JOURNAL OF BACTERIOLOGY, Sept. 2010, p. 4534 0021-9193/10/$12.00 doi:10.1128/JB.00651-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Vol. 192, No. 17
Whole Genome Sequences of Two Xylella fastidiosa Strains (M12 and M23) Causing Almond Leaf Scorch Disease in California䌤 J. Chen,1* G. Xie,2 S. Han,2 O. Chertkov,2 D. Sims,2 and E. L. Civerolo1 San Joaquin Valley Agricultural Sciences Center, U.S. Department of Agriculture, Parlier, California 93648,1 and Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 875452 Received 7 June 2010/Accepted 24 June 2010
Xylella fastidiosa is a Gram-negative plant-pathogenic bacterium causing many economically important diseases, including almond leaf scorch disease (ALSD) in California. Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23. numbers. Detailed information about the genome properties, genome annotation, and its related references can be obtained from the JGI Integrated Microbial Genomes website at http://img.jgi.doe.gov/pub/. The genome of X. fastidiosa M12 consists of a single, circular, 2,475,130-nucleotide (nt) chromosome that has a GC content of 51.9%. A total of 2,368 protein-encoding genes are predicted, 2,104 of which have been assigned a tentative function. The genome of X. fastidiosa M23 consists of a single, circular, 2,535,690-nt chromosome that has a GC content of 51.7%. A total of 2,280 protein-encoding genes are predicted, 2,161 of which have been assigned a tentative function. In addition, a circular plasmid of 38,297 nt, pXFAS01, with a GC content of 49%, was also identified in strain M23 but was absent in strain M12. Both strains had two identical rRNA operons in their chromosomes. Nucleotide sequence accession numbers. The genome sequences of X. fastidiosa strains M12 and M23 have been deposited in GenBank under the accession numbers CP000941 and CP001011, respectively. pXFAS01 has the accession number CP001012.
Xylella fastidiosa is a Gram-negative and nutritionally fastidious plant-pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce’s disease (PD) of grapevine. In 2003, we isolated two ALSD strains of X. fastidiosa from almond trees in Kern County in the San Joaquin Valley of California. Strain M12 caused only ALSD, and strain M23 caused both ALSD and PD. 16S rRNA gene sequences were analyzed; strain M12 was regarded as A genotype and strain M23 as G genotype (1), corresponding to X. fastidiosa subsp. multiplex and X. fastidiosa subsp. fastidiosa (4), respectively. Genomic DNAs of X. fastidiosa strains M12 and M23 were extracted from pure culture in PW medium (1). The random shotgun method was used for genome sequencing. Large-insert (40-kb), medium-insert (8-kb), and small-insert (3-kb) random libraries were partially sequenced, and sequences were assembled with parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected with the Dupfinisher software program (2). Gaps between contigs were closed by custom primer walking through PCR amplification. Annotation of the assembled genome sequence was carried out with the genome annotation system Oak Ridge Genome Annotation and Analysis (ORGAA) Pipelines and JGI Integrated Microbial Genomes (IMG) server (3). A combined gene prediction strategy was applied by means of the GLIMMER 2.0 system and the CRITICA program suite, along with postprocessing by the RBSfinder tool. tRNA genes were identified using the tRNAscan-SE server. The deduced proteins were functionally characterized by automated searches in public databases, including SWISS-PROT and TrEMBL, Pfam, TIGRFAM, InterPro, and KEGG. Additionally, the SignalP, helix-turn-helix, and TMHMM software programs were applied. Finally, each gene was functionally classified by assigning a clusters of orthologous groups (COG) number and corresponding COG category and gene ontology
This research was partially supported by the U.S. Department of Agriculture. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. We thank Greg Phillips and Rebecca Alvarez for technical assistance. REFERENCES 1. Chen, J., R. Groves, E. L. Civerolo, M. Viveros, M. Freeman, and Y. Zheng. 2005. Two Xylella fastidiosa genotypes associated with almond leaf scorch disease on the same location in California. Phytopathology 95:708–714. 2. Han, C. S., and P. Chain. 2006. Finishing repetitive regions automatically with Dupfinisher, p. 142–147. In H. R. Arabnia and H. Valafar (ed.), Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology. CSREA Press, Las Vegas, NV. 3. Markowitz, V. M., F. Korzeniewski, K. Palaniappan, E. Szeto, G. Werner, A. Padki, X. Zhao, I. Dubchak, P. Hugenholtz, I. Anderson, A. Lykidis, K. Mavromatis, N. Ivanova, and N. C. Kyrpides. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34:D344–D348. 4. Schaad, N. W., E. Postnikova, G. Lacy, M. Fatmi, and C. J. Chang. 2004. Xylella fastidiosa subspecies: X. fastidiosa subsp. [correction] fastidiosa [correction] subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov. Syst. Appl. Microbiol. 27:290–300.
* Corresponding author. Mailing address: San Joaquin Valley Agricultural Sciences Center, U.S. Department of Agriculture, Parlier, CA 93648. Phone: (559) 596-2924. Fax: (559) 596-2921. E-mail: jianchi
[email protected]. 䌤 Published ahead of print on 2 July 2010.
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