Principal component analyses (PCA) and heatmap analyses of CAZymes and lignocellulolytic genes
In PCA of CAZymes, organisms are cluster with others which have the similar nutrient patterns to determine the rot patterns of fungi (Riley et al., 2014). Here, PCA was used to cluster WR and BR fungi based on the diversity of their CAZymes. The CAZymes number matrix of wood decay fungi (WDF) from the following species was used as input: Galerina marginata (abbreviated as “gama”), A . orientale(“auor”),Heterobasidion annosum (“hean”),Stereum hirsutum (“sthi”), A . vulgare (“auvu”),Punctularia strigosozonata (“pust”), A .microsporum (“aumi”), Fomitiporia mediterranea(“fome”), S . pachycystidiatus (“stpa”), S .luchuensis (“stlu”), Dichomitus squalens (“disq”),Trametes versicolor (“trve”),Phanerochaete chrysosporium (“phch”), S . stephanocystis (“stst”),Phanerochaete carnosa (“phca”), S . orientalis(“stor”), Wolfiporia cocos (“woco”), Gloeophyllum trabeum (“gltr”), Fomitopsis pinicola (“fopi”),Dacryopinax primogenitus (“dapr”), Serpula lacrymans (“sela”) andConiophora puteana (“copu”) (Eastwood et al. 2011; Floudas et al. 2012; Martinez et al. 2004; Ohm et al. 2014; Olson et al., 2012; Riley et al., 2014; Suzuki et al. 2012).
Among these species, phca, phch, hean, sthi, gama, disq, trve, fome and pust belonged to WR fungi, while copu, gltr, fopi, woco, dapr and sela belonged to BR fungi (Chen et al., 2016; Riley et al., 2014). The online OmicShare tools (http://www.omicshare.com/tools) were used to generate the illustrations, heatmaps, and other outputs from PCA and statistical analysis. Adobe Photoshop (PS) and Adobe Illustrator (AI) were used for image editing and finalization.
Analyses of enzymes on resin decomposition
By adding latex to media, Oghenekaro, Kovalchuk, Raffaello, Camarero, & Asiegbu, (2020) identified that some genes had elevated expressions inR . microporus . Latex is a complex emulsion that includes a diversity of chemicals such as proteins, alkaloids, carbohydrates, oils, tannins, and resins that coagulate on exposure to air (Konno, 2011). It is commonly produced by plants after tissue injury and serve as a defense against pathogens and pests (Oghenekaro et al., 2020). Here we used the high expressed genes induced by latex treatment in R .microporus to infer the distributions of these genes in the seven fungi analyzed in our study. Using those genes in R .microporus as references, we identified the homologous genes in our genomes through BLASTP algorithms with a cut off e-value<1e-5 as showed above.