Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola.

Yazmín Rivera,Catalina Salgado-Salazar,Martha Malapi-Wight,Jo Anne Crouch,Daniel Veltri

doi:10.7717/peerj.5401

Abstract

Boxwood (Buxus spp.) are broad-leaved, evergreen landscape plants valued for their longevity and ornamental qualities. Volutella leaf and stem blight, caused by the ascomycete fungi Pseudonectria foliicola and P. buxi, is one of the major diseases affecting the health and ornamental qualities of boxwood. Although this disease is less severe than boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae, its widespread occurrence and disfiguring symptoms have caused substantial economic losses to the ornamental industry. In this study, we sequenced the genome of P. foliicola isolate ATCC13545 using Illumina technology and compared it to other publicly available fungal pathogen genomes to better understand the biology of this organism. A de novo assembly estimated the genome size of P. foliicola at 28.7 Mb (425 contigs; N50 = 184,987 bp; avg. coverage 188×), with just 9,272 protein-coding genes. To our knowledge, P. foliicola has the smallest known genome within the Nectriaceae. Consistent with the small size of the genome, the secretome, CAzyme and secondary metabolite profiles of this fungus are reduced relative to two other surveyed Nectriaceae fungal genomes: Dactylonectria macrodidyma JAC15-245 and Fusarium graminearum Ph-1. Interestingly, a large cohort of genes associated with reduced virulence and loss of pathogenicity was identified from the P. foliicola dataset. These data are consistent with the latest observations by plant pathologists that P. buxi and most likely P. foliicola, are opportunistic, latent pathogens that prey upon weak and stressed boxwood plants.

Highlights

Ascomycete fungi inhabit almost all known ecosystems, and play important roles as plant and insect pathogens, endophytes, mycoparasites, and saprobes (Arnold et al, 2009)
We report the first draft genome sequence assembly and annotation of P. foliicola and compare the genome characteristics against two other plant pathogenic fungi in the Nectriaceae, Fusarium graminearum and Dactylonectria macrodidyma
A de novo genome assembly of P. foliicola ATCC13545 R was generated from 19.5 million paired end, 300-bp reads, comprising a total of 5.4 Gb of raw sequence data

Summary

Introduction

Ascomycete fungi inhabit almost all known ecosystems, and play important roles as plant and insect pathogens, endophytes, mycoparasites, and saprobes (Arnold et al, 2009). Pseudonectria foliicola and P. buxi (the latter formerly known as Volutella buxi or P. rousseliana) are nectriaceous species causing a ubiquitous leaf and stem blight disease on boxwood (Buxus spp.), known as volutella blight (Fig. 1). To date, this disease has been reported worldwide, throughout the US, Armenia, Belgium, Bulgaria Canada, China, Greece, Portugal, Spain, UK and Ukraine, among others (Farr & Rossman, 2018), its distribution may extend further along with the distribution of boxwood plants. It is currently unclear to what extent previous sightings of volutella blight prior to the discovery of P. foliicola were caused by P. buxi, P. foliicola, or both of these pathogens

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