Lignin degradation potential and draft genome sequence of Trametes trogii S0301

Abstract

BackgroundTrametes trogii is a member of the white-rot fungi family, which has a unique ability to break down recalcitrant lignin polymers to CO2 and water, and they have enormous potential to biodegrade a wide range of toxic environmental pollutants. Because of its industrial potential, the identification of lignin-degrading enzyme systems in Trametes is an important area of research. Development and utilization of industrial value genes are suffering due to deficiency knowledge of genome available for their manipulation.ResultsIn the present study, Homokaryotic strains of T. trogii S0301 were screened and sequencing by PacBio Sequel II platform. The final draft genome is ~ 39.88 Mb, with a contig N50 size of 2.4 Mb, this was the first genome sequencing and assembly of T. trogii species. Further analyses predicted 14,508 protein-coding genes. Results showed that T. trogii S0301 contains 602 genes encoding CAZymes, include 211 glycoside hydrolase and 117 lignin-degrading family genes, nine laccases related genes. Small subunit ribosomal RNA gene (18S rRNA) sequencing confirms its phylogenetic position. Moreover, T. trogii S0301 has the largest number of cytochromes P450 (CYPs) superfamily genes compare to other fungi. All these results are consistent with enzymatic assays and transcriptome analysis results. We also analyzed other genome characteristics in the T. trogii S0301genome.ConclusionHere, we present a nearly complete genome for T. trogii S0301, which will help elucidate the biosynthetic pathways of the lignin-degrading enzyme, advancing the discovery, characterization, and modification of novel enzymes from this genus. This genome sequence will provide a valuable reference for the investigation of lignin degradation in the Trametes genus.

Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass

“…A total of 165 CYP genes in the SP02 genome were annotated and 149 of them were classified into 30 subfamilies. In comparison, this number is close to those such as Trametes trogii (158) and Phanerochaete chrysosporium (152), and far higher than Agaricus bisporus (109) [79,80]. NADPH-cytochrome P450 reductase, cytochrome b5, and cytochrome b5 reductase were also identified in SP02 genome as potential cytochrome P450 NADPH redox partners.…”

Haploid Genome Analysis Reveals a Tandem Cluster of Four HSP20 Genes Involved in the High-Temperature Adaptation of Coriolopsis trogii

“…A total of 283 BUSCOs (97.5% of genes in the fungal lineage of odb9) were identified in both assemblies, of which 282 were complete and only one was a fragment. These two genomes had comparable assembly quality with that of a previously published C. trogii draft genome (S0301) ( 30 ) in total genome size and N 50 value ( Table 1 ).…”

“… Global view of the Ct001_29 genome. (A) The longest 20 contigs of Ct001_29; (B) G+C percentage; (C) gene density; (D) repeat content; (E) variant density in Ct001_29 versus that in Ct001_31; (F) variant density in Ct001_29 versus that in S0301 ( 30 ); (G) syntenic blocks (sequence length, ≥5 kb) within the Ct001_29 genome. All of the statistics were calculated over 50-kb nonoverlapping windows.…”

“…However, considerable phenotypic and genetic diversity is found between different monokaryons, strains, or haplotypes ( 23 , 28 , 29 ), and thus more genomes may provide a more comprehensive genetic background of a single species. Currently, only one whole-genome sequence for a monokaryon of C. trogii (S0301) is available ( 30 ). Additional genomic resources are thus critically important for realizing a more comprehensive and in-depth understanding of C. trogii .…”

Insights into the cellulose degradation mechanism of the thermophilic fungus Chaetomium thermophilum based on integrated functional omics

“…Plant biomass is recognized as a sustainable source of mixed sugars for fermentation to second generation biofuels and high-value molecules. Fungi have evolved different strategies to degrade lignocellulose [53][54][55][56][57][58]. The genome of the thermophilic fungus C. thermophilum suggested that this fungus should prefer to degrade monocots that are rich in cellulose, xylan and β-glucan.…”