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United States Department of Agriculture

Agricultural Research Service

Title: Utilization of Bioinformatic Approaches for the Evaluation of a Bovine Expressed Sequence Tag (Est) Database

Authors
item Warren, W - MONSANTO CO. ST LOUIS MO
item Allison, T - MONSANTO CO. ST LOUIS MO
item Tao, N - MONSANTO CO. ST LOUIS MO
item Liu, J - MONSANTO CO. ST LOUIS MO
item Cao, Y - MONSANTO CO. ST LOUIS MO
item Shi, Y - MONSANTO CO. ST LOUIS MO
item Mathialagan, N - MONSANTO CO. ST LOUIS MO
item Wagner, S - MONSANTO CO. ST LOUIS MO
item Kappes, Steven
item Byatt, J - MONSANTO CO. ST LOUIS MO

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 1, 1999
Publication Date: N/A

Technical Abstract: In mammals whole genome and EST sequencing is ongoing in few target species. Bioinformatics is starting to enable biologist to organize, query and disseminate this information. For bovine, good genetic linkage maps exist, although a paucity of genes (ESTs) are available for study. We have targeted specific tissues and created non-normalized cDNA libraries for EST sequencing. Total 5' EST sequences generated thus far are 19753 within which 10365 (89%) singletons and 1392 (11%) clusters are found to create a 11667 bovine unigene database. Following annotation against a non-redundant amino acid and nucleic acid database, 52% singletons and 21% clusters were unique. Once this bovine unigene database was created three data mining approaches were employed: 1) pathway mapping against the yeast genome, 2) single nucleotide polymorphism (SNP) identification and 3) simple sequence repeat (SSR) identification. The KEGG database was used to identify bovine ESTs that were orthologous to yeast genes found in 7 metabolic pathways. The average representation of bovine genes within each pathway was 41%. For SNP identification, clusters of bovine ESTs (n > 10) were examined following alignment by the PHRAP program. A total of 130 potential SNPs were found with an average SNP representation of 1 in 583 nucleotides. A few SSR markers were found with the majority as CA repeats in the 3' untranslated region. A subset of both SSR and SNP markers will be mapped on the USDA reference family panel. In summary, these bioinformatic approaches are a start to understanding bovine gene polymorphism rate and sequence identify relative to other species.

Last Modified: 4/20/2014