Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut

O’Brien, Heath; Thakur, Shalabh; Gong, Yunchen; Fung, Pauline; Zhang, Jianfeng; Yuan, Liang; Wang, Pauline W.; Yong, Choseung; Scortichini, M.; Guttman, David S.

doi:10.1186/1471-2180-12-141

Cited by 54 publications

(56 citation statements)

References 46 publications

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“…For example, the core genome of P. syringae was recently estimated at 1,856 genes, approximately 740 genes smaller than that reported here (O’Brien et al 2012). Problems caused by protein fragments may be one reason for this discrepancy.…”

Section: Discussioncontrasting

confidence: 73%

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

Nowell

Green

Laue

et al. 2014

Genome Biology and Evolution

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Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.

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Section: Discussioncontrasting

confidence: 73%

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

Nowell

Green

Laue

et al. 2014

Genome Biology and Evolution

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“…manihotis or P. syringae pv. avellanae (35, 37). These observations contrast with earlier work performed with X. axonopodis where little variation in type III secretome composition was observed at the pathovar level (25).…”

Section: Discussionmentioning

confidence: 99%

Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity onArabidopsisRevealed by Association and Reverse Genetics

Guy

Génissel

Hajri

et al. 2013

mBio

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The pathogenic bacterium Xanthomonas campestris pv. campestris, the causal agent of black rot of Brassicaceae, manipulates the physiology and the innate immunity of its hosts. Association genetic and reverse-genetic analyses of a world panel of 45 X. campestris pv. campestris strains were used to gain understanding of the genetic basis of the bacterium’s pathogenicity to Arabidopsis thaliana. We found that the compositions of the minimal predicted type III secretome varied extensively, with 18 to 28 proteins per strain. There were clear differences in aggressiveness of those X. campestris pv. campestris strains on two Arabidopsis natural accessions. We identified 3 effector genes (xopAC, xopJ5, and xopAL2) and 67 amplified fragment length polymorphism (AFLP) markers that were associated with variations in disease symptoms. The nature and distribution of the AFLP markers remain to be determined, but we observed a low linkage disequilibrium level between predicted effectors and other significant markers, suggesting that additional genetic factors make a meaningful contribution to pathogenicity. Mutagenesis of type III effectors in X. campestris pv. campestris confirmed that xopAC functions as both a virulence and an avirulence gene in Arabidopsis and that xopAM functions as a second avirulence gene on plants of the Col-0 ecotype. However, we did not detect the effect of any other effector in the X. campestris pv. campestris 8004 strain, likely due to other genetic background effects. These results highlight the complex genetic basis of pathogenicity at the pathovar level and encourage us to challenge the agronomical relevance of some virulence determinants identified solely in model strains.

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“…For example we analysed the sequences of P. syringae pv. avellanae strains present in Genbank [35]. An ICE resembling Pac_ICE1 was present in the sequence of P. syringae pv.…”

Section: Resultsmentioning

confidence: 98%

“…avellanae Ve013 (Figure 7). Bacterial canker disease affecting hazelnut is a newly emerged disease, first described in Greece and Italy in the mid 1970s [35]. There are at least two, quite distinct, types of P .…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones That Originated in China

et al. 2013

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A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA). The disease was first reported in China and Japan in the 1980s. A severe outbreak of PSA began in Italy in 2008 and has spread to other European countries. PSA was found in both New Zealand and Chile in 2010. To study the evolution of the pathogen and analyse the transmission of PSA between countries, genomes of strains from China and Japan (where the genus Actinidia is endemic), Italy, New Zealand and Chile were sequenced. The genomes of PSA strains are very similar. However, all strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish them from all other PSA strains. Similarly, all the PSA strains from the 2008 Italian outbreak form a distinct clonal group and those from Chile form a third group. In addition to the rare SNPs present in the core genomes, there is abundant genetic diversity in a genomic island that is part of the accessory genome. The island from several Chinese strains is almost identical to the island present in the New Zealand strains. The island from a different Chinese strain is identical to the island present in the strains from the recent Italian outbreak. The Chilean strains of PSA carry a third variant of this island. These genomic islands are integrative conjugative elements (ICEs). Sequencing of these ICEs provides evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas syringae to PSA. The analyses of the core genome SNPs and the ICEs, combined with disease history, all support the hypothesis of an independent Chinese origin for both the Italian and the New Zealand outbreaks and suggest the Chilean strains also originate from China.

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Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut

Cited by 54 publications

References 46 publications

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages

Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity onArabidopsisRevealed by Association and Reverse Genetics

Pseudomonas syringae pv. actinidiae from Recent Outbreaks of Kiwifruit Bacterial Canker Belong to Different Clones That Originated in China

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