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

Gregory P Harhay,John W Keele,Shane C Burgess,Curtis P Van Tassell,Lakshmi K Matukumalli,Timothy Pl Smith,Susan M Bridges,Cathy R Gresham,Tad S Sonstegard,Steven G Schroeder,Leeson J Alexander,Christian D Haudenschild

doi:10.1186/gb-2010-11-10-r102

Abstract

BackgroundA 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.ResultsThe 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.ConclusionsThe 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.

Highlights

A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism
Most of these samples were from her male late-gestation fetus and juvenile daughter to reduce the impact of polymorphisms on analyses and capture changes in the transcriptomes early in the life cycle that may influence the adult state
The atlas consists in large part (58%) of endocrine (BRENDA [6,7] gland), alimentary (BRENDA viscus), and nervous tissues that provide for a wide diversity in expression profiles

Summary

Introduction

A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. 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. Two approaches to enumerate transcripts with NGS have been developed, either based on sequencing specific tags related to restriction sites in the cDNA (digital gene expression (DGE)) or random cDNA fragments (RNAseq) [2] The former approach was the only one available making use of NGS at the time of this transcriptome study based on restriction digestion of bovine cDNA with the enzyme DpnII and capture of 20-base tags (including the GATC restriction site) from the 3’-most restriction site. On the other hand, collapsing tag counts to a unique locus to precisely quantify transcript abundance using DGE tags can be more straightforward than the assembly of short, sometimes non-overlapping reads, especially for organisms lacking high quality genome sequences and annotation (as is the case for cattle)

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Conclusion