title: De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms.
abstract: BACKGROUND
  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.
authors.affiliation: Present Address: BIOEPAR, INRA, Oniris, La Chantrerie, F-44307, Nantes, France. claude.rispe@oniris-nantes.fr.|IGEPP, INRA, F-35653, Le Rheu cedex, France. claude.rispe@oniris-nantes.fr.
authors.forename: Claude
authors.initials: C
authors.lastname: Rispe
authors.affiliation: IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.|Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Legeai
authors.affiliation: SAVE, INRA, F-33883, Villenave d'Ornon, France.
authors.forename: Daciana
authors.initials: D
authors.lastname: Papura
authors.affiliation: IGEPP, BIPAA, INRA, Campus Beaulieu, Rennes, France.|Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genouest, Campus Beaulieu, Rennes, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Bretaudeau
authors.affiliation: IGEPP, INRA, F-35653, Le Rheu cedex, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Hudaverdian
authors.affiliation: IGEPP, INRA, F-35653, Le Rheu cedex, France.
authors.forename: Gaël
authors.initials: G
authors.lastname: Le Trionnaire
authors.affiliation: IGEPP, INRA, F-35653, Le Rheu cedex, France.
authors.forename: Denis
authors.initials: D
authors.lastname: Tagu
authors.affiliation: IGEPP, INRA, F-35653, Le Rheu cedex, France.|Present address: University of Rennes 1, UMR CNRS 6553 EcoBio, 35042, Rennes, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Jaquiéry
authors.affiliation: SAVE, INRA, F-33883, Villenave d'Ornon, France.
authors.forename: François
authors.initials: F
authors.lastname: Delmotte
mesh_terms: D000818:Animals; D020451:Contig Mapping; D005247:Feeding Behavior; D005260:Female; D017344:Genes, Insect; D007313:Insecta / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family; D052287:Oviparity; D010802:Phylogeny; D059467:Transcriptome; D027843:Vitis
keywords: Aphid; Daktulosphaira vitifoliae; Gallicole; Gene duplication; Oviparity; Polyphenism; Radicicole; Vitis