Transcriptomic Analysis of Olea europaea L. Roots during the Verticillium dahliae Early Infection Process

Abstract

Olive cultivation is affected by a wide range of biotic constraints. Verticillium wilt of olive is one of the most devastating diseases affecting this woody crop, inflicting major economic losses in many areas, particularly within the Mediterranean Basin. Little is known about gene-expression changes during plant infection by Verticillium dahliae of woody plants such as olive. A complete RNA-seq transcriptomic analysis of olive tree roots was made. Trinity assembler proved to be the best option to assemble the olive and V. dahliae transcriptomes. The olive transcriptome (Oleup) consisted of 68,259 unigenes (254,252 isoforms/transcripts), and the V. dahliae transcriptome (Vedah) consisted of 37,425 unigenes (52,119 isoforms/transcripts). Most unigenes of the Oleup transcriptome corresponded to cellular processes (12,339), metabolic processes (10,974), single-organism processes (7263), and responses to stimuli (5114). As for the Vedah transcriptome, most unigenes correspond to metabolic processes (25,372), cellular processes (23,718), localization (6385), and biological regulation (4801). Differential gene-expression analysis of both transcriptomes was made at 2 and 7 d post-infection. The induced genes of both organisms during the plant-pathogen interaction were clustered in six subclusters, depending on the expression patterns during the infection. Subclusters A to C correspond to plant genes, and subcluster D to F correspond to V. dahliae genes. A relevant finding was that the differentially expressed gene (DEGs) included in subclusters B and C were highly enriched in proteolysis as well as protein-folding and biosynthesis genes. In addition, a reactive oxygen species (ROS) defense was induced first in the pathogen and later in the plant roots. Core Ideas• A transcriptomic RNA-seq analysis was conducted to study the olive-V. dahliae interaction.• The transcriptomes of olive roots and V. dahliae were compiled at an early stage of infection.• A number of putative genes involved in the plant defense were found.• Most of the induced genes in response to the infection are related to protein turnover.• An ROS stress-defense response is induced first in the pathogen and later in the plant.

Tolerance of olive (Olea europaea) cv Frantoio to Verticillium dahliae relies on both basal and pathogen‐induced differential transcriptomic responses

“…The starting culture and the working inoculum (conidia suspension) of isolate V937I used in the bioassay (see later) were prepared as described by Jiménez‐Ruiz et al . ().…”

“…Plants were randomly distributed and maintained in a growth chamber adjusted to 24 : 21°C, day : night, 60% relative humidity, 14 h photoperiod of fluorescent light (360 μE m −2 s −1 ) during 15 d (for RNA sampling) or 2 months (for VWO symptoms observation). To ease plant stress after manipulation, inoculation and transplanting, the photoperiod was increased gradually (Gómez‐Lama Cabanás et al ., ; Jiménez‐Ruiz et al ., ). Roots of each ‘Frantoio’ plant were harvested at 0, 2 and 7 d (three plants per time point) after V937I inoculation (DAI).…”

“…Gene expression was carried out with RNA‐Seq by Arraystar Lasergene 13, using a 95% false discovery rate (FDR). The reference transcriptome was obtained from the Olea europaea L. cv Picual (Jiménez‐Ruiz et al ., ) to which 17 205 newly assembled unigenes from cv Frantoio that were absent in the cv Picual transcriptome were incorporated to generate the final ‘PicFra’ transcriptome consisting of 82 159 unigenes. Assembly and functional annotation of the cv Frantoio unigenes were performed following the same method as that for the ‘Picual’ transcriptome (Jiménez‐Ruiz et al ., ).…”

“…Recently, an RNA‐seq transcriptomic analysis of olive (cv ‘Picual’, highly susceptible to VWO) roots during the early interaction with V. dahliae (D pathotype) was conducted. An olive transcriptome (‘Oleup’) was thus obtained consisting of 68 259 unigenes (254 252 isoforms/transcripts) (Jiménez‐Ruiz et al ., ).…”

Not just BLAST nt: WGS database joins the party

“…We used the resulting Centrifuge database to analyze several samples from a transcriptomic study of the evolution of Verticillium wilt of olive (Jimenez-Ruiz et al 2017). Figure 2 shows a comparison of results with the nt versus nt+WGS databases for the sample corresponding to olive tree roots 15 days after Verticilium dahliae inoculation.…”