESTs. From a total of 5,008 unique sequences, 3,154 (62.98%) were similar to other sequences, and 1,854 (37.02%) were identified as having no hit or low identity (<95%) and 60% coverage in The Institute for Genomic Research (TIGR) gene index of Sus scrofa. Gene ontology (GO) annotation of unique sequences showed that approximately 31.7, 32.3, and 30.8% were assigned molecular function, biological process, and cellular component GO terms, respectively. A total of 1,854 putative novel transcripts resulted after comparison and filtering with the TIGR SsGI; these included a large percentage of singletons (80.64%) and a small proportion of contigs (13.36%).

Conclusion

The sequence data generated in this study will provide valuable information for studying expression profiles using EST-based microarrays and assist in the condensation of current pig TCs into clusters representing longer stretches of cDNA sequences. The isolation of genes expressed in backfat tissue is the first step toward a better understanding of backfat tissue on a genomic basis.