De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi
Identifieur interne : 000410 ( Main/Exploration ); précédent : 000409; suivant : 000411De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi
Auteurs : Aladje Baldé [Portugal, Guinée-Bissau] ; Dina Neves [Portugal] ; Francisco J. García-Breijo [Espagne] ; Maria Salomé Pais [Portugal] ; Alfredo Cravador [Portugal]Source :
- BMC Genomics [ 1471-2164 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phlomis.
- microbiologie : Phlomis.
- physiologie : Phytophthora.
- Analyse de profil d'expression de gènes, Annotation de séquence moléculaire, Gene Ontology, Génomique.
English descriptors
- KwdEn :
- MESH :
- genetics : Phlomis.
- microbiology : Phlomis.
- physiology : Phytophthora.
- Gene Expression Profiling, Gene Ontology, Genomics, Molecular Sequence Annotation.
Abstract
Using Illumina technology we obtained a de novo assembly of
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
The de novo assembly of transcriptome using short reads for a non-model plant,
The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from
The online version of this article (doi:10.1186/s12864-017-4042-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-017-4042-6
PubMed: 28877668
PubMed Central: 5585901
Affiliations:
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Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">De novo assembly of <italic>Phlomis purpurea</italic>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2017">2017</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Profiling (MeSH)</term>
<term>Gene Ontology (MeSH)</term>
<term>Genomics (MeSH)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Phlomis (genetics)</term>
<term>Phlomis (microbiology)</term>
<term>Phytophthora (physiology)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Gene Ontology (MeSH)</term>
<term>Génomique (MeSH)</term>
<term>Phlomis (génétique)</term>
<term>Phlomis (microbiologie)</term>
<term>Phytophthora (physiologie)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phlomis</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phlomis</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Phlomis</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Phlomis</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Phytophthora</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Phytophthora</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term>
<term>Gene Ontology</term>
<term>Genomics</term>
<term>Molecular Sequence Annotation</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p id="Par1"><italic>Phlomis</italic>
plants are a source of biological active substances with potential applications in the control of phytopathogens. <italic>Phlomis purpurea</italic>
(Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to <italic>Phytophthora cinnamomi. Phlomis purpurea</italic>
has revealed antagonistic effect in the rhizosphere of <italic>Quercus suber</italic>
and <italic>Q. ilex</italic>
against <italic>P. cinnamomi</italic>
. <italic>Phlomis purpurea</italic>
roots produce bioactive compounds exhibiting antitumor and anti-<italic>Phytophthora</italic>
activities with potential to protect susceptible plants. Although these important capacities of <italic>P. purpurea</italic>
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.</p>
</sec>
<sec><title>Results</title>
<p id="Par2">Using Illumina technology we obtained a de novo assembly of <italic>P. purpurea</italic>
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<italic>.</italic>
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.</p>
<p id="Par3">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.</p>
<p id="Par4">Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times.</p>
<p id="Par5">Comparative cyto-histological studies of <italic>P. purpurea</italic>
roots challenged with <italic>P. cinnamomi</italic>
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.</p>
</sec>
<sec><title>Conclusions</title>
<p id="Par6">The de novo assembly of transcriptome using short reads for a non-model plant, <italic>P. purpurea</italic>
, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies.</p>
<p id="Par7">The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from <italic>P. purpurea</italic>
when challenged with the pathogen<italic>.</italic>
This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with <italic>P. cinnamomi</italic>
.</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-017-4042-6) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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