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

RNA-Seq for Plant Pathogenic Bacteria

1,2email, 3email, 1,2email and 1,2,4,* email
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)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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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