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United States Department of Agriculture

Agricultural Research Service

Title: ANALYSIS OF BOVINE MAMMARY GLAND EST AND FUNCTIONAL ANNOTATION OF THE BOS TAURUS GENE INDEX

Authors
item SONSTEGARD, TAD
item Capuco, Anthony
item White, Joseph - INSTITUTE OF GENOMIC RES
item VAN TASSELL, CURTIS
item CONNOR, ERIN
item Cho, Jennifer - INSTITUTE OF GENOMIC RES
item Sultan, Razvan - INSTITUTE OF GENOMIC RES
item SHADE, LARRY
item Wray Jr, James
item Wells, Kevin

Submitted to: Mammalian Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 15, 2002
Publication Date: March 15, 2002
Citation: Sonstegard, T.S., Capuco, A.V., White, J., Van Tassell, C.P., Connor, E.E., Cho, J., Sultan, R., Shade, L.L., Wray Jr, J.E., Wells, K.D. 2002. Analysis of bovine mannary gland EST and functional annotation of the BOS taurus gene index. Mammalian Genome. vol.13, pp. 373-379.

Interpretive Summary: Functional genomic studies of the mammary gland require the construction of sequence resources based on genes expressed from the different developmental and operational states of this gland. As such, a normalized cDNA library constructed from pooled bovine mammary tissues was sequenced to generate over 23,000 expressed sequence tags (EST). These EST were placed in a publically available database and integrated into the Bos taurus Gene Index, a database that joins like sequence to form gene sequence assemblies. Assembly of similar EST helps define unique sequence elements or independent genes. Assembly of mammary gland EST identified over 5,500 different genes. Comparative sequence analysis was performed on all unique sequences in the BtGI to help assign a putative function for the sequences and to identify novel sequence elements with respect to human and rodent genomes. Approximately 42% of all gene sequences were assigned either the function of a known gene or a putative function based on similarity matches to other mammalian sequences. Functional classification was also performed to provide gene ontology assignments to more than 5,000 BtGI sequence elements. Approximately 4,000 sequence elements represent genes not currently identified in humans and rodents, or divergent genes potentially unique to cattle. These results underscore the importance of generating sequence expression data from livestock. This information serves as valuable resource for functional genomic studies of the mammary gland across species.

Technical Abstract: The mammary gland is a dynamic tissue that undergoes many physiological transitions. Functional genomic studies of this system require an appropriate collection of cDNA sequences to assess gene expression patterns from the different developmental and operational states of underlying cell types. To generate such a resource, a normalized cDNA library constructed from pooled bovine mammary tissues was sequenced and annotated. Over 23,000 mammary derived expressed sequence tags (EST) were produced and integrated into an existing Bos taurus Gene Index (BtGI). While 20 % of these EST populated eight TC sequences corresponding to genes expressed in support of lactation, the majority of these 5,551 TC sequences contained only one to three mammary derived EST. These results suggested library normalization was partially effective. Comparative sequence analysis was performed to provide evidence for functional annotation and to assess the number of novel sequence elements with respect to the human genome, human and rodent gene indices, and an index of orthologous alignments of genes across eukaryotes. Approximately 42% of all TC sequences were assigned either the function of a known gene or a putative function based on similarity matches to mammalian orthologs. Functional classification was performed to provide gene ontology assignments to more than 5,000 BtGI sequence elements. This analysis revealed that approximately 4,000 TC sequences represent expressed genes not currently identified in humans and rodents, or divergent orthologs potentially unique to cattle. These results underscore the importance of sequence expression data from livestock for characterizing mammalian transcriptomes.

Last Modified: 8/27/2014
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