De novo transcriptome sequencing and comprehensive analysis of the heat stress response genes in the basidiomycetes fungus Ganoderma lucidum

Xiaoyan Tan; Junshe Sun; Huijuan Ning; Zifang Qin; Yuxin Miao; Tian Sun; Xiuqing Zhang

doi:10.1016/j.gene.2018.03.093

De novo transcriptome sequencing and comprehensive analysis of the heat stress response genes in the basidiomycetes fungus Ganoderma lucidum

Gene. 2018 Jun 30:661:139-151. doi: 10.1016/j.gene.2018.03.093. Epub 2018 Mar 29.

Authors

Xiaoyan Tan¹, Junshe Sun², Huijuan Ning¹, Zifang Qin¹, Yuxin Miao¹, Tian Sun³, Xiuqing Zhang⁴

Affiliations

¹ Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
² Chinese Academy of Agricultural Engineering, Beijing 100125, China.
³ Tianfangjian (China) Pharma Company Ltd, Guangzhou 510623, China. Electronic address: Elaine.Sun@tianfangjian.com.cn.
⁴ Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: xiuqingzhang@cau.edu.cn.

PMID: 29605602
DOI: 10.1016/j.gene.2018.03.093

Abstract

Ganoderma lucidum is a valuable basidiomycete with numerous pharmacological compounds, which is widely consumed throughout China. We previously found that the polysaccharide content of Ganoderma lucidum fruiting bodies could be significantly improved by 45.63% with treatment of 42 °C heat stress (HS) for 2 h. To further investigate genes involved in HS response and explore the mechanisms of HS regulating the carbohydrate metabolism in Ganoderma lucidum, high-throughput RNA-Seq was conducted to analyse the difference between control and heat-treated mycelia at transcriptome level. We sequenced six cDNA libraries with three from control group (mycelia cultivated at 28 °C) and three from heat-treated group (mycelia subjected to 42 °C for 2 h). A total of 99,899 transcripts were generated using Trinity method and 59,136 unigenes were annotated by seven public databases. Among them, 2790 genes were identified to be differential expressed genes (DEGs) under HS condition, which included 1991 up-regulated and 799 down-regulated. 176 DEGs were then manually classified into five main responsive-related categories according to their putative functions and possible metabolic pathways. These groups include stress resistance-related factors; protein assembly, transportation and degradation; signal transduction; carbohydrate metabolism and energy provision-related process; other related functions, suggesting that a series of metabolic pathways in Ganoderma lucidum are activated by HS and the response mechanism involves a complex molecular network which needs further study. Remarkably, 48 DEGs were found to regulate carbohydrate metabolism, both in carbohydrate hydrolysis for energy provision and polysaccharide synthesis. In summary, this comprehensive transcriptome analysis will provide enlarged resource for further investigation into the molecular mechanisms of basidiomycete under HS condition.

Keywords: Differential gene expression; Ganoderma lucidum; Heat stress; RNA-Seq; Transcriptome.

MeSH terms

Gene Expression Profiling
Gene Expression Regulation, Fungal
Genes, Fungal
Heat-Shock Response / genetics*
High-Throughput Nucleotide Sequencing
Metabolic Networks and Pathways / genetics
Molecular Sequence Annotation
Reishi / genetics*
Reishi / metabolism
Sequence Analysis, DNA
Stress, Physiological / genetics*
Transcriptome*