De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

Baldé, Aladje; Neves, Dina; García-Breijo, Francisco J; Pais, Maria S; Cravador, A.

Publication

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

2017-09-06Journal article

dc.contributor.author	Baldé, Aladje
dc.contributor.author	Neves, Dina
dc.contributor.author	García-Breijo, Francisco J
dc.contributor.author	Pais, Maria S
dc.contributor.author	Cravador, A.
dc.date.accessioned	2017-10-10T09:14:49Z
dc.date.available	2017-10-10T09:14:49Z
dc.date.issued	2017-09-06
dc.date.updated	2017-10-01T03:52:09Z
dc.description.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. 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.	pt_PT
dc.description.version	info:eu-repo/semantics/publishedVersion	pt_PT
dc.identifier.citation	BMC Genomics. 2017 Sep 06;18(1):700	pt_PT
dc.identifier.doi	http://dx.doi.org/10.1186/s12864-017-4042-6	pt_PT
dc.identifier.other	AUT: ACR00659;
dc.identifier.uri	http://hdl.handle.net/10400.1/10085
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	BioMed Central	pt_PT
dc.relation	Production of active compounds against Phytophthora cinnamomi by Phlomis purpurea, Metabolite and transcript profiling
dc.rights.holder	The Author(s).
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	Phlomis purpurea	pt_PT
dc.subject	Cutin	pt_PT
dc.subject	Transcriptomics	pt_PT
dc.subject	Phytophthora cinnamomi	pt_PT
dc.subject	Resistance	pt_PT
dc.subject	Defence response	pt_PT
dc.subject	Time course challenge	pt_PT
dc.subject	Casparian strips	pt_PT
dc.title	De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	Production of active compounds against Phytophthora cinnamomi by Phlomis purpurea, Metabolite and transcript profiling
oaire.awardURI	info:eu-repo/grantAgreement/FCT/SFRH/SFRH%2FBD%2F66016%2F2009/PT
oaire.awardURI	info:eu-repo/grantAgreement/FCT/5876/UID%2FBIA%2F04325%2F2013/PT
oaire.awardURI	info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FAGR-CFL%2F100217%2F2008/PT
oaire.citation.issue	(1):700	pt_PT
oaire.citation.title	BMC Genomics	pt_PT
oaire.citation.volume	18	pt_PT
oaire.fundingStream	SFRH
oaire.fundingStream	5876
oaire.fundingStream	3599-PPCDT
person.familyName	Cravador
person.givenName	Alfredo
person.identifier.orcid	0000-0002-9831-9815
person.identifier.rid	K-7247-2012
person.identifier.scopus-author-id	6602537257
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
relation.isAuthorOfPublication	8c84a9e6-6b7f-4b50-93a2-152c85901722
relation.isAuthorOfPublication.latestForDiscovery	8c84a9e6-6b7f-4b50-93a2-152c85901722
relation.isProjectOfPublication	35092430-c060-4270-92f7-33ba132f8b49
relation.isProjectOfPublication	6d3f02ba-fdcb-47d4-9822-726bf3da94d9
relation.isProjectOfPublication	2b7be6c6-5360-47c6-892d-77a15b7896fd
relation.isProjectOfPublication.latestForDiscovery	2b7be6c6-5360-47c6-892d-77a15b7896fd