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

RNA-Seq for Plant Pathogenic Bacteria

Received: 16 September 2011 / Revised: 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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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 next generation sequencing; transcriptomics; differential gene expression; overdispersion; negative binomial
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.

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

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