Comparison between complete genomes of an isolate of Pseudomonas syringae pv. actinidiae from Japan and a New Zealand isolate of the pandemic lineage

Scientific Reports
Russell T M PoulterMargi I Butler

Abstract

The modern pandemic of the bacterial kiwifruit pathogen Pseudomonas syringae pv actinidiae (Psa) is caused by a particular Psa lineage. To better understand the genetic basis of the virulence of this lineage, we compare the completely assembled genome of a pandemic New Zealand strain with that of the Psa type strain first isolated in Japan in 1983. Aligning the two genomes shows numerous translocations, constrained so as to retain the appropriate orientation of the Architecture Imparting Sequences (AIMs). There are several large horizontally acquired regions, some of which include Type I, Type II or Type III restriction systems. The activity of these systems is reflected in the methylation patterns of the two strains. The pandemic strain carries an Integrative Conjugative Element (ICE) located at a tRNA-Lys site. Two other complex elements are also present at tRNA-Lys sites in the genome. These elements are derived from ICE but have now acquired some alternative secretion function. There are numerous types of mobile element in the two genomes. Analysis of these elements reveals no evidence of recombination between the two Psa lineages.

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Citations

Jan 15, 2020·Journal of Medical Microbiology·Joycelyn HoRussell Poulter

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Datasets Mentioned

BETA
CP018203
CP012180
CP018204
CM002754
KY362373
KY362372
CP012179
CP018202
ICMP9853

Methods Mentioned

BETA
restriction modification
ICE
ICEs
454 sequencing
PCR

Software Mentioned

SMRT Analysis
ISsaga
Geneious
progressiveMauve
FLASH
Island Viewer
kineticsTools
BLASTn
FastQC
BLAST

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