Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome.

Hye-Won Yu,Ji-Hoon Im,Won-Sik Kong,Young-Jin Park

doi:10.3390/microorganisms9010020

Hye-Won Yu, Ji-Hoon Im + Show 2 more

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https://doi.org/10.3390/microorganisms9010020

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Abstract

The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F. velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54–95 AAs, 145–188 GHs, 55–73 GTs, 6–19 PLs, 13–59 CEs, and 7–67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.

Highlights

Flammulina velutipes var. lupinicola (Physalacriaceae) was first identified in 1999 by Redhead and Petersen [1]
Flammulina species and S. commune were found to have only the PL9 family (Table S4). These results suggest that F. velutipes var. lupinicola might be a potential candidate for future research focused on polysaccharide lyase as the number of genes encoding polysaccharide lyases (PLs) family members 1, 3, and 9 is similar to that of S. commune
Our results showed to that copper-binding and β-α-β dinucleotide-binding motifs are present in the 9 (AA1 families) and 16 genes (AA3 families) of F. velutipes var. lupinicola, respectively, indicating that these genes may act as laccases and GMC oxidoreductases (Table 7)

Summary

Introduction

Flammulina velutipes var. lupinicola (Physalacriaceae) was first identified in 1999 by Redhead and Petersen [1]. Except for the following characteristics, its molecular biology and biological properties were not well known; first, basidiospores are larger (7−14.5 × 3.7–6.5 μm) than those of the typical F. velutipes variety. It seems to be limited geographically (from southern to northern California) in ecologically distinctive zone (in costal dunes) largely on a specific host (Lupinus arboreus) native to the region. Enzymes, including carbohydrate esterases (CEs), glycoside hydrolases (GHs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AAs), are collectively known as carbohydrate-active enzymes (CAZymes), and these enzymes are involved in the catabolism of carbohydrates [2]. Many fungal species that exist extensively in nature, including basidiomycetes, can efficiently degrade

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