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

Gregory P Harhay1*, Timothy PL Smith1, Leeson J Alexander2, Christian D Haudenschild3, John W Keele1, Lakshmi K Matukumalli45, Steven G Schroeder5, Curtis P Van Tassell5, Cathy R Gresham6, Susan M Bridges6, Shane C Burgess7 and Tad S Sonstegard5

Author Affiliations

1 USDA-ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA

2 USDA-ARS Fort Keogh Livestock and Range Research Laboratory, 243 Fort Keogh Road, Miles City, MT 59301, USA

3 Illumina, Inc., 25861 Industrial Boulevard, Hayward, CA 94545, USA

4 Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA

5 USDA-ARS Bovine Functional Genomics Laboratory, 10300 Baltimore Avenue, Bldg 200 Rm 2A BARC-East, Beltsville, MD 20705, USA

6 Department of Computer Science, Mississippi State University, Mississippi State, MS 39762, USA

7 Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

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Genome Biology 2010, 11:R102  doi:10.1186/gb-2010-11-10-r102

Published: 20 October 2010



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.


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 accounting 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.


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.