RNA‐Seq reveals infection‐related global gene changes in <i>Phytophthora phaseoli</i>, the causal agent of lima bean downy mildew

Kunjeti, Sridhara G.; Evans, T. A.; Marsh, Adam G.; Gregory, Nancy; Kunjeti, Saritha; Kalavacharla, Venugopal; Donofrio, Nicole

doi:10.1111/j.1364-3703.2011.00761.x

Cited by 40 publications

(34 citation statements)

References 41 publications

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“…We tested whether they could individually induce necrosis in N. benthamiana using infiltration of A. tumefaciens cells with pGR107 carrying each of the genes. These methods have been widely used for transient expression of genes in N. benthamiana and for determining whether particular genes can induce or suppress cell death [18], [32], [34], [37], [59], [66]–[68]. The known elicitor of cell death, P. infestans INF1 , was used as a positive control.…”

Section: Resultsmentioning

confidence: 99%

RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

Chen

Xing

et al. 2013

PLoS ONE

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Phytophthora capsici is a soilborne plant pathogen capable of infecting a wide range of plants, including many solanaceous crops. However, genetic resistance and fungicides often fail to manage P. capsici due to limited knowledge on the molecular biology and basis of P. capsici pathogenicity. To begin to rectify this situation, Illumina RNA-Seq was used to perform massively parallel sequencing of three cDNA samples derived from P. capsici mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). Over 11 million reads were generated for each cDNA library analyzed. After read mapping to the gene models of P. capsici reference genome, 13,901, 14,633 and 14,695 putative genes were identified from the reads of the MY, ZO and GC libraries, respectively. Comparative analysis between two of samples showed major differences between the expressed gene content of MY, ZO and GC stages. A large number of genes associated with specific stages and pathogenicity were identified, including 98 predicted effector genes. The transcriptional levels of 19 effector genes during the developmental and host infection stages of P. capsici were validated by RT-PCR. Ectopic expression in Nicotiana benthamiana showed that P. capsici RXLR and Crinkler effectors can suppress host cell death triggered by diverse elicitors including P. capsici elicitin and NLP effectors. This study provides a first look at the transcriptome and effector arsenal of P. capsici during the important pre-infection stages.

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Section: Resultsmentioning

confidence: 99%

RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

Chen

Xing

et al. 2013

PLoS ONE

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“…Recently, the term "dual RNA-seq" was coined to refer to the use of RNA-seq in transcriptomic analyses in which gene expression changes in both the pathogen and the host are analyzed simultaneously (Westermann et al, 2012). Whereas numerous studies have focused on either the pathogen or the host (Xu et al, 2011;Kunjeti et al, 2012;Petre et al, 2012;Weßling et al, 2012;Garnica et al, 2013;Link et al, 2014), only a few have involved the comprehensive analysis of both organisms (Kawahara et al, 2012;Tierney et al, 2012;Fernandez et al, 2012;Lowe et al, 2014;Yamagishi et al, 2014). Here, we present an in-depth transcriptomic analysis of the M. perniciosa-cacao interaction, which vastly expands our current knowledge of WBD and also contributes to our general understanding of plant-pathogen interactions.…”

Section: Discussionmentioning

confidence: 99%

High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa

et al. 2014

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Witches' broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.

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“…In P. infestans, mRNA levels for nearly one-half of genes change Ͼ2-fold during life stage changes, with about 14% being expressed exclusively in one stage or another (35). Studies in P. infestans, the lima bean pathogen Phytophthora phaseoli, and the cucumber downy mildew agent Pseudoperonospora cubensis also documented changes during different stages of growth (31,49). the major orders based on 28S rRNA sequences.…”

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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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RNA‐Seq reveals infection‐related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew

Cited by 40 publications

References 41 publications

RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

RNA-Seq Reveals Infection-Related Gene Expression Changes in Phytophthora capsici

High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa

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

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