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RNA-Seq for Plant Pathogenic Bacteria
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
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
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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Kimbrel, J.A.; Di, Y.; Cumbie, J.S.; Chang, J.H. RNA-Seq for Plant Pathogenic Bacteria. Genes 2011, 2, 689-705.
Kimbrel JA, Di Y, Cumbie JS, Chang JH. RNA-Seq for Plant Pathogenic Bacteria. Genes. 2011; 2(4):689-705.
Kimbrel, Jeffrey A.; Di, Yanming; Cumbie, Jason S.; Chang, Jeff H. 2011. "RNA-Seq for Plant Pathogenic Bacteria." Genes 2, no. 4: 689-705.