Abstract
SummaryHybrid assembly strategies that combine long‐read sequencing reads from Oxford Nanopore's MinION device combined with high‐depth Illumina paired‐end reads have enabled completion and circularization of both plasmids and chromosomes from multiple bacterial strains. Here we demonstrate the utility of supplementing Illumina paired‐end reads from a previously published draft genome of P. syringae pv. pisi PP1 with long reads to generate a complete genome sequence for this strain. The phylogenetic placement and genomic repertoire of virulence factors within this strain provides a unique perspective on virulence evolution within P. syringae phylogroup 2, and highlights that strains can rapidly acquire virulence factors through horizontal gene transfer by acquisition of plasmids as well as through chromosomal recombination.
Highlights
We originally reported assembly of a draft genome for this strain using Illumina paired-end reads (Baltrus et al, 2014), but have completed this genome by employing a hybrid approach involving long reads from an Oxford Nanopore MinION
Access to this complete genome sequence, which consists of one chromosome and three plasmids, enables definitive placement of type III effectors onto replicons and allows investigation into how these effectors were acquired. Using this genome sequence we can demonstrate that, even though numerous type III effectors have been acquired in concert with loss of at least two of three phytotoxins present in other group II strains, horizontal transfers of these effectors have taken place through recombination of chromosomal segments as well through plasmid acquisition
We have originally reported a draft genome sequence for this strain, using only 100 bp paired-end reads from an Illumina HiSeq, which consisted of an assembly of 5 949 520 bp spread over 256 contigs (Baltrus et al, 2014)
Summary
We originally reported assembly of a draft genome for this strain using Illumina paired-end reads (Baltrus et al, 2014), but have completed this genome by employing a hybrid approach involving long reads from an Oxford Nanopore MinION. Using this genome sequence we can demonstrate that, even though numerous type III effectors have been acquired in concert with loss of at least two of three phytotoxins present in other group II strains, horizontal transfers of these effectors have taken place through recombination of chromosomal segments as well through plasmid acquisition.
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