Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

Thidiazuron-induced efficient biosynthesis of phenolic compounds in callus culture of Ipomoea turbinata Lagasca and Segura

International audienceIpomoea turbinata Lagasca and Segura (Purple Moonflower) belongs to the largest flowering genus Ipomoea in the Convolvulaceae family. Ipomoea turbinata has not been previously explored for its in vitro potential. This is the first study focused on thidiazuron-induced callus culture for efficient biosynthesis of commercially important phenolic compounds in this plant species. Among the two plant growth regulators tested on leaf, stem, and root explants, 5 mg L−1 thidiazuron (TDZ) induced the highest biomass accumulation (61.4 g L−1 fresh weight, 6.3 g L−1 dry weight) in leaf-derived callus cultures after 5 wk of culture. The highest total phenolic and flavonoid contents recorded were 9.04 mg g−1 and 1.16 mg g−1, respectively, in optimized callus cultures. High-performance liquid chromatography analysis indicated high levels of pharmacologically important anticancer compounds such as chlorogenic acid (13.48 mg g−1), arctigenin (11.67 mg g−1), quercetin (6.19 mg g−1), and kaempferol (5.48 mg g−1), along with other phenolic acids. Furthermore, the antioxidant activity was also evaluated, and leaf-derived callus culture displayed a maximum of 62.6% antioxidant potential. The induction of improved biomass accumulation in callus culture and the production of multipotent bioactive metabolites shows the potential of the multifunctional thidiazuron hormone as an efficient elicitation tool in callus culture of I. turbinata