|Baldwin, Ransom - Randy|
|Van Tassell, Curtis - Curt|
Submitted to: Animal Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2004
Publication Date: 5/1/2005
Citation: Baumann, R.G., Baldwin, R.L., Van Tassell, C.P., Matukumalli, L.K., Sonstegard, T.S. 2005. Characterization of a normalized cDNA library from bovine intestinal muscle and epithelial tissues. Animal Biotechnology. 16(1):17-30.
Interpretive Summary: This paper describes the construction and characterization of a cDNA library from bovine intestinal tissues which we have named BARC-8BOV. Holstein dairy cattle from the BARC dairy herd were used to develop this library derived from small intestinal and colon tissues of a mature, lactating dairy cow and from small intestinal tissues of a neonatal calf. This library has contributed over 19,000 new 5'-EST to public databases, over 1,100 of which are analogous to physiologically relevant gene sequences from other animal species that have not yet been seen before in cattle. Analyses show this library has an excellent representation of EST sequences from genes involved in a large variety of critical cellular processes, particularly those relating to metabolism. This library of clones, containing transcripts of bovine genes expressed in the gut, serves as a valuable resource for scientists studying animal nutrition and health by a variety of different experimental approaches. Our aim is to develop this library resource for use in second-generation research tools, particularly microarrays, and specific experiments designed to understand how gene expression patterns and control are coupled with cellular, tissue and whole animal nutrient-use profiles. Developing this resource, therefore, expands classical approaches to understanding bovine nutrition by complementing ongoing whole animal, tissue and cellular experiments on growing and lactating cattle by providing gene-level information necessary to characterize the molecular controls of producing ruminants. Ultimately this work will facilitate development of new nutritional management and selection strategies to optimize animal production.
Technical Abstract: Tissue-specific cDNA library sequences (expressed sequence tags, or EST) yield a detailed snapshot of gene expression and are useful in developing second-generation molecular resources (i.e. microarrays) for gene expression profiling. The objective of this study was to develop and characterize an intestine-specific cDNA library to examine the transcriptome of the bovine gut and identify expressed genes that influence ruminant nutrition and health. We describe BARC-8BOV, a normalized cDNA library developed from mRNA isolated from four distinct intestinal locations (duodenal, jejunal and ileal small intestine, colon) of Holstein dairy cattle resulting in 19,110 EST deposited into the NCBI Genbank EST database. Assembly and clustering of these 19,110 clone sequences yielded 11,208 unique elements (3,419 contigs and 7,789 singletons) with an average length of 695 base pairs. Analysis strongly suggests normalization and tissue-pooling were effective at increasing the discovery rate of new bovine sequence. A total of 1,123 sequence elements not previously identified in cattle, but with similarity to known genes in other animal species, were identified and shown to be involved in numerous critical biological processes. An additional 745 transcripts were not represented in nucleotide or protein data bases, and further analysis of these could lead to the identification of gut-specific transcript variants of known genes or potentially the discovery of novel bovine genes. Of the 11,208 assembled sequences, 11,034, or 98.4%, match sequences present in the bovine DNA trace archive at NCBI, and add to a bovine EST database previously lacking significant gut tissue representation. Ultimately, these data will also contribute in efforts to annotate the bovine genome.