RNA-Seq profile of flavescence dorée phytoplasma in grapevine

Autor: Sébastien Carrère, Massimo Delledonne, Luciana Galetto, Cristina Marzachì, F. Veratti, Simona Abbà, Xavier Foissac, Sabrina Palmano, Patricia Carle
Přispěvatelé: Istituto per la Protezione delle Piante (IPP), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Dipartimento di Biotecnologie, University of Verona (UNIVR), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)
Jazyk: angličtina
Rok vydání: 2014
Předmět:
Zdroj: BMC Genomics 1 (15), 1-13. (2014)
BMC Genomics
BMC Genomics, BioMed Central, 2014, 15 (1), pp.1-13. ⟨10.1186/1471-2164-15-1088⟩
BMC genomics 15 (2014): 1088. doi:10.1186/1471-2164-15-1088
info:cnr-pdr/source/autori:Abbà S., Galetto L., Carle P., Carrère S., Delledonne M., Foissac X., Palmano S., Veratti F., Marzachì C./titolo:RNA-Seq profile of flavescence doree phytoplasma in grapevine/doi:10.1186%2F1471-2164-15-1088/rivista:BMC genomics/anno:2014/pagina_da:1088/pagina_a:/intervallo_pagine:1088/volume:15
ISSN: 1471-2164
Popis: The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insecticides. Further studies of the pathogen, the vector and the mechanisms of phytoplasma-host interactions could improve our understanding of the disease. In this work, RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting field-grown Vitis vinifera leaves.
With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 215 annotated genes, and identified 10 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 draft genome. Furthermore, we improved the annotation of 44 genes with the addition of 5'/3' untranslated regions. Functional classification revealed that the most expressed genes were either related to translation and protein biosynthesis or hypothetical proteins with unknown function. Some of these hypothetical proteins were predicted to be secreted, so they could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies.
The RNA-Seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine infection. Our results provided new insights into the transcriptional organization and gene structure of FD. This may represent the starting point for the application of high-throughput sequencing technologies to study differential expression in FD and in other phytoplasmas with an unprecedented resolution.
Databáze: OpenAIRE
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