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De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms

hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorRISPE, Claude
hal.structure.identifierScalable, Optimized and Parallel Algorithms for Genomics [GenScale]
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorLEGEAI, Fabrice
hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorPAPURA, Daciana
hal.structure.identifierService Expérimentation et Développement [SED [Rennes]]
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorBRETAUDEAU, Anthony
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorHUDAVERDIAN, Sylvie
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorLE TRIONNAIRE, Gaël
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorTAGU, Denis
hal.structure.identifierEcosystèmes, biodiversité, évolution [Rennes] [ECOBIO]
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorJAQUIÉRY, Julie
hal.structure.identifierSanté et agroécologie du vignoble [UMR SAVE]
dc.contributor.authorDELMOTTE, François
dc.date.accessioned2024-04-08T12:36:10Z
dc.date.available2024-04-08T12:36:10Z
dc.date.issued2016-12
dc.identifier.issn1471-2164
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197362
dc.description.abstractEnBackground - Grapevine phylloxera, an insect related to true aphids, is a major historic pest of viticulture only controlled through the selection of resistant rootstocks or through quarantine regulations where grapevine is cultivated own-rooted. Transcriptomic data could help understand the bases of its original life-traits, including a striking case of polyphenism, with forms feeding on roots and forms feeding in leaf-galls. Comparisons with true aphids (for which complete genomes have been sequenced) should also allow to link differences in life-traits of the two groups with changes in gene repertoires or shifts in patterns of expression. Results - We sequenced transcriptomes of the grapevine phylloxera (Illumina technology), choosing three life-stages (adults on roots or on leaf galls, and eggs) to cover a large catalogue of transcripts, and performed a de novo assembly. This resulted in 105,697 contigs, which were annotated: most contigs had a best blastx hit to the pea aphid (phylogenetically closest complete genome), while very few bacterial hits were recorded (except for Probionibacterium acnes). Coding sequences were predicted from this data set (17,372 sequences), revealing an extremely high AT-bias (at the third codon position). Differential expression (DE) analysis among root-feeding and gall-feeding showed that i) the root-feeding form displayed a much larger number of differentially expressed transcripts ii) root-feeding biased genes were enriched in some categories, for example cuticular proteins and genes associated with cell-cell signaling iii) leaf-galling-biased genes were enriched in genes associated with the nucleus and DNA-replication, suggesting a metabolism more oriented towards fast and active multiplication. We also identified a gene family with a very high expression level (copies totaling nearly 10% of the reads) in the grapevine phylloxera (both in root and leaf galling forms), but usually expressed at very low levels in true aphids (except in sexual oviparous females). These transcripts thus appear to be associated with oviparity. Conclusions - Our study illustrated major intraspecific changes in transcriptome profiles, related with different life-styles (and the feeding on roots versus in leaf-galls). At a different scale, we could also illustrate one major shift in expression levels associated with changes in life-traits that occurred along evolution and that respectively characterize (strictly oviparous) grapevine phylloxera and (mostly viviparous) true aphids.
dc.language.isoen
dc.publisherBioMed Central
dc.subject.enRadicicole
dc.subject.enGallicole
dc.subject.enOviparity
dc.subject.enGene duplication
dc.subject.enPolyphenism
dc.subject.enVitis
dc.subject.enAphid
dc.subject.enDaktulosphaira vitifoliae
dc.title.enDe novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms
dc.typeArticle de revue
dc.identifier.doi10.1186/s12864-016-2530-8
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalBMC Genomics
bordeaux.page219
bordeaux.volume17
bordeaux.hal.laboratoriesSanté et Agro-Ecologie du Vignoble (SAVE) - UMR 1065*
bordeaux.issue1
bordeaux.institutionBordeaux Sciences Agro
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-01286528
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01286528v1
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