Comparative Analysis of Carbohydrate Active Enzymes of Fungal Genomes Across Taxonomic Orders

Carbohydrate active enzymes, or CAZymes, are enzymes that are important for the breakdown of carbohydrates. Fungi produce many of these enzymes as they cycle essential nutrients. For this study, we compared the abundance of CAZymes families among fungal genomes from the taxonomic orders Capnodiales, Dothideales, Eurotiales, Filobasidiales, Pleosporales, Tremellales, and Ustilaginales that were isolated from different sources including plant, soil, and food, among others. Our objective was to address the following questions: 1) How does the alpha diversity or number of CAZymes differ between the fungal orders? 2) Are closely-related fungi more likely to have similar CAZyme profiles as compared to distantly-related fungi? 3) Which CAZymes are significantly enriched or depleted between these fungal groups? Alpha diversity, measured as the effective number of CAZymes, showed that Eurotiales had the largest average number of CAZymes present (79) while Filobasidiales had the least (55). Additionally, we found a correlation of R2 = 0.64 between the effective number of CAZymes and the assembly size of the analysed genomes; however, it was insufficient to explain the differences in CAZymes across orders. Beta diversity analyses visualized with Non-metric Multidimensional Scaling (NMDS) showed clear compositional clustering of the CAZyme profiles among the taxonomic orders, indicating that closely related fungi have similar CAZyme profiles. In contrast, there was no relationship among different sampling sources. While the Glycoside Hydrolase and Carbohydrate-Binding Module CAZymes were relatively similar in enrichment across the seven orders, differential abundance analysis using ANCOM II at 0.7 cut off showed that there were more than 30 differentially abundant CAZymes across different fungal orders. Ustilaginales and Filobasidiales had fewer differentially abundant CAZymes than other groups. Auxiliary Activities (AA) were noticeably more enriched in the Eurotiales, Capnodiales, and Pleosporales orders, and the Carbohydrate Esterase (CE) CAZymes had lower overall abundances across the groups. CAZymes are important for microbes, and these results indicate that different fungal orders have evolved to have different sets of them, likely due to ecological specialization or adaptation to specific niches. The fact that we did not see differences in CAZyme profiles across environmental sources suggests that they do not evolve and change quickly enough to be distinct among closely-related species growing in different habitats.