Genes 2011, 2(4), 689-705; doi:10.3390/genes2040689
Review

RNA-Seq for Plant Pathogenic Bacteria

1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA 2 Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA 3 Department of Statistics, Oregon State University, Corvallis, OR 97331, USA 4 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
* Author to whom correspondence should be addressed.
Received: 16 September 2011; in revised form: 30 September 2011 / Accepted: 30 September 2011 / Published: 13 October 2011
(This article belongs to the Special Issue Genes and Genomes of Plant Pathogenic Bacteria)
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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.
Keywords: next generation sequencing; transcriptomics; differential gene expression; overdispersion; negative binomial

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MDPI and ACS Style

Kimbrel, J.A.; Di, Y.; Cumbie, J.S.; Chang, J.H. RNA-Seq for Plant Pathogenic Bacteria. Genes 2011, 2, 689-705.

AMA Style

Kimbrel JA, Di Y, Cumbie JS, Chang JH. RNA-Seq for Plant Pathogenic Bacteria. Genes. 2011; 2(4):689-705.

Chicago/Turabian Style

Kimbrel, Jeffrey A.; Di, Yanming; Cumbie, Jason S.; Chang, Jeff H. 2011. "RNA-Seq for Plant Pathogenic Bacteria." Genes 2, no. 4: 689-705.

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