Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes

Figures & data

Figure 1. Genetic diversity of strains in Trametes. (a) Size of pan-genome (red) and core genome (blue) shared by different genomes, respectively; (b) Core and specific genes families of nine Trametes strains. Number of core genome shared by all strains is in the center (8518). Number of non-overlapping portions of each oval represents the size of specific families; (c) Phylogenetic tree based on the ITS1 sequences of nine Trametes strains and Coriolopsis caperata; (d) Phylogenetic tree based on the ITS2 sequences of nine Trametes strains and C. caperata. Coriolopsis caperata was selected as an outgroup to root the topology of phylogenetic tree; (e) UPGMA tree of Manhattan distance based on the pan-genome composition of nine Trametes strains.

Table 1. Comparison of the genomic features of nine strains in Trametes genus.

Organism	DB accession number	Contigs/scaffolds	Genome size (bp)	CDSs/ORFs^a	Reference
T. cinnabarina BRFM137	CCBP010000001	776	33,668,918	59,163	[39,40]
T. cinnabarina FP 104138-Sp	JSYY01000001	9,648	31,621,284	61,560	[41]
T. coccinea BRFM310	KZ084086	222	32,757,859	56,735	[42]
T. hirsuta	CP019371	13	37,433,966	61,150	[43]
T. polyzona	MKKQ01000001	5,321	36,629,716	65,446	[44]
T. pubescens	MNAD01000001	1,731	39,739,821	67,916	[45]
Trametes sp. AH28-2	LJJJ01000001	306	38,904,488	65,191	[46]
T. versicolor FP-101664 SS1	NW_007360321	283	44,794,008	71,443	[47]
T. villosa CCMB561	PUDQ01000001	10,327	57,987,392	101,817	[4]

^a The CDSs/ORFs were predicted by Prodigal.

Figure 2. COG and GO annotation of gene families. (a) Distribution of COG annotation of pan-genome that assigned in 25 functional categories; (b) Distribution of GO annotation of pan-genome in biological process, molecular function and cellular component. Accessory clusters (pink), core clusters (green), and specific genes (wathet).

Figure 3. Distributions of CAZymes in nine Trametes strains of Trametes. (a) Distribution of CAZymes in Trametes pan-genome; (b) Distribution of CAZymes of pan-genome in each Trametes strain grouped by accessory clusters, core clusters and specific genes. The numbers shown in subgraph represents the orthologous genes assigned by CAZymes and grouped by accessory clusters (pink), core clusters (green), and specific genes (wathet); (c) Distribution of CAZymes of accessory clusters in each Trametes strain; (d) Distribution of CAZymes of core clusters in each Trametes strain; (e) Distribution of CAZymes of specific genes in each Trametes strain. The numbers shown in subgraphs represent the orthologous genes assigned by CAZymes. GT: glycosyltransferase; GH: glycoside hydrolase; CE: carbohydrate esterase; CBM: carbohydrate-binding molecule; AA: auxiliary activities; PL: polysaccharide lyases.

Figure 4. Distribution of biosynthetic gene clusters in nine Trametes strains of Trametes. The distribution of biosynthetic gene clusters in each Trametes strain. The numbers shown in graph represent the counts of different types of biosynthetic gene clusters predicted by antiSMASH for each Trametes strain. Note: cf_putative, putative cluster of unknown type identified with the ClusterFinder algorithm; terpene, terpene cluster; nrps, nonribosomal peptide synthetase cluster; cf_fatty_acid, putative fatty acid cluster identified with the ClusterFinder algorithm; t1pks, type I PKS cluster; lantipeptide, lanthipeptide cluster; other, cluster containing a secondary metabolite-related protein that does not fit into any other category.

Figure 5. Probability and homologous gene clusters for three putative BGCs of T. pubescens. The probability and homologous gene clusters for the putative BGCs of (a) no. 13; (b) no. 15; (c) no. 20. In the subgraph, the same colors of the boxes with arrows are similar genes.

Lomascolo A, Cayol JL, Roche M, et al. Molecular clustering of Pycnoporus strains from various geographic origins and isolation of monokaryotic strains for laccase hyperproduction. Mycol Res. 2002;106:1193–1203.

 Google Scholar

Levasseur A, Lomascolo A, Chabrol O, et al. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics. 2014;15:486.

 PubMed Web of Science ®Google Scholar

Busk PK, Lange M, Pilgaard B, et al. Several genes encoding enzymes with the same activity are necessary for aerobic fungal degradation of cellulose in nature. PLoS One. 2014;9:e114138.

 Web of Science ®Google Scholar

Couturier M, Navarro D, Chevret D, et al. Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. Biotechnol Biofuels. 2015;8:216.

 Web of Science ®Google Scholar

Pavlov AR, Tyazhelova TV, Moiseenko KV, et al. Draft genome sequence of the fungus Trametes hirsuta 072. Genome Announc. 2015;3:e01287–01215.

 Google Scholar

Cerrón LM, Romero-Suárez D, Vera N, et al. Decolorization of textile reactive dyes and effluents by biofilms of Trametes polyzona LMB-TM5 and Ceriporia sp. LMB-TM1 isolated from the Peruvian Rainforest. Water Air Soil Pollut. 2015;226:235.

 Web of Science ®Google Scholar

Granchi Z, Peng M, Chi-A-Woeng T, et al. Genome sequence of the basidiomycete white-rot fungus Trametes pubescens FBCC735. Genome Announc. 2017;5:e0164301616.

 Google Scholar

Wang J, Zhang Y, Xu Y, et al. Genome sequence of a laccase producing fungus Trametes sp. AH28-2. J Biotechnol. 2015;216:167–168.

 Web of Science ®Google Scholar

Floudas D, Binder M, Riley R, et al. The Paleozoic origin of enzymatic mechanisms for decay of lignin reconstructed using 31 fungal genomes. Science. 2012;336:1715–1719.

 PubMed Web of Science ®Google Scholar

Ferreira DSS, Kato RB, Miranda FM, et al. Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil. Data Brief. 2018;18:1581–1587.

 Web of Science ®Google Scholar