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.

Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil

“…The DNA library was prepared with ligation Sequencing kit (SQKRAD004, Oxford Nanopore Technologies, Oxford, UK) according to the manufacturer’s instructions. Libraries were sequenced with qualified FLO-MIN106 flow cells (the initial bias voltage was −210 mV and the active pores number around 516) for 36 h (basecalling function was used, the reads sequences was filtered using a min_score = 9) on a MinION (Oxford Nanopore Technologies, Oxford, UK) [ 22 ].…”

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

“…Specific primers ( Table 2 ) for the amplification of Laccase (Lac), Lignin peroxidase (LiP), Manganese peroxidase (MnP), and Actin (actin1) were designed based on the genome and functional annotations of T. villosa CCMB561 [ 33 ]. The Geneious® software version 9.0.5 (Auckland, New Zealand) and the OligoAnalyzer™ tool ( https://www.idtdna.com/ ) were used to design and analyze the primers, respectively.…”

“…Recently, the complete genome of T . villosa CCMB561 was sequenced using the high-throughput sequencing platforms Illumina HiSeq and Oxford Nanopore MinION (hybrid assembly strategy) [ 33 ]. The obtained high-quality genome revealed an arsenal of genes encoding peroxidases, cellulases, hemicellulases, and pectinases that act synergistically in the degradation of all lignocellulose polymers.…”

“…The obtained high-quality genome revealed an arsenal of genes encoding peroxidases, cellulases, hemicellulases, and pectinases that act synergistically in the degradation of all lignocellulose polymers. Furthermore, the comparative genomic analyses showed that T. villosa CCMB561 was the species with the highest number of genes encoding lignin-modifying enzymes when compared to other species of the same genus [ 33 ].…”

Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics

“…Conversely, long-read HTS platforms (e.g. : Oxford Nanopore Technologies) can sequence long DNA segments (Kbp to Mbp; Tomé et al, 2022 ). Long-read sequencing may help not only in alignment-based taxonomic and functional assignment due to its increased information content but also in bridging within- and between-genome repetitive sequences ( Wommack et al, 2008 ; Bertrand et al, 2018 ).…”