Abstract
Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.
Highlights
The pan-GWAS approach predicted the genes associated with onion-pathogenicity in Pantoea stewartii subsp. indologenes (Psi) strains, in Psi pv. cepacicola
We found a cluster of genes different from the HiVir/PASVIL cluster linked to onion pathogenicity in Psi pv. cepacicola
We concluded that there might be several pathogenicity factors involved in onion pathogenicity and to some extent these might be specific to some Pantoea spp
Summary
The Pantoea complex is constituted by four species, namely, P. ananatis, P. stewartii, P. allii and P. agglomerans that cause center rot of onions [1,2,3,4]. Three out of the four species in the Pantoea species complex Indologenes) are responsible for more than 80% of the reported cases of disease in onions [5]. Mergaert et al [6] reclassified Eriwinia stewartii as P. stewartii and proposed two subspecies namely, P. stewartii subsp. We phenotypically and genotypically characterized seventeen Psi strains that are either pathogenic on both onions and millets or on millets only [7]. Based on a host-range evaluation, we proposed two new pathovars of Psi, namely, Psi pv. Based on a host-range evaluation, we proposed two new pathovars of Psi, namely, Psi pv. cepacicola pv. nov. and
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