Metatranscriptomic approach to characterize the microbiome and identify molecular markers for early detection of ?Hoja de malvón? disease in Vitis vinifera cv. Malbec.

CESARI CECILIA; GARCÍA LAMPASONA SANDRA; PAOLINELLI MARCOS; HERNÁNDEZ-MARTÍNEZ RUFINA; ESCORIAZA GEORGINA; SEBASTIÁN GOMEZ TALQUENCA

Penticton

Workshop; 11TH INTERNATIONAL WORKSHOP ON GRAPEVINE TRUNK DISEASES; 2019

Argentinian viticulture is markedly affected by the grapevine trunk disease ?Hoja de malvón?. Similar to Esca disease, Phaeoacremonium spp., Phaeomoniella chlamydospora and Botryosphaeriaceae are the pioneer fungi, but in a secondary stage of the disease become involved the Basidiomycota Arambarria sp. (formerly, Inocutis jamaicensis). Currently, detection of the pathogens is done through culture-dependent techniques since molecular culture-independent methods are poorly developed. The objective of this work was to design a metatranscriptomic approach for the simultaneous exploration of the microbiome and the host gene expression, with the aim to identify molecular markers that help with the early detection and the monitoring of the disease progression in vineyards. Twenty-three years old own-rooted Vitis vinifera cv. Malbec plants were selected to obtain a pool of wood chips from the trunk and arms from either symptomatic or asymptomatic plants. Total RNA was extracted and processed for RNAseq using Illumina HiSeq4000. The metatranscriptome renders an average of 37 million 100 bp PE reads per sample. Around 81% of reads were mapped on the genome of Vitis vinifera cv. Pinot Noir and used for gene expression analysis. The remaining unmapped reads were used for microbiome characterization through two bioinformatics strategies: 1) rRNA reads assembly and taxonomic assignment using SILVASSU and RDP_ITS database 2) Taxonomic assignment and relative quantification based on uniquely kmer mapping of reads on microbial genome database. Culture-based and culture-independent methods coincide in the detection of the most abundant species (i.e., Alternaria sp.), but culture-independent and kmer-based technique detect a vast diversity of microorganisms never identified before using culture-based strategies. Based on the differential abundance of disease-associated pathogens, host functional enrichment on differential expressed genes was evaluated. Results indicate that polyamines genes are candidates for molecular markers of the disease.