RNA-Seq for Plant Pathogenic Bacteria

Jeffrey A Kimbrel; Yanming Di; Jason S Cumbie; Jeff H Chang

doi:10.3390/genes2040689

RNA-Seq for Plant Pathogenic Bacteria

Genes (Basel). 2011 Oct 13;2(4):689-705. doi: 10.3390/genes2040689.

Authors

Jeffrey A Kimbrel¹, Yanming Di², Jason S Cumbie³, Jeff H Chang⁴

Affiliations

¹ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. kimbreje@science.oregonstate.edu.
² Department of Statistics, Oregon State University, Corvallis, OR 97331, USA. diy@stat.oregonstate.edu.
³ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. cumbiej@onid.orst.edu.
⁴ Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. changj@science.oregonstate.edu.

Abstract

The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions.