Comparative genomics of plant pathogenic Botrytis species with distinct host specificity

Abstract

BackgroundFungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae.ResultsBioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed.ConclusionsComparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5580-x) contains supplementary material, which is available to authorized users.

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

“…In Zymoseptoria, most of the predicted effectors are shared among all species, although they show presence-absence variation. In the Botrytis genus (Dothideomycetes), sister species infecting different hosts share effectors with confirmed functions [43]. Likewise, in Microbotrym, a fungal plant pathogen including several species specialized on different hosts a large set of genes encoding conserved and shared secreted proteins was identified.…”

The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations

“…This may rely on functional variations into the diverse and sophisticated biochemical arsenal of B. cinerea. Indeed, this pathogen shows a large repertoire of secreted proteins, secondary metabolites and small interfering RNA (siRNA) that act as effectors in the interactions with its hosts (Amselem et al, 2011; Mbengue et al, 2016; Reino et al, 2004; Siewers et al, 2005; Valero-Jiménez et al, 2019; Weiberg et al, 2013). The possible role of the different fungal effectors in host specialization remain to be investigated, as well as the possible role of the host phytoalexins.…”

The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host‐specialized and generalist populations

“…This may rely on functional variations into the diverse and sophisticated biochemical arsenal of B. cinerea. Indeed, this pathogen shows a large repertoire of secreted proteins, secondary metabolites and small interfering RNA (siRNA) that act as effectors in the interactions with its hosts (Reino et al, 2004;Siewers et al, 2005;Amselem et al, 2011;Weiberg et al, 2013;Mbengue et al, 2016;Valero-Jiménez et al, 2019). The possible role of the different fungal effectors in host specialization remains to be investigated, as well as the possible role of the host phytoalexins.…”