Dataset Information

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.

ABSTRACT: Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction.

SUBMITTER: Meyer FE

PROVIDER: S-EPMC4773608 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.

Meyer Febé E FE Shuey Louise S LS Naidoo Sitha S Mamni Thandekile T Berger Dave K DK Myburg Alexander A AA van den Berg Noëlani N Naidoo Sanushka S

Frontiers in plant science 20160302

Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nite ...[more]

PMID: 26973660

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Project description:Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5000 species of plants, including many of importance in agriculture, forestry and horticulture. The inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognized Global Biodiversity Hotspots, has had disastrous consequences for the environment and the biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores. Disease control is difficult in agricultural and forestry situations and even more challenging in natural ecosystems as a result of the scale of the problem and the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires a comprehensive understanding of the cellular and molecular basis of pathogen development and pathogenicity. The application of next-generation sequencing technologies to generate genomic and transcriptomic data promises to underpin a new era in P. cinnamomi research and discovery. The aim of this review is to integrate bioinformatic analyses of P. cinnamomi sequence data with current knowledge of the cellular and molecular basis of P. cinnamomi growth, development and plant infection. The goal is to provide a framework for future research by highlighting potential pathogenicity genes, shedding light on their possible functions and identifying suitable targets for future control measures.TaxonomyPhytophthora cinnamomi Rands; Kingdom Chromista; Phylum Oomycota or Pseudofungi; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; genus Phytophthora.Host rangeInfects about 5000 species of plants, including 4000 Australian native species. Host plants important for agriculture and forestry include avocado, chestnut, macadamia, oak, peach and pineapple.Disease symptomsA root pathogen which causes rotting of fine and fibrous roots, but which can also cause stem cankers. Root damage may inhibit water movement from roots to shoots, leading to dieback of young shoots. USEFUL WEBSITES: http://fungidb.org/fungidb/; http://genome.jgi.doe.gov/Phyci1/Phyci1.home.html; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314365.1; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314505.1.

Project description:Genomic selection (GS) is being increasingly adopted by the tree breeding community. Most of the GS studies in trees are focused on estimating additive genetic effects. Exploiting the dominance effects offers additional opportunities to improve genetic gain. To detect dominance effects, trait-relevant markers may be important compared to nonselected markers. Here, we used preselected markers to study the dominance effects in a Eucalyptus nitens (E. nitens) breeding population consisting of open-pollinated (OP) and controlled-pollinated (CP) families. We used 8221 trees from six progeny trials in this study. Of these, 868 progeny and 255 parents were genotyped with the E. nitens marker panel. Three traits; diameter at breast height (DBH), wood basic density (DEN), and kraft pulp yield (KPY) were analyzed. Two types of genomic relationship matrices based on identity-by-state (IBS) and identity-by-descent (IBD) were tested. Performance of the genomic best linear unbiased prediction (GBLUP) models with IBS and IBD matrices were compared with pedigree-based additive best linear unbiased prediction (ABLUP) models with and without the pedigree reconstruction. Similarly, the performance of the single-step GBLUP (ssGBLUP) with IBS and IBD matrices were compared with ABLUP models using all 8221 trees. Significant dominance effects were observed with the GBLUP-AD model for DBH. The predictive ability of DBH is higher with the GBLUP-AD model compared to other models. Similarly, the prediction accuracy of genotypic values is higher with GBLUP-AD compared to the GBLUP-A model. Among the two GBLUP models (IBS and IBD), no differences were observed in predictive abilities and prediction accuracies. While the estimates of predictive ability with additive effects were similar among all four models, prediction accuracies of ABLUP were lower than the GBLUP models. The prediction accuracy of ssGBLUP-IBD is higher than the other three models while the theoretical accuracy of ssGBLUP-IBS is consistently higher than the other three models across all three groups tested (parents, genotyped, and nongenotyped). Significant inbreeding depression was observed for DBH and KPY. While there is a linear relationship between inbreeding and DBH, the relationship between inbreeding and KPY is nonlinear and quadratic. These results indicate that the inbreeding depression of DBH is mainly due to directional dominance while in KPY it may be due to epistasis. Inbreeding depression may be the main source of the observed dominance effects in DBH. The significant dominance effect observed for DBH may be used to select complementary parents to improve the genetic merit of the progeny in E. nitens.

Dataset Information

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.

Publications

Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility.

Similar Datasets

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