%0 Journal Article
%T An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
%A Gregory P Harhay
%A Timothy PL Smith
%A Leeson J Alexander
%A Christian D Haudenschild
%A John W Keele
%A Lakshmi K Matukumalli
%A Steven G Schroeder
%A Curtis P Van Tassell
%A Cathy R Gresham
%A Susan M Bridges
%A Shane C Burgess
%A Tad S Sonstegard
%J Genome Biology
%D 2010
%I BioMed Central
%R 10.1186/gb-2010-11-10-r102
%X 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.Comprehensive surveys of transcript abundance among tissues, often referred to as gene atlases, are relatively few [1-10], but provide novel and detailed insights into the genomic biology of the organism surveyed. For example, genomic studies often reveal chromosomal segments harboring variation affecting a trait, and knowledge of the expression profiles of genes lying in these segments enhances selection of candidate genes for further investigation. From another perspective, knowledge of the tissues in which a particular transcript is expressed may provide additional evidence about gene function. The utility a
%U http://genomebiology.com/2010/11/10/R102