Abstract
Here, we report the draft genome sequences for 7 phylogenetically diverse isolates of Pseudomonas syringae, obtained from numerous environmental sources and geographically proximate crop species. Overall, these sequences provide a wealth of information about the differences (or lack thereof) between isolates from disease outbreaks and those from other sources.
GENOME ANNOUNCEMENT
Pseudomonas syringae is well known as a facultative phytopathogen of many plant species, including crops, such as tomato, bean, and wheat, as well as the laboratory model Arabidopsis (1). Therefore, a majority of P. syringae-related research has focused on identifying and understanding the virulence factors that enable this bacterium to cause disease in planta. More recently, increased emphasis has been placed on understanding how P. syringae strains survive in the environment outside plants, and greater environmental sampling has driven the collection of strains from noncrop sources and symptomless plants (2–4). Here, we describe the draft genome sequences for phylogenetically diverse isolates of P. syringae collected from various sources in the United States and France. The sampled locations include nonagricultural environmental sources as well as plants lacking disease symptoms. These sequences provide a wealth of data for genomic comparisons between geographically similar isolates and enable a greater understanding of the evolutionary forces that lead to the emergence of phyopathogens from environmental reservoirs.
The collection of these isolates has been previously described (3–5). Genomic DNA was prepared from populations initiated with single colonies and purified as per Baltrus et al. (6). The sequencing of each isolate except P. syringae USA011 was performed on an Illumina GAII from 36-bp paired-end libraries. A genomic library from USA011 was sequenced using a portion of one Illumina HiSeq lane using 36-bp paired-end libraries. The draft genomes were assembled using SPAdes 2.5.0 without trimming for quality (7). These assemblies are part of a larger project that includes draft genome assemblies for P. syringae strains (and their respective accession no.) UB246 (AVEQ00000000), CC1543 (AVEJ00000000), CC94 (AVEA00000000), UB303 (AVDZ00000000), CC1416 (AVEP00000000), CC1458 (AVEN00000000), CC1544 (AVEI00000000), CC1559 (AVEG00000000), CC440 (AVEC00000000), CC457 (AVEB00000000), CC1557 (AVEH00000000), USA007 (AVDY00000000), and CC1583 (AVEF00000000), as well as P. viridiflava strains CC1582 (AVDW00000000) and TA043 (AVDV00000000). These assemblies are not included within this announcement due to poor assembly quality.
Nucleotide sequence accession numbers.
The nucleotide sequence accession numbers for Genbank are found in Table 1. These sequences and associated metadata can be publicly found at the Joint Genome Institute (JGI) portal (http://img.jgi.doe.gov/) with the JGI taxon IDs listed in Table 1.
TABLE 1.
Characteristics of the seven P. syringae isolates
| Isolate | NCBI accession no.a | JGI taxon ID | Genome size (bp) | No. of contigs | N50 | Substrate of isolation | Country of isolation | Reference |
|---|---|---|---|---|---|---|---|---|
| Pseudomonas syringae CC1417 | AVEO00000000 | 2506783030 | 5,648,464 | 210 | 50,166 | Epilithon | USA | 3 |
| Pseudomonas syringae CC1466 | AVEM00000000 | 2506783019 | 5,591,749 | 294 | 60,479 | Dodecatheon pulchellum | USA | 3 |
| Pseudomonas syringae CC1513 | AVEL00000000 | 2506783020 | 5,725,032 | 164 | 85,568 | Hutchinsia alpina | France | 3 |
| Pseudomonas syringae CC1524 | AVEK00000000 | 2506783021 | 5,828,366 | 264 | 44,224 | Stream water | France | 4 |
| Pseudomonas syringae CC1629 | AVEE00000000 | 2524614586 | 5,932,928 | 261 | 75,208 | Oats | USA | 4 |
| Pseudomonas syringae CC1630 | AVED00000000 | 2524614587 | 6,056,064 | 283 | 52,218 | Sainfoin | USA | 4 |
| Pseudomonas syringae USA011 | AVDX00000000 | 2509276053 | 6,429,288 | 198 | 91,862 | Stream water | USA | 4 |
Projects have been deposited at GenBank under these accession numbers, but the version described in this paper is version XXXX02000000.
ACKNOWLEDGMENTS
Funding was provided by National Institutes of Health (NIH) grant no. GM066025 and the Department of Energy Basic Energy Sciences grant no. ER20187 to J. L. Dangl and by NIH National Research Service Ruth Kirchstein Award no. GM082279-01 and startup funds from the University of Arizona to D. A. Baltrus.
J. L. Dangl is an Investigator of the Howard Hughes Medical Institute.
We thank P. Miecskowski, H. Kelkar, and J. Walsh of the UNC-CH HTS core and Amy Chen, Susannah Tringe, and Konstantinos Liolios of the Lawrence Berkeley National Laboratory for their technical assistance.
Footnotes
Citation Baltrus DA, Yourstone S, Lind A, Guilbaud C, Sands DC, Jones CD, Morris CE, Dangl JL. 2014. Draft genome sequences of a phylogenetically diverse suite of Pseudomonas syringae strains from multiple source populations. Genome Announc. 2(1):e01195-13. doi:10.1128/genomeA.01195-13.
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