Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags

Jan Gorodkin¹ , Susanna Cirera¹ , Jakob Hedegaard² , Michael J Gilchrist³ , Frank Panitz² , Claus Jørgensen¹ , Karsten Scheibye-Knudsen¹ , Troels Arvin¹ , Steen Lumholdt¹ , Milena Sawera¹ , Trine Green¹ , Bente J Nielsen¹ , Jakob H Havgaard¹ , Carina Rosenkilde¹ , Jun Wang⁴^,5^,6 , Heng Li⁴^,5 , Ruiqiang Li⁴^,6 , Bin Liu⁴ , Songnian Hu⁴ , Wei Dong⁴ , Wei Li⁴ , Jun Yu⁴ , Jian Wang⁴ , Hans-Henrik Stærfeldt⁷ , Rasmus Wernersson⁷ , Lone B Madsen² , Bo Thomsen² , Henrik Hornshøj² , Zhan Bujie² , Xuegang Wang² , Xuefei Wang² , Lars Bolund⁴^,5 , Søren Brunak⁷ , Huanming Yang⁴ , Christian Bendixen² and Merete Fredholm¹

¹Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark

²Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark

³The Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK

⁴Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China

⁵Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark

⁶Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campus Vej 55, DK-5230 Odense M, Denmark

⁷Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark

author email corresponding author email

Genome Biology 2007, 8:R45doi:10.1186/gb-2007-8-4-r45


Published:	2 April 2007

Subject areas: Bioinformatics, Genome studies

Abstract

Background

Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages.

Results

Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories.

Conclusion

This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.