De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

Abstract

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.ResultsUsing 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4042-6) contains supplementary material, which is available to authorized users.

A Metabolome Analysis and the Immunity of Phlomis purpurea against Phytophthora cinnamomi

“…The integration of metabolome with transcriptome data is crucial for understanding plants’ molecular mechanisms underlying the Phlomis purpurea immunity against Phytophthora cinnamomi. Transcription factors such as WRKY, MYB, AP2, ERF, bZIP, bHLH, CYP, and NAC, known to be involved in the biosynthesis of secondary metabolites [ 30 , 31 ], were up-regulated in Phlomis purpurea upon a challenge with Phytophthora cinnamomi , and their role in the innate immunity of Phlomis purpurea has been previously reported [ 25 , 26 ]. A metabolome screening of Phlomis purpurea leaves and roots challenged with Phytophthora cinnamomi revealed a set of secondary metabolites that were differentially produced along the challenge time course.…”

“…The transcriptome analysis of Phlomis purpurea challenged with Phytophthora cinnamomi revealed the up- regulation of several transcripts related to the production of terpenoids, namely the monoterpenes, limonene, terpineol, myrcene, geraniol, and linalool, as well as of sesquiterpenes and their precursor germacrene. Their over-expression value decreased from 24 hpc [ 25 ] in a similar way to the metabolome profile of the terpenoids in leaves, opposite to the terpenoids profile in the roots. These data suggest their translocation from the leaves to the roots, from where they are released into the soil infested by P. cinnamomi, inhibiting its growth.…”

“…In order to understand the mechanisms underlying the ability of Phlomis purpurea to reduce disease spread, a transcriptome analysis of Phlomis purpurea challenged with Phytophthora cinnamomi has been produced and a set of genes and hormones acting in a concerted manner has been identified, accounting for both elicited and constitutive defense [ 25 , 26 ]. Among them, several transcriptional factors shown to regulate the secondary metabolite biosynthesis in plants under stress conditions have been identified by other authors [ 25 , 26 ]. In addition, terpenoids and polyketides, as well as other secondary metabolites, lipids, and carbohydrate metabolism were among the top six pathways more represented by the unigenes annotated [ 25 ].…”

“…Among them, several transcriptional factors shown to regulate the secondary metabolite biosynthesis in plants under stress conditions have been identified by other authors [ 25 , 26 ]. In addition, terpenoids and polyketides, as well as other secondary metabolites, lipids, and carbohydrate metabolism were among the top six pathways more represented by the unigenes annotated [ 25 ]. Altogether, these results raised the expectations of discovering the putative metabolites overproduced as a response to the stress imposed by a pathogen.…”

“…The receptors involved in pathogen recognition and the resistance proteins detecting the pathogen effectors, as well as the defense-related genes transcriptionally activated by downstream signaling, have been disclosed [ 25 , 26 , 27 ]. However, the contribution of secondary metabolites to plant immunity has been less studied.…”