Abstract
Pseudomonas syringae is a ubiquitous bacterium that readily persists in environmental habitats as a saprophyte and also is responsible for numerous diseases of crops. Here, we report the whole-genome sequences of 10 strains isolated from both woody and herbaceous plants that will contribute to the elucidation of the determinants of their host ranges.
GENOME ANNOUNCEMENT
The Pseudomonas syringae complex is composed of 13 phylogenetic groups (1) collectively able to cause disease on more than one hundred plant species (2, 3). P. syringae strains have also been isolated from substrates other than plants in various habitats linked to the water cycle. Many of these environmental strains, when tested in the laboratory, are also pathogenic for several plant species (4, 5). Here, we sequenced, assembled, and annotated the whole genomes of 10 strains of P. syringae isolated from diverse plants and representing 3 phylogenetic groups. These strains were chosen to represent different host range spectra based on the results of research to be reported elsewhere. From phylogroup 1, the strains included CFBP 1657 (pv. maculicola) isolated from Brassica oleracea, CFBP 1702 (pv. viburni) isolated from Viburnum sp., and PaVt10 (5) (pv. avellanae) isolated from Corylus avellana. From phylogroup 2, the strains were 41a from Prunus armeniaca and CFBP 1754 (pv. papulans) from Malus sylvestris. From phylogroup 3, we sequenced the genomes of strains CFBP 3205 (pv. amygdali) from Prunus dulcis, CFBP 3225 (pv. meliae) from Melia azedarach, CFBP 3226 (pv. dendropanacis) from Dendropanax trifidus, CFBP 4219 (pv. daphniphylli) from Daphniphyllum sp., and PseNe107 (5) (pv. savastanoi) from Olea europaea. With the exception of strain 41a, all other strains were from reference collections and were described previously. For all strains, DNA was extracted by using the Qiagen Genomic-tip 100/G kit after growing strains overnight at 26°C in a liquid nutrient broth. Illumina libraries were constructed with the NEXTflex PCR-free DNA sequencing kit and NEXTflex PCR-free barcodes, and genomes were sequenced by using MiSeq M00185 (250-bp paired-end reads). The insert sizes for each genome are reported in Table 1. Overall, the average insert size was 389 bp. De novo assembly was performed by using a pipeline that consists of a combination of Velvet (6), SOAPdenovo, and SOAPGapCloser (7). The structural annotation of the contigs was achieved as previously described (8). The features for each genome are reported in Table 1. Analysis of the 10 P. syringae genomes showed that all strains present a complete type III secretion system.
TABLE 1.
Genome characteristics
| Strain name | Phylogroup | Accession no. | Genome size (bp) | Insert size (bp) | No. of contigs | N50 (bp) | No. of protein-coding genes | G+C content (%) |
|---|---|---|---|---|---|---|---|---|
| CFBP 1657 | 1 | JYHH00000000 | 891,415,000 | 374 | 138 | 122,411 | 5,209 | 58.43 |
| CFBP 1702 | 1 | JYHK00000000 | 944,775,000 | 397 | 265 | 98,077 | 5,595 | 58.60 |
| PaVt10 | 1 | JYHC00000000 | 899,519,500 | 392 | 455 | 30,706 | 4,807 | 58.82 |
| 41a | 2 | JYHJ00000000 | 930,312,000 | 372 | 24 | 665,729 | 5,126 | 59.11 |
| CFBP 1754 | 2 | JYHI00000000 | 735,876,000 | 394 | 182 | 132,813 | 2,378 | 58.97 |
| CFBP 3205 | 3 | JYHB00000000 | 697,222,500 | 404 | 343 | 35,334 | 4,934 | 58.29 |
| CFBP 3225 | 3 | JYHE00000000 | 733,793,000 | 390 | 360 | 34,681 | 4,344 | 58.40 |
| CFBP 3226 | 3 | JYHG00000000 | 545,040,500 | 370 | 247 | 73,921 | 4,988 | 58.11 |
| CFBP 4219 | 3 | JYHD00000000 | 614,308,500 | 403 | 377 | 47,492 | 5,100 | 58.12 |
| PseNe107 | 3 | JYHF00000000 | 853,186,500 | 396 | 247 | 109,046 | 5,303 | 58.02 |
Nucleotide sequence accession numbers.
These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
We thank the GetPlage Platform (INRA-Toulouse) for assistance in genome sequencing. Genome assembly and annotation were performed by using the informatics facilities of INRA-Toulouse LIPM Research Unit.
Support for this work came from in-house funding from UR0407 of INRA and from DAFNE of Tuscia University and from contract no. 21000546 to UR0407 from the French Ministry of Agriculture for the RESIBAC project.
Footnotes
Citation Bartoli C, Carrere S, Lamichhane JR, Varvaro L, Morris CE. 2015. Whole-genome sequencing of 10 Pseudomonas syringae strains representing different host range spectra. Genome Announc 3(2):e00379-15. doi:10.1128/genomeA.00379-15.
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