Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown

Abstract

Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.