Abstract
Dickeya dianthicola and “Dickeya solani” are currently the dominant bacterial pathogens of potatoes in Europe. Here, we present the draft genome sequences of four strains of each pathogen.
GENOME ANNOUNCEMENT
Enterobacterial plant pathogens belonging to the Dickeya genus (previously Erwinia chrysanthemi) cause disease worldwide in a wide range of plant species, including crops (1). The Dickeya genus is currently considered to comprise 5 species: Dickeya dianthicola, Dickeya dadantii, Dickeya zeae, Dickeya chrysanthemi, and Dickeya paradisiaca (2, 3). D. dianthicola, although causing disease worldwide on a range of crops and ornamentals, has had great impact on potato production in Europe from the early 1970s onward (1). In addition to the five assigned Dickeya species, several isolates were identified that formed distinct clades, e.g., DUC-1 (also referred to as group 1, clade IV), DUC-2, DUC-3, SLC-1, and SLC-2, which may represent previously unidentified species. Since 2004, DUC-1, for which the name “Dickeya solani” has been proposed, has been identified across Europe as causing disease in potatoes, and it was also isolated recently from hyacinth (4–8).
Currently, there are four complete sequenced Dickeya strains deposited in GenBank, one each from D. paradisiaca, D. zeae, D. chrysanthemi, and D. dadantii, as well as a draft D. zeae strain. Here, we announce draft genome sequences of the following eight strains from previously unsequenced Dickeya species: D. dianthicola NCPPB 453T, a type strain from Dianthus; NCPPB 3534, from potato in the Netherlands; IPO 980, from potato in the Netherlands; LMG 25864, from potato in Belgium; and D. solani strain IPO 2222 from potato in the Netherlands; MK10, from potato in Israel; MK16, from river water in the United Kingdom; and LMG 25865, from potato in Belgium.
Six strains were sequenced using 454 pyrosequencing (Roche, Branford, CT): IPO 2222, MK10, MK16, NCPPB 453T, NCPPB 3534, and IPO 980. Three strains were sequenced using Illumina GAIIx: LMG 25864, LMG 25865, and NCPPB 3534. Three strains were assembled de novo using 454 Life Sciences Newbler v2.5.3 (IPO 2222, NCPPB 453T, and IPO 980); strain LMG25865 was assembled by reference mapping to the IPO 2222 assembly using CLC bio assembly module, strain NCPPB 3534 was assembled as a hybrid of 454 and Illumina reads using MIRA, strains MK10 and MK16 were assembled as a meta-assembly of Newbler de novo and reference-guided assemblies to the IPO 2222 assembly, and the LMG 25864 strain was assembled as a meta-assembly of CLC and Velvet de novo assemblies.
Sequences were annotated using a combination of Prodigal and RAST gene callers, BLAST searches using query sequences known to be missed by those packages, and tRNAScan-SE. A total of 4,571 (for strain LMG 25864), 4,477 (strain LMG 25865), 4,642 (strain NCPPB 3534), 4,365 (strain NCPPB 453T), 4,516 (strain IPO 980), 4,519 (strain MK10), 4,401 (strain MK16), and 4,471 (strain IPO 2222) genes were determined.
A detailed comparative genomic analysis of the eight draft sequences will follow in a future publication.
Nucleotide sequence accession numbers.
The draft sequences of these eight Dickeya strains are available in GenBank under the accession no. AONU00000000 (IPO 2222), AOOP00000000 (MK10), AOOQ00000000 (MK16), AOOB00000000 (NCPPB 453T), AOOK00000000 (NCPPB 3534), AOOS00000000 (IPO 980), AOOM00000000 (LMG 25864), and AONX00000000 (LMG 25865). See Table 1 for statistics for the eight draft Dickeya genomes.
TABLE 1 .
Statistics for the eight draft Dickeya genomes
| Species | Strain | Accession no. | No. of contigs | No. of assembled bases | N50 |
|---|---|---|---|---|---|
| D. dianthicola | LMG 25864, GBBC 2039 | AOOM00000000 | 237 | 4,767,435 | 35,250 |
| D. dianthicola | NCPPB 3534 | AOOK00000000 | 52 | 4,832,425 | 213,434 |
| D. dianthicola | NCPPB 453T | AOOB00000000 | 47 | 4,668,129 | 235,227 |
| D. dianthicola | IPO 980 | AOOS00000000 | 63 | 4,825,313 | 181,825 |
| D. solani | LMG 25865, GBBC 2040 | AONX00000000 | 224 | 4,812,070 | 40,901 |
| D. solani | MK10 | AOOP00000000 | 39 | 4,930,219 | 295,556 |
| D. solani | MK16 | AOOQ00000000 | 23 | 4,867,774 | 485,700 |
| D. solani | IPO 2222 | AONU00000000 | 91 | 4,857,348 | 99,673 |
ACKNOWLEDGMENTS
This study was funded by the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS) (SCR/0919/07 and SCR/0927/09) and the Agriculture, Horticulture Development Board (AHDB) through the Potato Council (R437).
We thank members of the Centre for Genomics Research at the University of Liverpool for sequencing 6 of the 8 Dickeya strains used in the study.
Footnotes
Citation Pritchard L, Humphris S, Baeyen S, Maes M, Van Vaerenbergh J, Elphinstone J, Saddler G, Toth I. 2013. Draft genome sequences of four Dickeya dianthicola and four Dickeya solani strains. Genome Announc. 1(4):e00087-12. doi:10.1128/genomeA.00087-12.
REFERENCES
- 1. Toth IK, van der Wolf JM, Saddler G, Lojkowska E, Helias V, Pirhonen M, Tsror (Lahkim) L, Elphinstone JH. 2011. Dickeya species: an emerging problem for potato production in Europe. Plant Pathol. 60:385–399 [Google Scholar]
- 2. Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, Gardan L. 2005. Transfer of Pectobacterium chrysanthemi (Burkholder et al., 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int. J. Syst. Evol. Microbiol. 55:1415–1427 [DOI] [PubMed] [Google Scholar]
- 3. Brady C, Cleenwerck I, Denman S, Venter S, Rodríguez-Palenzuela P, Coutinho TA, de Vos P. 2011. Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. Int. J. Syst. Evol. Microbiol. 62:1592–1602. 10.1099/ijs.0.035055-0 [DOI] [PubMed] [Google Scholar]
- 4. Parkinson N, Stead D, Bew J, Heeney J, Tsror Lahkim L, Elphinstone J. 2009. Dickeya species relatedness and clade structure determined by comparison of recA sequences. Int. J. Syst. Evol. Microbiol. 59:2388–2393 [DOI] [PubMed] [Google Scholar]
- 5. Cahill G, Fraser K, Kowalewska MJ, Kenyon DM, Saddler GS. 2010. Recent findings from the Dickeya survey and monitoring programme. The Dundee Conference: crop protection in northern Britain 2010, Bayer CropScience, Dundee, United Kingdom [Google Scholar]
- 6. Laurila J, Ahola V, Lehtinen A, Joutsjoki T, Hannukkala A, Rahkonen A, Pirhonen M. 2008. Characterisation of Dickeya strains isolated from potato and river water samples in Finland. Eur. J. Plant Pathol. 122:213–225 [Google Scholar]
- 7. Sławiak M, van Beckhoven JRCM, Speksnijder AGCL, Czajkowski R, Grabe G, van derWolf JM. 2009. Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. Strains isolated from potato in Europe. Eur. J. Plant Pathol. 125:245–261 [Google Scholar]
- 8. Czajkowski R, van Veen JA, van der Wolf JM. 2009. New biovar 3 Dickeya spp. strain (syn. Erwinia chrysanthemi) as a causative agent of blackleg in seed potato in Europe. Phytopathology 99:S27 [Google Scholar]