Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle.

David Gramaje,Livio Antonielli,Carmen Berlanas,Monika Schmoll,Sabrina Beier,María del Pilar Martínez-Diz,Emilia Diaz-Losada,Stéphane Compant,Markus Gorfer

doi:10.3390/jof6040255

Abstract

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusarium fujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.

Highlights

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe [1,2,3], one of the most important destructive diseases in grapevine (Vitis vinifera L.), which has a devastating effect on grapevine production worldwide [4]
The Bayesian Information Criterion (BIC) best-fit nucleotide substitution model identified by jModelTest was Hasegawa-Kishino-Yano model (HKY) with gamma distributed with invariant sites rates (G + I) for the Dactylonectria analysis
Recent studies have suggested that black-foot fungi have a non-pathogenic endophytic phase [12,13] and may become pathogenic to grapevine after different abiotic and/or biotic stresses conditions and they are considered as latent pathogens in grapevine

Summary

Introduction

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe [1,2,3], one of the most important destructive diseases in grapevine (Vitis vinifera L.), which has a devastating effect on grapevine production worldwide [4]. It is well known that D. torresensis is common in the soil and causes infection of grafted vines after some months of growth in nursery soils and in young vineyards, especially during the first five years after planting [1,2]. Young vines affected by D. torresensis generally appear normal at planting but differences in vigour become marked with reduced trunk growth, shortened internodes, and reduced foliage/canopy. Foliar symptoms may appear as small leaves with interveinal chlorosis, followed by necrosis and early defoliation [5]. Removal of the rootstock bark of declining plants reveals further black discolouration and necrosis of wood tissues that develop from the base of the rootstock. Symptoms include reduced total root biomass, low numbers of feeder roots, and black, sunken and necrotic root lesions [4]

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