rna-seq for plant pathogenic bacteriarna-seq对植物病原菌.pdfVIP

Genes 2011, 2, 689-705; doi:10.3390/genes2040689 OPEN ACCESS genes ISSN 2073-4425 /journal/genes Review RNA-Seq for Plant Pathogenic Bacteria Jeffrey A. Kimbrel 1,2, Yanming Di 3, Jason S. Cumbie 1,2 and Jeff H. Chang 1,2,4,* 1 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; E-Mails: kimbreje@ (J.A.K.); cumbiej@ (J.S.C.) 2 Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA 3 Department of Statistics, Oregon State University, Corvallis, OR 97331, USA; E-Mail: diy@ 4 Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA * Author to whom correspondence should be addressed; E-Mail: changj@; Tel.: +1-541-737-5278; Fax: +1-541-737-3573. 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 challen