Abstract
Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the ‘alt’ gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P. ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.
Highlights
The genus Pantoea currently has 27 recognized species; five of which are known to cause disease-associated losses in several crops (Arnold et al, 2003; Cruz et al, 2007; Coutinho and Venter, 2009; Bankevich et al, 2012; De Maayer et al, 2014)
We describe the use of a pan-genome wide association study (GWAS) approach that predicted novel genes associated with onion-pathogenicity in P. ananatis and provide genomic evidence that presence of entire HiVir/PASVIL and ‘alt’ clusters do not warrant an onion pathogenic phenotypic
We used the pan-GWAS approach to predict genes associated with onion-pathogenicity in P. ananatis
Summary
The genus Pantoea currently has 27 recognized species; five of which are known to cause disease-associated losses in several crops (Arnold et al, 2003; Cruz et al, 2007; Coutinho and Venter, 2009; Bankevich et al, 2012; De Maayer et al, 2014). Indologenes), which causes center rot of onion (Gitaitis et al, 2002; Walcott et al, 2002; Stumpf et al, 2018). Out of the four species in the Pantoea spp. complex, P. ananatis has been associated predominantly with center rot, in Georgia (Dutta et al, 2014). The bacterium can be found as an epiphyte on crop and weed plants (Gitaitis et al, 2002) or as an endophyte in maize kernels and rice seeds (Okunishi et al, 2005; Rijavec et al, 2007). Apart from its epiphytic and endophytic niche in crops and weeds, P. ananatis can be disseminated through infected onion seed and contaminated insect vectors (thrips) to onion crops (Gitaitis et al, 2003; Dutta et al, 2014)
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