Genomic overview of closely related fungi with different Protea host ranges

• Published in: Fungal biology 2018-12, Vol.122 (12), p.1201-1214
• Main Authors: Aylward, Janneke, Wingfield, Brenda D., Dreyer, Léanne L., Roets, Francois, Wingfield, Michael J., Steenkamp, Emma T.
• Format: Article
• Language: English
• Subjects: Competition; Genomes; Interactions; Knoxdaviesia; Secretome
• ISSN: 1878-6146; 1878-6162
• DOI: 10.1016/j.funbio.2018.10.001

Genome comparisons of species with distinctive ecological traits can elucidate genetic divergence that influenced their differentiation. The interaction of a microorganism with its biotic environment is largely regulated by secreted compounds, and these can be predicted from genome sequences. In this study, we considered Knoxdaviesia capensis and Knoxdaviesia proteae, two closely related saprotrophic fungi found exclusively in Protea plants. We investigated their genome structure to compare their potential inter-specific interactions based on gene content. Their genomes displayed macrosynteny and were approximately 10 % repetitive. Both species had fewer secreted proteins than pathogens and other saprotrophs, reflecting their specialized habitat. The bulk of the predicted species-specific and secreted proteins coded for carbohydrate metabolism, with a slightly higher number of unique carbohydrate-degrading proteins in the broad host-range K. capensis. These fungi have few secondary metabolite gene clusters, suggesting minimal competition with other microbes and symbiosis with antibiotic-producing bacteria common in this niche. Secreted proteins associated with detoxification and iron sequestration likely enable these Knoxdaviesia species to tolerate antifungal compounds and compete for resources, facilitating their unusual dominance. This study confirms the genetic cohesion between Protea-associated Knoxdaviesia species and reveals aspects of their ecology that have likely evolved in response to their specialist niche. •We compared the genomes of two Knoxdaviesia species with different Protea hosts.•Similarity was apparent at a structural and gene content level.•Few secreted proteins and secondary metabolite gene clusters were identified.•A degraded secondary metabolite gene suggests limited competition in K. proteae.•The specialist Protea niche has likely facilitated a smaller genetic complement.