Abstract
Here, we report the draft genome sequence of Pseudomonas viridiflava strain CDRTc14 a pectinolytic bacterium showing herbicidal activity, isolated from the root of Lepidium draba L. growing as a weed in an Austrian vineyard. The availability of this genome sequence allows us to investigate the genetic basis of plant–microbe interactions.
GENOME ANNOUNCEMENT
The pectinolytic species Pseudomonas viridiflava represents one of the many phylogroups in the P. syringae species complex (1). It has a worldwide distribution and an extensive host range that includes numerous cultivated crops and weeds, including the model plant Arabidopsis thaliana (2, 3). This organism causes both compatible (disease) and incompatible (resistance) responses in A. thaliana that have triggered great interest in plant–pathogen interaction studies (3, 4).
P. viridiflava shows a high level of adaptability, both as a saprophyte and as a pathogen. Pathogenicity of this bacterium is correlated with the presence/absence of the avrE effector gene in two paralogous pathogenicity islands (T-PAI and S-PAI) of type III secretion systems (5). This bacterium was shown to display variability in phenotypic traits and genomic content, with all isolated P. viridiflava strains parting into two distinct phylogroups, causing disease symptoms of differing severities (6).
The P. viridiflava strain CDRTc14 was isolated from surface-sterilized roots of the weed Lepidium draba, sampled from an Austrian vineyard. This bacterium significantly inhibited germination and root growth of L. draba in vitro and under greenhouse conditions. It also shows indole acetic acid production and phosphate solubilization. Its genomic DNA was extracted following the standard phenol-chloroform method (7). Whole-genome shotgun sequencing was carried out on an Illumina HiSeq (GATC Biotech, Konstanz, Germany), producing 6,728,600 paired-end (2 × 125-bp) reads. Assembly was carried out with SPAdes version 3.8.0 (8). This resulted in 38 contigs (>500 bp), with a 221-fold mean coverage of a 5,963,467-bp genome length and yielded a contig N50 of 29,5098. One contig (67,392 bp) belonging to a plasmid was found by means of Blobtools (http://drl.github.io/blobtools/). The assembly quality was estimated in QUAST version 3.1 (9) and quality control of the mapping data was performed in Qualimap version 2.2 (10). PhyloSift version 1.0.1 (11) was used to verify the genome completeness, assessing a list of 40 highly conserved single-copy marker genes, all of which were found to be present.
Genome assembly was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (12). The chromosome and plasmid of P. viridiflava CDRTc14 had GC contents of 59.31% and 55%, respectively. A total of 5,330 genes and 5,219 protein-coding genes were observed, along with seven genes encoding 5S rRNA, one gene encoding 16S rRNA, one gene encoding 23S rRNA, and 58 genes encoding tRNA.
Regarding pathogenicity, no complete pathogenicity islands or pathogenicity-related effector gene (avrE) was found in this strain. These results are consistent with a previous study showing P. viridiflava strain UASWS0038 as a valuable biological control agent due to the absence of pathogenicity islands (13). Strain CDRTc14 is equipped with several genes related to metal and semimetal resistance (54 genes), stress response (193 genes), and auxin biosynthesis (5 genes).
In-depth genomic comparison between P. viridiflava strain CDRTc14 and pathogenic strains will enable a better understanding of pathogen evolution and determinants of pathogenicity.
Accession number(s).
The draft genome sequence for P. viridiflava strain CDRTc14 has been deposited in GenBank under the accession number MBPF00000000.
ACKNOWLEDGMENT
We gratefully acknowledge the Higher Education Commission (HEC) of Pakistan for financial support for A. Samad.
Footnotes
Citation Samad A, Trognitz F, Antonielli L, Compant S, Sessitsch A. 2016. High-quality draft genome sequence of an endophytic Pseudomonas viridiflava strain with herbicidal properties against its host, the weed Lepidium draba L. Genome Announc 4(5):e01170-16. doi:10.1128/genomeA.01170-16.
REFERENCES
- 1.Parkinson N, Bryant R, Bew J, Elphinstone J. 2011. Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus. Plant Pathol 60:338–344. doi: 10.1111/j.1365-3059.2010.02366.x. [DOI] [Google Scholar]
- 2.Gitaitis R, MacDonald G, Torrance R, Hartley R, Sumner DR, Gay JD, Johnson WC III. 1998. Bacterial streak and bulb rot of sweet onion: II. Epiphytic survival of Pseudomonas viridiflava in association with multiple weed hosts. Plant Dis 82:935–938. doi: 10.1094/PDIS.1998.82.8.935. [DOI] [PubMed] [Google Scholar]
- 3.Jakob K, Goss EM, Araki H, Van T, Kreitman M, Bergelson J. 2002. Pseudomonas viridiflava and P. syringae—natural pathogens of Arabidopsis thaliana. Mol Plant Microbe Interact 15:1195–1203. doi: 10.1094/MPMI.2002.15.12.1195. [DOI] [PubMed] [Google Scholar]
- 4.Goss EM, Bergelson J. 2007. Fitness consequences of infection of Arabidopsis thaliana with its natural bacterial pathogen Pseudomonas viridiflava. Oecologia 152:71–81. doi: 10.1007/s00442-006-0631-9. [DOI] [PubMed] [Google Scholar]
- 5.Bartoli C, Berge O, Monteil CL, Guilbaud C, Balestra GM, Varvaro L, Jones C, Dangl JL, Baltrus DA, Sands DC, Morris CE. 2014. The Pseudomonas viridiflava phylogroups in the P. syringae species complex are characterized by genetic variability and phenotypic plasticity of pathogenicity–related traits. Environ Microbiol 16:2301–2315. doi: 10.1111/1462-2920.12433. [DOI] [PubMed] [Google Scholar]
- 6.Goss EM, Kreitman M, Bergelson J. 2005. Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana. Genetics 169:21–35. doi: 10.1534/genetics.104.031351. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Neumann B, Pospiech A, Schairer HU. 1992. Rapid isolation of genomic DNA from Gram-negative bacteria. Trends Genet 8:332–333. [DOI] [PubMed] [Google Scholar]
- 8.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 assembly algorithm 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]
- 9.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. 2012. Qualimap: evaluating next-generation sequencing alignment data. BioInformatics 28:2678–2679. doi: 10.1093/bioinformatics/bts503. [DOI] [PubMed] [Google Scholar]
- 11.Darling AE, Jospin G, Lowe E, Matsen FA IV, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e01170-16. doi: 10.7717/peerj.243. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Pruitt KD, Tatusova T, Brown GR, Maglott DR. 2012. NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130–D135. doi: 10.1093/nar/gkr1079. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Lefort F, Calmin G, Crovadore J, Osteras M, Farinelli L. 2013. Whole-genome shotgun sequence of Pseudomonas viridiflava, a bacterium species pathogenic to Ararabidopsis thaliana. Genome Announc 1(1):e01170-16. doi: 10.1128/genomeA.00116-12. [DOI] [PMC free article] [PubMed] [Google Scholar]