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

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. Olive (Olea europaea L.) was one of the first tree species to be domesticated and cultivated. Wild and cultivated olives are diploid (2n = 46) and have a genome size of approximately 1800 Mb (De la Rosa et al., 2003). Today, olive cultivation has spread worldwide and has far-reaching economic, social, and ecological implications within the Mediterranean Basin. In fact, according to International Olive Oil Council data (http://www. Published in Plant Genome Volume 10. doi: 10.3835/plantgenome2016.07.0060 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). J. Jiménez-Ruiz, M.O. Leyva-Pérez, J.B. Barroso, and F. Luque, Center for Advanced Studies in Olive Grove and Olive Oils, Dep. of Experimental Biology, Univ. Jaén, 23071-Jaén, Spain; E. Schilirò and J. Mercado-Blanco, Dep. de Protección de Cultivos, Institute for Sustainable Agriculture (CSIC), 14004-Córdoba, Spain; A. Bombarely, Virginia Polytechnic Institute and State Univ., Blacksburg, VA, 24061; L. Mueller, Boyce Thompson Institute for Plant Research, Ithaca, NY 14853-1801. Received 6 July 2016. Accepted 13 Nov. 2016. *Corresponding author ([email protected]). Assigned to Associate Editor Stephen Moose. Abbreviations: D, defoliating; DEG, differentially expressed gene; GO, Gene Ontology; NGS, next-generation sequencing; qPCR, quantitative polymerase chain reaction; ROS, reactive oxygen species; SNP, single-nucleotide polymorphism; SOD, superoxide dismutase; VWO, verticillium wilt of olive. 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. Published February 9, 2017