Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes

PLoS One. 2014 Feb 26;9(2):e89817. doi: 10.1371/journal.pone.0089817. eCollection 2014.

Abstract

In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 1,300 DEGs were involved in cellular processes, metabolic pathways, and the actin cytoskeleton pathway. Importantly, we identified 34 DEGs related to muscle cell development and differentiation. Additionally, we were able to optimize the gene structure and predict the untranslated regions (UTRs) for some of the DEGs. Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences. The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes. These results will provide useful information for functional genetic research in the future.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / genetics
  • Cell Differentiation / physiology
  • DNA Primers / genetics
  • Gene Expression Profiling / veterinary
  • Gene Ontology
  • High-Throughput Nucleotide Sequencing
  • Muscle Cells / physiology
  • Muscle, Skeletal / metabolism*
  • Protein Interaction Maps
  • Real-Time Polymerase Chain Reaction
  • Sheep / genetics*
  • Sheep / metabolism*
  • Species Specificity
  • Transcriptome / genetics*
  • Untranslated Regions / genetics

Substances

  • DNA Primers
  • Untranslated Regions

Grants and funding

This work was financially supported by the Innovation Research of Agriculture and Biology Resources (No. 2011186125) and the Shandong Provincial Modern Agriculture Industry Technology System Sheep Industry Innovation Team (No. SATS2012263). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.