Draft Genome Sequences of Four Dickeya dianthicola and Four Dickeya solani Strains.

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