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Open Access Research article

Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

Hirohide Uenishi123*, Takeya Morozumi34, Daisuke Toki34, Tomoko Eguchi-Ogawa13, Lauretta A Rund5 and Lawrence B Schook5

Author Affiliations

1 Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan

2 Division of Animal Sciences, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan

3 Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan

4 Animal Research Division, Japan Institute of Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

5 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA

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BMC Genomics 2012, 13:581  doi:10.1186/1471-2164-13-581

Published: 15 November 2012

Abstract

Background

Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits.

Results

We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5′-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome.

Conclusions

ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs.

Keywords:
Sus scrofa; Full-length cDNA; Sequencing; Genome annotation