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United States Department of Agriculture

Agricultural Research Service

Title: Porcine Gene-Discovery by Normalized Cdna-Library Sequencing and Est Cluster Assembly

Authors
item Fahrenkrug, Scott
item Smith, Timothy
item Freking, Bradley
item Cho, Jennifer - TIGR, ROCKVILLE, MD
item White, Joseph - TIGR, ROCKVILLE, MD
item Vallet, Jeffrey
item Wise, Thomas
item Rohrer, Gary
item Keele, John

Submitted to: Mammalian Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 5, 2002
Publication Date: August 1, 2003
Citation: FAHRENKRUG, S.C., SMITH, T.P., FREKING, B.A., CHO, J., WHITE, J., VALLET, J.L., WISE, T.H., ROHRER, G.A., KEELE, J.W. PORCINE GENE-DISCOVERY BY NORMALIZED CDNA-LIBRARY SEQUENCING AND EST CLUSTER ASSEMBLY. MAMMALIAN GENOME. 2002. v. 13. p. 475-478.

Interpretive Summary: We constructed, arrayed, and extensively sequenced two normalized pig cDNA libraries derived from embryonic and reproductive tissues. Over 20,000 clones from each library have been sequenced and currently represent nearly 90% of the porcine expressed sequence data in public sequence repositories. The sequences generated from these libraries will play a valuable role in future efforts towards swine comparative mapping, the construction of microarrays for gene-expression analysis, and for functional genomics research aimed at understanding the molecular regulation of pig reproduction, growth and development. Continuing analysis of the cDNA clones in these libraries is likely to further these efforts through unique gene discovery and further consensus sequence development.

Technical Abstract: Genetic and environmental factors affect the efficiency of pork production by influencing gene expression during porcine reproduction, tissue development and growth. The identification and functional analysis of gene-products important to these processes would be greatly enhanced by the development of an index of expressed porcine genes. Towards this end we have constructed, arrayed, and extensively sequenced two normalized pig cDNA libraries, MARC1PIG and MARC2PIG, derived from embryonic and reproductive tissues. Over 20,000 clones from each library have been 5'-end sequenced and currently represent nearly 90% of the porcine expressed sequence data in public sequence repositories. Cluster analysis revealed that within-library redundancy is low and comparison of all porcine ESTs suggests the discovery of up to 25,000 pig genes from these two libraries. A TIGR porcine gene-index (PGI) comprised of 29,092 unique sequences includes all sequences in public repositories, and has been developed to facilitate further comparative map development and characterization of porcine genes. These libraries have provided an excellent resource for establishing a catalog of expressed porcine genes and will be instrumental in the development of high-density hybridization arrays for transcriptional profiling of porcine tissues. In addition, comparison of porcine ESTs to sequences from other species serves as a valuable resource for comparative map development. Both arrayed cDNA libraries are available for unrestricted public use.

Last Modified: 9/22/2014