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

Luiz Marcelo Ribeiro Tomé,Aristóteles Góes-Neto,Thairine Mendes-Pereira,Vasco Ariston De Carvalho Azevedo,Fernanda Badotti,Paula Luize Camargos Fonseca,Bertram Brenig,Felipe Ferreira Da Silva

doi:10.3390/jof8020142

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.

Highlights

IntroductionLignocellulosic biomass (LB), including agro-industrial residues, municipal solid wastes, and forest litter is one of the largest stocks of carbon and energy on Earth [1]
According to the estimated genome size of the CCMB561 strain, coverages of 129× and 93× were obtained through sequencing on the Illumina and Oxford Nanopore platforms, respectively
Genomes with lengths similar to the estimated length of T. villosa CCMB561 were assembled with good contiguity and completeness using even smaller coverages than those obtained in this study

Summary

Introduction

Lignocellulosic biomass (LB), including agro-industrial residues, municipal solid wastes, and forest litter is one of the largest stocks of carbon and energy on Earth [1]. These are a sustainable, renewable, and abundant source of raw material, which can be (bio-). Lignocellulosic materials are inexpensive, abundant, and considered a valuable feedstock for biorefineries (bio-based industry), a major challenge for their use is the degradation of lignin, which is a highly recalcitrant polymer, and the consecutive depolymerization of cellulose and hemicellulose (polysaccharides) to fermentable sugars (oligosaccharides and monosaccharides) [3,4,5]. Biomass needs to undergo physical, chemical, and/or biological pretreatment [4]

Methods

Results

Conclusion