Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen <i>Phytophthora capsici</i>

Lamour, Kurt; Mudge, Joann; Gobena, Daniel; Hurtado‐Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana; Bharti, Arvind K.; Donahoo, Ryan S.; Finley, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Storey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James; Affourtit, Jason P.; Han, Cliff; Chertkov, Olga; Lindquist, Erika; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

doi:10.1094/mpmi-02-12-0028-r

Cited by 239 publications

(218 citation statements)

References 56 publications

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“…Recent research indicates that mating type may be a poor characteristic for describing diversity in P. capsici and that spontaneous mating type changes (particularly A2 to A1 changes) can occur and may be associated with a genetic phenomenon known as loss of heterozygosity (LOH) (24). Three of the five isolates with mating types different from their group occurred within the context of identical MLGs and it is possible that the underlying mechanism is LOH (Fig.…”

Section: Discussionmentioning

confidence: 99%

Genetically Diverse Long-Lived Clonal Lineages ofPhytophthora capsicifrom Pepper in Gansu, China

Hu¹,

Pang²,

Bi³

et al. 2013

Phytopathology®

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Phytophthora capsici causes significant loss to pepper production in China, and our objective was to investigate the population structure in Gansu province. Between 2007 and 2011, 279 isolates were collected from pepper at 24 locations. Isolates (or subsets) were assessed for simple sequence repeat (SSR) genotype, metalaxyl resistance, mating type, and physiological race using cultivars from the World Vegetable Center (AVRDC) and New Mexico recombinant inbred lines (NMRILs). The A1 and A2 mating types were recovered from nine locations and metalaxyl-resistant isolates from three locations. A total of 104 isolates tested on the AVRDC panel resolved five physiological races. None of 42 isolates tested on the NMRIL panel caused visible infection. SSR genotyping of 127 isolates revealed 59 unique genotypes, with 42 present as singletons and 17 having 2 to 13 isolates. Isolates with identical genotypes were recovered from multiple sites across multiple years and, in many cases, had different race types or metalaxyl sensitivities. Isolates clustered into three groups with each group having almost exclusively the A1 or A2 mating type. Overall it appears long-lived genetically diverse clonal lineages are dispersed across Gansu, outcrossing is rare, and functionally important variation exists within a clonal framework.

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Section: Discussionmentioning

confidence: 99%

Genetically Diverse Long-Lived Clonal Lineages ofPhytophthora capsicifrom Pepper in Gansu, China

Hu¹,

Pang²,

Bi³

et al. 2013

Phytopathology®

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“…Changes in ploidy, gene conversion, and loss of heterozygosity are reported in several species (11,30,50). Unstable supernumerary chromosomes have also been described in Pythium (56).…”

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confidence: 97%

“…Assemblies annotated with gene models are now available publicly for nine plant pathogens, including six Phytophthora spp. (Phytophthora capsici, P. cinnamomi, P. infestans, Phytophthora parasitica, P. ramorum, and P. sojae), Pythium ultimum, H. arabidopsidis, and A. laibachii (6,31,45,50,51,86). Data are also released for one animal pathogen, S. parasitica, but not for an exclusively saprophytic species.…”

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confidence: 99%

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

Judelson

2012

Eukaryot Cell

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The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.

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“…EST mining resulted in the identification of various putative extracellular proteins (9). With the elucidation of various Phytophthora and other oomycete genomes, a wealth of information was retrieved from genome sequences by in silico gene annotation (4,5,(11)(12)(13)(14). Genome mining resulted in the identification of many novel genes and a large repertoire of potential virulence factors (4,5,15,16).…”

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confidence: 99%

Profiling the Secretome and Extracellular Proteome of the Potato Late Blight Pathogen Phytophthora infestans

Meijer

Mancuso

Espadas

et al. 2014

Molecular & Cellular Proteomics

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Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes, and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focused on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyze P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses, and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment. Molecular & Cellular

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Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

Cited by 239 publications

References 56 publications

Genetically Diverse Long-Lived Clonal Lineages ofPhytophthora capsicifrom Pepper in Gansu, China

Genetically Diverse Long-Lived Clonal Lineages ofPhytophthora capsicifrom Pepper in Gansu, China

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

Profiling the Secretome and Extracellular Proteome of the Potato Late Blight Pathogen Phytophthora infestans

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