Identification of Two Novel Pathovars of Pantoea stewartii subsp. indologenes Affecting Allium sp. and Millets

Koirala, Santosh; Zhao, Mei; Agarwal, Gaurav; Gitaitis, R. D.; Stice, Shaun; Kvitko, Brian H.; Dutta, Bhabesh

doi:10.1094/phyto-11-20-0508-r

Cited by 18 publications

(32 citation statements)

References 29 publications

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“…cepacicola (n= 4) and pv. setariae (n=13)] (Table 1) were used in this study that were phenotypically characterized in our earlier study [7]. Out of the 17 strains, two strains were previously sequenced Psi pv.…”

Section: Bacterial Strains Identification and Culture Preparationmentioning

confidence: 99%

“…Genomic features of all 21 strains used in this study are listed in Table 1. The gbk (genebank format) files of the draft-assembled and annotated genomes of Psi strains [7] were used for pan-genome analyses using get_homologues [20]. These gbk files were used to get the syntenic sequence clusters by get_homologues.pl using Or-thoMCL (OMCL) algorithm.…”

Section: Bacterial Strains Identification and Culture Preparationmentioning

confidence: 99%

“…We utilized phenotypic data from the Koirala et al (2021) study [7]where both Psi pv. cepacicola and Psi pv.…”

Section: Pan-genome-wide Association Analysis and Annotationsmentioning

confidence: 99%

“…cepacicola strains were pathogenic on Allium spp. (onion, leek, chive and bunching onion) and Poacea (oat, rye, foxtail millet) species [7]. Rest of the strains belonged to Psi pv.…”

Section: The P Stewartii Subsp Indologenes Pan-genome Architecture and Phylogenymentioning

confidence: 99%

“…indologenes (Psi). Recently, we phenotypically and genotypically characterized seventeen Psi strains that are either pathogenic on both onions and millets or on millets only [7]. Based on the host-range evaluation we proposed two new pathovars of Psi namely Psi pv.…”

Section: Introductionmentioning

confidence: 99%

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Pan-genome of Novel Pantoea stewartii subsp. indologenes Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Agarwal¹,

Gitaitis²,

Dutta³

2021

Preprint

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Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. 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 onion 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 7,030 genes. Among these, 3,546 (present in genomes of all 17 strains) were the core genes that were a subset of 3,682 soft-core genes (present in ≥16 strains). The accessory genome included 1,308 shell genes and 2,040 cloud genes (present in ≤ 2 strains). The pan-genome showed a clear liner progression with >6,000 genes, suggesting the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison to core genome SNP-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study including four 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 transfers observed between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes including seven cluster of genes associated with the pathogenicity phenotype on onion. One of the clusters contain 11 genes with known functions and are found to be chromosomally located.

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Section: Bacterial Strains Identification and Culture Preparationmentioning

confidence: 99%

Section: Bacterial Strains Identification and Culture Preparationmentioning

confidence: 99%

“…We utilized phenotypic data from the Koirala et al (2021) study [7]where both Psi pv. cepacicola and Psi pv.…”

Section: Pan-genome-wide Association Analysis and Annotationsmentioning

confidence: 99%

“…cepacicola strains were pathogenic on Allium spp. (onion, leek, chive and bunching onion) and Poacea (oat, rye, foxtail millet) species [7]. Rest of the strains belonged to Psi pv.…”

Section: The P Stewartii Subsp Indologenes Pan-genome Architecture and Phylogenymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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