Abstract
Pseudomonas syringae pv. tomato race 1 strains have evolved to overcome genetic resistance in tomato. Here, we present the draft genome sequences of two race 1 P. syringae pv. tomato strains, A9 and 407, isolated from diseased tomato plants in California.
GENOME ANNOUNCEMENT
Pseudomonas syringae pv. tomato causes bacterial speck of tomato, which is one of the most persistent bacterial diseases in tomato worldwide. In resistant genotypes, the race 0 P. syringae pv. tomato type III effectors AvrPto and AvrPtoB are recognized by the tomato proteins Pto and Prf (1, 2). However, P. syringae pv. tomato race 1 strains are able to overcome genetic resistance in tomato by modifying the presence and expression of AvrPto and AvrPtoB (3, 4). Despite the historical success of Pto-mediated resistance, race 1 strains now predominate (4, 5). P. syringae pv. tomato race 1 was first detected in 1986 in Canada and in 1993 in California, the primary production area for processing tomato cultivars in the United States (6, 7). The vast majority of strains collected from 2005 to 2007 were race 1, and we were unable to identify any race 0 strains in 2007, 2008, or 2009 from infected tomato plants in California (4, 5). Here, we report the draft genome sequences of P. syringae pv. tomato A9 and P. syringae pv. tomato 407, isolated from infected tomato plants in California. Both strains are race 1, but P. syringae pv. tomato A9 exhibits enhanced bacterial growth and disease symptoms in tomato compared to P. syringae pv. tomato 407 (8).
Genomic DNA was sequenced using the Illumina HiSeq 2500 (2 × 150-bp paired-end reads) at the Genome Center at the UC Davis DNA Technologies Core Facility. After the raw sequences were trimmed and their quality filtered (>Q30), the remaining reads were assembled de novo using the SPAdes assembler and draft genomes were generated for each isolate (9). Each genome was annotated with PROKKA (10) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok).
The final draft assembly of the P. syringae pv. tomato A9 genome consists of 188 contigs (>200 bp) with 70-fold genome coverage. P. syringae pv. tomato A9 harbors a single circular genome of 6,314,445 bp, with a G+C content of 57.9%. The genome of the P. syringae pv. tomato A9 strain contains 5,749 predicted coding sequences (CDSs), 1 rRNA operon, and 60 tRNA genes; and the genome of P. syringae pv. tomato 407 contains 5,702 predicted CDSs, 1 rRNA operon, and 57 tRNA genes. The final draft assembly of the P. syringae pv. tomato 407 genome consists of 192 contigs (>200 bp) with 65-fold genome coverage. P. syringae pv. tomato 407 harbors a single circular genome of 6,264,873 bp with a G+C content of 55.8%. Among the 57 type III effectors present in the P. syringae pangenome (11), 27 are present in both P. syringae pv. tomato A9 and P. syringae pv. tomato 407. Detailed comparisons of related Pseudomonas strains exhibiting variable virulence will facilitate insight into molecular mechanisms regulating virulence and adaptation.
Nucleotide sequence accession numbers.
The sequences have been deposited as whole-genome shotgun projects in GenBank under the accession numbers LNKY00000000 for P. syringae pv. tomato A9 and LNKZ00000000 for P. syringae pv. tomato 407.
ACKNOWLEDGMENT
This work was supported by the California Tomato Research Institute, grant 196. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Thapa SP, Coaker G. 2016. Genome sequences of two Pseudomonas syringae pv. tomato race 1 strains, isolated from tomato fields in California. Genome Announc 4(2):e01671-15. doi:10.1128/genomeA.01671-15.
REFERENCES
- 1.Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD. 1993. Map based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436. doi: 10.1126/science.7902614. [DOI] [PubMed] [Google Scholar]
- 2.Salmeron JM, Oldroyd GE, Rommens CM, Scofield SR, Kim HS, Lavelle DT, Dahlbeck D, Staskawicz BJ. 1996. Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster. Cell 86:123–133. doi: 10.1016/S0092-8674(00)80083-5. [DOI] [PubMed] [Google Scholar]
- 3.Lin NC, Martin GB. 2007. Pto- and Prf-mediated recognition of AvrPto and AvrPtoB restricts the ability of diverse Pseudomonas syringae pathovars to infect tomato. Mol Plant Microbe Interact 20:806–815. doi: 10.1094/MPMI-20-7-0806. [DOI] [PubMed] [Google Scholar]
- 4.Kunkeaw S, Tan S, Coaker G. 2010. Molecular and evolutionary analyses of Pseudomonas syringae pv. tomato race 1. Mol Plant Microbe Interact 23:415–424. doi: 10.1094/MPMI-23-4-0415. [DOI] [PubMed] [Google Scholar]
- 5.Cai R, Lewis J, Yan S, Liu H, Clarke CR, Campanile F, Almeida NF, Studholme DJ, Lindeberg M, Schneider D, Zaccardelli M, Setubal JC, Morales-Lizcano NP, Bernal A, Coaker G, Baker C, Bender CL, Leman S, Vinatzer BA. 2011. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathog. 7:e1002130. doi: 10.1371/journal.ppat.1002130. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Lawton MB, MacNeill BH. 1986. Occurrence of race 1 of Pseudomonas syringae on field tomato in south western Ontario. Can J Plant Pathol 8:85–88. doi: 10.1080/07060668609501847. [DOI] [Google Scholar]
- 7.Arredondo CR, Davis RM. 2000. First report of Pseudomonas syringae pv. tomato race 1 on tomato in California. Plant Dis 84:370–371. doi: 10.1094/PDIS.2000.84.3.371A. [DOI] [PubMed] [Google Scholar]
- 8.Thapa SP, Miyao EM, Davis M, Coaker G. 2015. Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777. Theor Appl Genet 128:681–692. doi: 10.1007/s00122-015-2463-7. [DOI] [PubMed] [Google Scholar]
- 9.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembler and its applications to single cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 11.Lindeberg M, Cunnac S, Collmer A. 2012. Pseudomonas syringae type III effector repertoires: last words in endless arguments. Trends Microbiol 20:199–208. doi: 10.1016/j.tim.2012.01.003. [DOI] [PubMed] [Google Scholar]