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Characterization of Erwinia amylovora strains from different host plants using repetitive‐sequences PCR analysis, and restriction fragment length polymorphism and short‐sequence DNA repeats of plasmid pEA29
Author(s) -
Barionovi D.,
Giorgi S.,
Stoeger A.R.,
Ruppitsch W.,
Scortichini M.
Publication year - 2006
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/j.1365-2672.2006.02813.x
Subject(s) - biology , genetics , restriction fragment length polymorphism , plasmid , erwinia , repeated sequence , dna , restriction fragment , inverted repeat , polymerase chain reaction , cleaved amplified polymorphic sequence , sequence analysis , microbiology and biotechnology , gene , genome
Aims: The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the Pst I fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short‐sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. Methods and Results: Ninety‐three strains obtained from 12 plant genera and different geographical locations were examined by repetitive‐sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using Msp I and Sau 3A restriction enzymes showed a higher variability than that previously observed and no clear‐cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. Conclusions: The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. Significance and Impact of the Study: The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree‐fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic features of deviating E. amylovora strains have to be studied in detail.