Genome-Wide Analysis of Secondary Metabolite Gene Clusters in Ophiostoma ulmi and Ophiostoma novo-ulmi Reveals a Fujikurin-Like Gene Cluster with a Putative Role in Infection

Abstract

The emergence of new microbial pathogens can result in destructive outbreaks, since their hosts have limited resistance and pathogens may be excessively aggressive. Described as the major ecological incident of the twentieth century, Dutch elm disease, caused by ascomycete fungi from the Ophiostoma genus, has caused a significant decline in elm tree populations (Ulmus sp.) in North America and Europe. Genome sequencing of the two main causative agents of Dutch elm disease (Ophiostoma ulmi and Ophiostoma novo-ulmi), along with closely related species with different lifestyles, allows for unique comparisons to be made to identify how pathogens and virulence determinants have emerged. Among several established virulence determinants, secondary metabolites (SMs) have been suggested to play significant roles during phytopathogen infection. Interestingly, the secondary metabolism of Dutch elm pathogens remains almost unexplored, and little is known about how SM biosynthetic genes are organized in these species. To better understand the metabolic potential of O. ulmi and O. novo-ulmi, we performed a deep survey and description of SM biosynthetic gene clusters (BGCs) in these species and assessed their conservation among eight species from the Ophiostomataceae family. Among 19 identified BGCs, a fujikurin-like gene cluster (OpPKS8) was unique to Dutch elm pathogens. Phylogenetic analysis revealed that orthologs for this gene cluster are widespread among phytopathogens and plant-associated fungi, suggesting that OpPKS8 may have been horizontally acquired by the Ophiostoma genus. Moreover, the detailed identification of several BGCs paves the way for future in-depth research and supports the potential impact of secondary metabolism on Ophiostoma genus’ lifestyle.

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae

“…2009) on predicted protein databases (e-value < 1 × 10 −5 , query coverage > 60% and identity > 50% (Sbaraini et al . 2017).…”

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae

“…The conservation of predicted SMCs among Verticillium spp. was assessed based on core enzyme conservation, using BLAST+ tool protein blast (blastp) (Camacho et al, 2009) on predicted protein databases (e-value < 1 x 10 -5 , query coverage > 60 % and identity > 50 % (Sbaraini et al, 2017).…”

CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology

“…In plant pathogenic fungi, secondary metabolites such as host-selective toxins are well known to play an important role in disease development ( Macheleidt et al., 2016 ). Bioinformatic annotations have identified O. novo-ulmi gene clusters putatively involved in biosynthesis of secondary metabolites, and interspecific comparative genomic analyses uncovered a fujikurin-like gene cluster (OpPKS8), found in the DED pathogens ( O. ulmi and O. novo-ulmi ) but absent in related non-phytopathogenic species ( Sbaraini et al., 2017 ). According to phylogenetic analyses the authors suggested that this toxin-related cluster may have been horizontally acquired by DED pathogens ( Sbaraini et al., 2017 ).…”

“…Bioinformatic annotations have identified O. novo-ulmi gene clusters putatively involved in biosynthesis of secondary metabolites, and interspecific comparative genomic analyses uncovered a fujikurin-like gene cluster (OpPKS8), found in the DED pathogens ( O. ulmi and O. novo-ulmi ) but absent in related non-phytopathogenic species ( Sbaraini et al., 2017 ). According to phylogenetic analyses the authors suggested that this toxin-related cluster may have been horizontally acquired by DED pathogens ( Sbaraini et al., 2017 ). Genes in the OpPKS8 cluster are good candidates for exploration with CRISPR/Cas9, which could be used as an additional tool to elucidate the functions of this secondary metabolite cluster and its potential role in pathogenicity.…”