Transcriptome Analysis in Domesticated Species: Challenges and Strategies

Jessica P. Hekman, Jennifer L. Johnson, Anna V. Kukekova

Research output: Contribution to journalReview articlepeer-review

Abstract

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

Original languageEnglish (US)
Pages (from-to)21-31
Number of pages11
JournalBioinformatics and Biology Insights
Volume9S4
DOIs
StatePublished - Jan 1 2015

Keywords

  • NGS
  • RNA-seq
  • domestication
  • transcriptomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Mathematics
  • Applied Mathematics

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