ARS | Publication request: Searching for small RNA genes in Xylella fastidiosa genomes

Submitted to: American Phytopathological Society Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: May 20, 2011
Publication Date: June 24, 2011
Citation: Chen, J., Huang, H. 2011. Searching for small RNA genes in Xylella fastidiosa genomes. American Phytopathological Society Abstracts. 101:S34.

Technical Abstract: Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and roles in controlling numerous cellular processes including survival, adaptation and pathogenesis. Xylella fastidiosa is a bacterial pathogen causing many economically important diseases such as almond leaf scorch, citrus variegated chlorosis and Pierce’s disease of grapevine. However, little is known about small RNA in this bacterium, despite of the fact that several whole genome sequences of X. fastidiosa strains have been published. To fill in this gap, a research project was initiated to search for small RNAs in X. fastidiosa. The complete genome sequences of four X. fastidiosa strains (9a5c, M12, M23, and Temecula1) were selected for in silico analysis to scan for small RNA using the sRNAscanner program (PLoS ONE 5:e11970). Candidate small RNA genes were identified in all four strains, with 46 for 9a5c, 50 for M12, 49 for M23, and 47 for Temecula1. Size of candidate small RNA ranged from 40 to 350 bp. Results from BLAST analysis showed that 34 small RNA genes were shared by all four X. fastidiosa strains. Species-, subspecies- and pathotype-specific small RNAs also were identified.