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

Susceptibility of grapevine tissues to Neofusicoccum luteum conidial infection

This study investigated the ability of Neofusicoccum luteum to infect wounded shoots, trunks, pruned cane ends, leaf surfaces, buds, berries and roots, and its further progression into stem tissues. All tissue types were susceptible to infection except roots, with highest incidences in trunks (100%), cane ends (100%), shoots (92%) and buds (88%), indicating that in New Zealand, N. luteum is primarily a trunk and shoot pathogen. In trunks, there were no external symptoms, although N. luteum could be reisolated from 60 to 70 cm acropetally from the inoculation site after 4 months, by which time the pathogen had progressed into side shoots which became necrotic. Wounded and non-wounded buds became infected; most were killed, with basipetal progression of the pathogen into the supporting shoots. Berries wounded and inoculated at the pre-bunch closure stage were susceptible to N. luteum infection, with isolation incidence increasing over the season and peaking at harvest, when infected berries became mummified and produced pycnidia with many conidia. The pathogen was also able to progress from berries into bunch stems and supporting canes. Results from this research have indicated that N. luteum infection can occur in all aerial grapevine tissues and progress to young stem tissues where it causes wood necrosis. Growers should remove mummified berries from vineyard trash to ensure that pruning and trimming times do not coincide with rainy periods when conidia are released and dispersed. Furthermore, the susceptibility of buds to N. luteum infection indicates the need for fungicide sprays before budburst in spring

Factors affecting Neofusicoccum luteum infection and disease progression in grapevines

© 2014, Australasian Plant Pathology Society Inc.This study investigated some factors that affect Neofusicoccum luteum infection and disease progression in grapevines, on which it causes cankers and die-back. Inoculation of green shoots with each of the conidial suspensions (20 μL of 10²–10⁶ conidia/mL) caused 100 % infection, but significant differences in lesion lengths among concentrations (P < 0.001). Lesion lengths increased with conidial concentrations to a maximum of 41.7 mm, in tissue inoculated with 10⁴/conidial. Lesions then decreased for 10⁵ and 10⁶ conidial/mL (28.6 and 27.8 mm, respectively). The different wetness durations (0–24 h) tested after inoculating trunks of 1-year old vines with conidia did not affect pathogen incidence or lesion lengths, however continued incubation at 95 % RH caused greater pathogen progression (maximum isolation distances from point of inoculation; P < 0.001; 100.6 mm) than at ambient 78 % RH (77.0 mm) within 3 months after inoculation. Inoculation of trunks, canes and green shoots caused different rates of pathogen colonisation (P < 0.001); by 5 months after N. luteum inoculation mean maximum distances were 39.1, 31.6 and 23.2 mm, respectively. Wound age at the time of inoculation significantly affected (P < 0.001) infection incidence by N. luteum, which decreased as wounds aged. Conidial inoculum caused 100-0 % incidence over 0–14 days and mycelial inoculum caused 100-40 % infection over 0–30 days. Soil moistures affected lesion development, with 15 and 100 % soil moisture causing greatest dieback and bud death during winter. This study has shown how some features of the natural infection environment can affect infection by Botryosphaeria spp. inoculum and symptom development, which could underpin improvements in vineyard management

Dispersal of conidia of Fusicladium eriobotryae and spatial patterns of scab in loquat orchards in Spain.

Dispersal of conidia of Fusicladium eriobotryae, the causal agent of loquat scab, was investigated in two loquat orchards in Spain from 2010 to 2012. A volumetric spore sampler, horizontally and vertically orientated microscope slides, and rain collectors were placed in loquat fields to trap conidia of F. eriobotryae. No conidia were collected in the volumetric sampler, and highly variable numbers of conidia were collected in the rain gatherers. Large numbers of conidia were collected by microscope slides, particularly by those held in a horizontal orientation compared with those held in a vertical orientation. Approximately 90%of the F. eriobotryae conidia were collected during rainy periods. Based on ROC and Bayesian analysis, using 65 0.2 mm rainfall as a cut-off value resulted in a high probability of correctly predicting actual conidial dispersal, and had a low probability of failing to predict actual conidial dispersal. Based on the index of dispersion and the binary power law, the incidence of loquat scab on fruit was highly aggregated in space between and within trees, and aggregation was influenced by disease incidence. Our results demonstrate, for the first time, that F. eriobotryae is dispersed mainly in rain splash. The results will be integrated into a mechanistic, weather-driven, disease prediction model that should help growers to minimize fungicide application for the management of loquat scab