Whole-Genome Sequencing and Transcriptome Analysis of Ganoderma lucidum Strain Yw-1-5 Provides New Insights into the Enhanced Effect of Tween80 on Exopolysaccharide Production

Abstract

Ganoderma lucidum is an important medicinal mushroom widely cultured in Asian countries. Exopolysaccharides are bioactive compounds of G. lucidum with health benefits. Limited exopolysaccharide content hinders its extraction from G. lucidum. The addition of Tween80 had an enhanced effect on G. lucidum exopolysaccharide production in submerged fermentation. However, the mechanism of this effect remains unclear. In this study, we report on a high-quality assembly of G. lucidum strain yw-1-5 to lay the foundation for further transcriptome analysis. The genome sequence was 58.16 Mb and consisted of 58 scaffolds with an N50 of 4.78 Mb. A total of 13,957 protein-coding genes were annotated and Hi-C data mapped to 12 pseudo-chromosomes. Genes encoding glycosyltransferases and glycoside hydrolases were also obtained. Furthermore, RNA-seq was performed in a Tween80-treated group and control group for revealing the enhanced effect of Tween80 on exopolysaccharide production. In total, 655 genes were identified as differentially expressed, including 341 up-regulated and 314 down-regulated. Further analysis of differentially expressed genes showed that groups of MAPK, amino sugar and nucleotide sugar metabolism, autophagy, ubiquitin-mediated proteolysis, peroxisome, starch and sucrose metabolism, TCA cycle, glycolysis/gluconeogenesis KEGG pathway, glycosyltransferases and glycoside hydrolases played important roles in the enhanced effect of Tween80 on exopolysaccharide production. This work provides a valuable resource for facilitating our understanding of the synthesis of polysaccharides and accelerating the breeding of new strains with a high content of exopolysaccharides.

Keywords: Ganoderma lucidum; Tween80; functional gene analysis; genome sequencing; polysaccharides; transcriptome.

Figure 1

Hi-C interaction heat map and genomic features of the Ganoderma lucidum yw-1-5. (A), Hi-C interaction heat map of Ganoderma lucidum yw-1-5 haploid genome. (B), Global view of the yw-1-5 genomic features. The names marked outside the circle were identified as gene clusters and the cluster names in red represent the terpene clusters. The detailed information of these gene clusters was listed in Table S6. Circle I represents the 12 pseudo-chromosomes of G. lucidum (Mb). Circle II represents gene density on every pseudo-chromosome. Circle III represents repetitive sequence density on each pseudo-chromosome. Circle IV represents large segmental duplications: regions sharing more than 90% sequence similarity over 10 kb were connected by red lines; those over 5 kb were connected by dark blue lines.

Figure 2

Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of the Ganoderma lucidum yw-1-5 genome. GO functional enrichment (A) and KEGG pathway (B) enrichment of putative genes in yw-1-5.

Figure 3

Genes functional classification of yw-1-5 by KOG.

Figure 4

The content of exopolysaccharides (A) and the comparison of DEG expression between Tween80-treated group and control group (B).

Figure 5

A model of the enhanced effect of Tween80 on exopolysaccharide production.