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.