TY - JOUR
T1 - An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
AU - Harhay, Gregory P.
AU - Smith, Timothy P.L.
AU - Alexander, Leeson J.
AU - Haudenschild, Christian D.
AU - Keele, John W.
AU - Matukumalli, Lakshmi K.
AU - Schroeder, Steven G.
AU - Van Tassell, Curtis P.
AU - Gresham, Cathy R.
AU - Bridges, Susan M.
AU - Burgess, Shane C.
AU - Sonstegard, Tad S.
N1 - Funding Information:
This project was supported by NRI-Animal genome reagent and tool development no. 2006-35616-16648 from the USDA Cooperative State Research, Education, and Extension and by projects 1265-31000-098 D (BFGL) and 5438-31000-073 D (USMARC) from the USDA Agricultural Research Service. We thank Andy Roberts, Richard Waterman (USDA, LARRL), Steve Moore (University of Alberta), Mike Brownstein (Venter Institute), Steve Smith (TAMU), and Anthony Capuco (USDA, BFGL) for collecting and contributing tissue samples. We also thank Alicia Bertles (USDA, BFGL) for RNA standardization and Keith Moon (Illumina, Inc., formerly Solexa) for cDNA synthesis and next generation sequence analysis of these DGE library samples. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.
PY - 2010/10/20
Y1 - 2010/10/20
N2 - 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 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.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.
AB - 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 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.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.
UR - http://www.scopus.com/inward/record.url?scp=77957991364&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77957991364&partnerID=8YFLogxK
U2 - 10.1186/gb-2010-11-10-r102
DO - 10.1186/gb-2010-11-10-r102
M3 - Article
C2 - 20961407
AN - SCOPUS:77957991364
SN - 1474-7596
VL - 11
JO - Genome biology
JF - Genome biology
IS - 10
M1 - R102
ER -