An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

Authors: Harhay, Gregory; Smith, Timothy - Tim; Alexander, Leeson; HAUDENSCHILD, CHRISTIAN - Illumina, Inc; Keele, John; MATUKUMALLI, LAKSHMI - George Mason University; Schroeder, Steven - Steve; Van Tassell, Curtis - Curt; GRESHAM, CATHY - Mississippi State University; BRIDGES, SUSAN - Mississippi State University; BURGESS, SHANE - Mississippi State University; Sonstegard, Tad

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/20/2010
Publication Date: 10/20/2010
Citation: Harhay, G.P., Smith, T.P.L., Alexander, L.J., Haudenschild, C.D., Keele, J.W., Matukumalli, L.K., Schroeder, S.G., Van Tassell, C.P., Gresham, C.R., Bridges, S.M., Burgess, S.C., Sonstegard, T.S. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biology [online serial]. 11:R102.

Interpretive Summary: In this study, 93 cattle tissues were individually surveyed to identify which genes were active and to quantify the extent of their activity. This study examined the most cattle tissues and yielded the most detailed description of the extent of gene activity of any single livestock study to date. The results of this study are directly applicable to cattle research in economically important production and health traits associated with muscles, fat depots, nervous and digestive system tissues.

Technical Abstract: Background A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. Results The Bovine Gene Atlas was generated from 7.2 million unique digital gene expression tag sequences (300.2 million total raw tag sequences), from which 1.59 million unique tag sequences were identified that mapped to the draft bovine genome accounting for 85% of the total raw tag abundance. Filtering these tags yielded 87,764 unique tag sequences that unambiguously mapped to 16,517 annotated protein-coding loci in the draft genome accounted for 45% of the total raw tag abundance. Clustering of tissues based on tag abundance profiles generally confirmed ontology classification based on anatomy. There were 5,429 constitutively expressed loci and 3,445 constitutively expressed unique tag sequences mapping outside annotated gene boundaries that represent a resource for enhancing current gene models. Physical measures such as inferred transcript length or antisense tag abundance identified tissues with atypical transcriptional tag profiles. We report for the first time the tissue-specific variation in the proportion of mitochondrial transcriptional tag abundance. Conclusions The Bovine Gene Atlas is the deepest and broadest transcriptome survey of any livestock genome to date. Commonalities and variation in sense and antisense transcript tag profiles identified in different tissues facilitate the examination of the relationship between gene expression, tissue, and gene function.