AUTHOR=Lee Robert C. , Farfan-Caceres Lina M. , Debler Johannes W. , Syme Robert A. 

TITLE=Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean (Vicia faba L.)

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.00217

DOI=10.3389/fmicb.2020.00217

ISSN=1664-302X

ABSTRACT=<p>Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, <italic>Botrytis fabae</italic>. <italic>B. fabae</italic> is also implicated in botrytis gray mold disease in lentils, along with <italic>B. cinerea</italic>. Here we have isolated and characterized two <italic>B. fabae</italic> isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, <italic>B. fabae</italic> was more aggressive than <italic>B. cinerea</italic> and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward <italic>B. fabae</italic>. In contrast, the plant response to <italic>B. cinerea</italic> was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of <italic>B. fabae</italic>, we produced genome assemblies for both <italic>B. fabae</italic> isolates using Illumina sequencing. Genome sequencing coverage and assembly size for <italic>B. fabae</italic> isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for <italic>B. fabae</italic>, and using the same selection criteria for <italic>B. cinerea</italic>, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from <italic>B. fabae</italic> and <italic>B. cinerea</italic> was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in <italic>B. fabae</italic>. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the <italic>B. cinerea</italic> phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from <italic>B. fabae</italic>. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in <italic>B. fabae</italic> was double that of <italic>B. cinerea</italic>.</p>