Population Genomics of Bacterial Plant Pathogens

Straub, Christina; Colombi, Elena; McCann, Honour C.

doi:10.1094/phyto-09-20-0412-rvw

Cited by 18 publications

(9 citation statements)

References 64 publications

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“…In the same study, the authors demonstrated that PAVs from the pan-genome analysis of 10 P. ananatis strains separated the pathogenic strains from the non-pathogenic strains, which was not observed when the core genome was used. Phylogenetic studies conducted so far in P. ananatis have relied only on PAVs, which are mainly horizontally acquired ( Welch et al, 2002 ) contrary to the vertically inherited SNPs ( Straub et al, 2021 ). In the current study, we therefore conducted a comparative phylogenetic study using core genome SNPs, PAVs and wgMLST approach.…”

Section: Discussionmentioning

confidence: 99%

“…In the current study, we therefore conducted a comparative phylogenetic study using core genome SNPs, PAVs and wgMLST approach. Core SNPs are relied to infer phylogeny as they represent the vertically inherited portion of the genome in the population ( Didelot and Wilson, 2015 ; Straub et al, 2021 ). It was however observed that pathogenic strains clustered together with the non-pathogenic strains (in some groups in the phylogenetic tree) based on core SNPs.…”

Section: Discussionmentioning

confidence: 99%

“…However, the possibility of HGT based distortion can be ruled out because our core SNP analysis was not based on a single reference genome. Use of a reference genome-based SNP calling approach can result in SNPs that are present in core genome of some strains that have horizontally acquired genes similar to reference genome but not present in other strains that do not have such horizontally acquired genes ( Straub et al, 2021 ). In the current study, the core genome region of 81 strains was aligned (non-reference based) to identify the variant and invariant sites in all the strains.…”

Section: Discussionmentioning

confidence: 99%

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Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

et al. 2021

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“…However, the number of input genomes may have a role to play and core genes-based phylogeny could probably change if the number of strains/genomes is further increased. It could also be possible that the core genome is impacted by HGT or homologous recombination and, as a result, the phylogenetic relationship based on core genes is obscured or distorted [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

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

2021

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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.

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“…However, number of input genomes may have a role to play and probably core genes-based phylogeny could change if the number of strains/genomes are further added. It could also be possible that core genome is impacted by HGT or homologous recombination and as a result phylogenetic relationship based on core genes is obscured or distorted [34].…”

Section: An Open Pan-genome Of Pantoea Stewartii Subsp Indologenesmentioning

confidence: 99%

Pan-genome of Novel <em>Pantoea stewartii</em> subsp. <em>indologenes</em> 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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Population Genomics of Bacterial Plant Pathogens

Cited by 18 publications

References 64 publications

Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

Pan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion

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

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

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