De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi
Autor: | Francisco J. García-Breijo, Aladje Baldé, Maria Salomé Pais, Alfredo Cravador, Dina Neves |
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Jazyk: | angličtina |
Rok vydání: | 2017 |
Předmět: |
0301 basic medicine
Defence response Phytophthora lcsh:QH426-470 lcsh:Biotechnology BOTANICA Resistance Sequence assembly Phytophthora cinnamomi Cutin Transcriptome 03 medical and health sciences Phlomis lcsh:TP248.13-248.65 Botany Genetics Time course challenge Casparian strips Phlomis purpurea Transcriptomics 2. Zero hunger Oomycete biology cDNA library Gene Expression Profiling Molecular Sequence Annotation Genomics 15. Life on land biology.organism_classification lcsh:Genetics 030104 developmental biology Gene Ontology DNA microarray Functional genomics Biotechnology Research Article |
Zdroj: | BMC Genomics RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia instname Repositório Científico de Acesso Aberto de Portugal Repositório Científico de Acesso Aberto de Portugal (RCAAP) instacron:RCAAP BMC Genomics, Vol 18, Iss 1, Pp 1-17 (2017) |
ISSN: | 1471-2164 |
Popis: | [EN] Background: Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity. Results: Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated. Conclusions: The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi. This work was supported by the project PTDC/AGR-CFL/100217/2008 and the grant SFRH/BD/66016/2009, both funded by Fundacao para a Ciencia e Tecnologia (FCT). The APC charge was supported by the project UID/BIA/04325/2013 - MEDTBIO (FCT). The COST Office and the European Council provided financial support to the Short Term Scientific Mission (COST-STSM-FP0801-10084). |
Databáze: | OpenAIRE |
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