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Oct 13, 2011;2 (4): 689-705.

RNA-Seq for Plant Pathogenic Bacteria.

Jeffrey A Kimbrel, Yanming Di, Jason S Cumbie, Jeff H Chang
Author Information
  1. Jeffrey A Kimbrel: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. kimbreje@science.oregonstate.edu.
  2. Yanming Di: Department of Statistics, Oregon State University, Corvallis, OR 97331, USA. diy@stat.oregonstate.edu.
  3. Jason S Cumbie: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. cumbiej@onid.orst.edu.
  4. Jeff H Chang: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA. changj@science.oregonstate.edu.
PMID: 24710287 DOI: 10.3390/genes2040689

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.

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Journal Article
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