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Dickeya species relatedness and clade structure determined by comparison of recA sequences
Year:
2009
Authors :
Tsror, Leah
;
.
Volume :
59
Co-Authors:
Parkinson, N., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Stead, D., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Bew, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Heeney, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Tsror, L., Agricultural Research Organisation, Gilat Research Centre, MP Negev 85280, Israel
Elphinstone, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Facilitators :
From page:
2388
To page:
2393
(
Total pages:
6
)
Abstract:
Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance. © 2009 IUMS.
Note:
Related Files :
bacterial strain
Chrysanthemum
Dianthus
Dickeya paradisiaca
Plants
Rec A Recombinases
Solanum tuberosum
Zea mays
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Related Content
More details
DOI :
10.1099/ijs.0.009258-0
Article number:
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
27379
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 00:30
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Scientific Publication
Dickeya species relatedness and clade structure determined by comparison of recA sequences
59
Parkinson, N., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Stead, D., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Bew, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Heeney, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Tsror, L., Agricultural Research Organisation, Gilat Research Centre, MP Negev 85280, Israel
Elphinstone, J., Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom
Dickeya species relatedness and clade structure determined by comparison of recA sequences
Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance. © 2009 IUMS.
Scientific Publication
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