Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host

Abstract

Bacterial etiolation and decline (BED), caused by Acidovorax avenae, is an emerging disease of creeping bentgrass on golf courses in the United States. We performed the first comprehensive analysis of A. avenae on a nationwide collection of turfgrass- and maize-pathogenic A. avenae. Surprisingly, our results reveal that the turfgrass-pathogenic A. avenae in North America are not only highly divergent but also belong to two distinct phylogroups. Both phylogroups specifically infect turfgrass but are more closely related to maize pathogens than to each other. This suggests that, although the disease is only recently reported, it has likely been infecting turfgrass for a long time. To identify a genetic basis for the host specificity, we searched for genes closely related among turfgrass strains but distantly related to their homologs from maize strains. We found a cluster of 11 such genes generated by three ancient recombination events within the type III secretion system (T3SS) pathogenicity island. Ever since the recombination, the cluster has been conserved by strong purifying selection, hinting at its selective importance. Together our analyses suggest that BED is an ancient disease that may owe its host specificity to a highly conserved cluster of 11 T3SS genes.

Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

“…We believe that the genetic diversity calculated from this study is a better representation of the true scenario of the SI E. amylovora strains. Despite this, the overall diversity of SI E. amylovora strains was still very low in comparison with other pathogens that have emerged in recent years (McCann et al ., ; Potnis et al ., ; Zeng et al ., ).…”

“…The overall diversity of the 30 SI E. amylovora genomes, as determined by Watterson's theta (Watterson, 1975), was 8.18 310 24 per site, which is at least 100-fold lower than that of other bacterial plant pathogens, such as the kiwifruit pathogen Pseudomonas syringae pv. actinidiae and the turfgrass pathogen Acidovorax avenae (Watterson's theta values determined as 0.008 and 0.0279, respectively) (McCann et al, 2013;Zeng et al, 2017). However, when compared with a previous comparative genomics study of E. amylovora, the genetic diversity of E. amylovora determined by our study was approximately 33 times higher (nucleotide pairwise identity was 99.90% in this study, compared with the amino acid pairwise identity of 99.98% of coding regions, or nucleotide pairwise identity of 99.997% on the whole genome, in the previous study).…”

“…Homologous recombination, defined as a segment of DNA from one microorganism being transferred and recombined with the genome of another microorganism in prokaryotes, has been commonly observed in plant-pathogenic bacteria, and is thought to play a critical role in pathogen evolution and host adaptation (Awadalla, 2003;Baltrus et al, 2017;Mhedbi-Hajri et al, 2013;Yan et al, 2008;Zeng et al, 2017). We determined the level of recombination that occurred between the four clades of SI E. amylovora (Fig.…”

“…The quality and quantity of the purified DNA were checked with a Nanodrop 2000C (Nanodrop Products, Wilmington, DE, USA). Genomic DNA was sequenced by either an Illumina MiSeq instrument (Illumina Inc, San Diego, CA, USA) or a Pacific Bioscience RS II instrument (Pacific Biosciences, Menlo Park, CA, USA) at the Yale Center for Genome Analysis using the same procedure as described in our previous work (Zeng et al, 2017).…”

Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash

“…A phylogenetic analysis confirmed that the recombinant hrp/hrc genes shared a common evolutionary history with that of phylogroup 2a (Figure 4) and therefore, may be a significant factor contributing to the convergent pathogenicity of 2a and 2b-a lineages to cucurbit hosts. This finding was reminiscent of bacterial etiolation and decline of creeping bentgrass, for which the host-specificity of two phylogenetically distinct Acidovorax avenae populations was associated with three ancestral recombination events affecting the hrp/hrc gene cluster (Zeng et al, 2017).…”