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.
Supplementary File 1: Summary of repeat-induced-point mutation (RIP) per scaffold.
Supplementary File 2: Examples of the sequence depth and number of mismatches across
repetitive regions in Knoxdaviesia capensis and K. proteae.
Supplementary File 3: Overview of the classification of Knoxdaviesia genome-wide speciesspecific
proteins in Functional Catalogue categories.
Supplementary File 4: Classification and annotation of the genome-wide species-specific
proteins of Knoxdaviesia capensis and K. proteae.
Supplementary File 6: Summary of proteins excluded from and included in the final
Supplementary File 7: Overview of the classification of Knoxdaviesia secreted proteins in
Functional Catalogue categories.
Supplementary File 8: Classification and annotation of the putative secreted proteins of
Knoxdaviesia capensis and K. proteae.
Supplementary File 9: Classification and annotation of the small secreted cysteine-rich
proteins (SSCPs) identified in the two Knoxdaviesia genomes.
Supplementary Table S1: Occurrence of the TTAGGGTTAC / GTAACCCTAA
Knoxdaviesia telomere repeat in K. capensis and K. proteae.
Supplementary Table S2: Populous orthogroups in the Knoxdaviesia genomes.
Supplementary Table S3: Outcome of the protein BLAST for the Knoxdaviesia capensis
and K. proteae species-specific proteins.
Supplementary Table S4: Cysteine-rich secreted proteins and proteins with hits to the
Pathogen Host Interaction (PHI) database in Knoxdaviesia capensis and K. proteae.
Supplementary Table S5: Amplification of the T1PKS-4 cluster deletion in Knoxdaviesia
capensis and K. proteae.
The predicted proteins of Knoxdaviesia capensis and K. proteae in FASTA format and the
gff3 annotation files of the transposable elements identified by the REPET package have been
made available on Mendeley Data (https://data.mendeley.com/), DOI:10.17632/rbx32w7crp.1