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

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.

Transcriptional profiling of threePseudomonas syringaepv.actinidiaebiovars reveals different responses to apoplast-like conditions related to strain virulence

“…Our Psa2 and Psa3 strains featured the canonical EEL structure (including tRNA Leu , queA and tgt sequences) although two of the three Psa2 genomes (ICMP 19071 and ICMP 19072) contained a phage insertion within the EEL, supporting the observation that tRNA genes are often found at phage integration sites (75). Multiple rearrangements have been reported in Psa1 and Psa3 biovars (76), and accordingly we found that the tRNA Leu , queA and tgt sequences were dispersed to other chromosomal locations in Psa1 (ICMP9617 and ICMP9853). Such rearrangements may be selectively neutral, but the genome structure may affect transcriptional regulation (76).…”

The application of the CRISPR–Cas9 system in Pseudomonas syringae pv. actinidiae

“…Genome sequencing yielded an average of 1.05 million paired sequence reads for each genome, equivalent to an average 40-fold read coverage. The sequence reads from the Psa3 isolates were mapped to the completely assembled 6 555 571 bp chromosome and 74 432 bp plasmid of a pandemic Psa3 strain from New Zealand, ICMP18708 (GenBank accessions CP012179-chromosome and CP012180-plasmid [26]), using Geneious 11.0.3 [39]. Read mapping was performed with the Geneious 6.0.3 Read Mapper [40] using the following parameter values: maximum mismatches per read=10 %, minimum mapping quality=Phred 30, maximum gaps per read=10 % read length, maximum gap length=3 bp and minimum overlap=25 bp.…”

“…The genomes of several isolates of Psa have been fully sequenced using the PacBio platform [26,41]. This permitted the identification of RM systems specific to different types of Psa.…”

“…The sequence of pJH1 has been submitted to GenBank and assigned the accession number MN346704. To confirm the activity and specificity of the type I RM system suggested by the PacBio methylation data [26], a modified version of the pJH1 was constructed. This plasmid, designated pMZ5-103, has a single base change that generated a restriction site for the type I enzyme (AGCANNNNNGTC).…”

“…More recently, Pseudomonas putida was also found to employ NHEJ to repair DNA during the stationary phase [24]. A variety of Psa strains have now been fully sequenced and annotated [6,25,26]. This has revealed the presence of Ku-and ATPdependent ligase genes arranged in an operon in these Psa genomes.…”