Transcriptome Analysis of Antrodia cinnamomea Mycelia from Different Wood Substrates

Abstract

Antrodia cinnamomea, an edible and medicinal fungus with significant economic value and application prospects, is rich in terpenoids, benzenoids, lignans, polysaccharides, and benzoquinone, succinic and maleic derivatives. In this study, the transcriptome of A. cinnamomea cultured on the wood substrates of Cinnamomum glanduliferum (YZM), C. camphora (XZM), and C. kanehirae (NZM) was sequenced using the high-throughput sequencing technology Illumina HiSeq 2000, and the data were assembled by de novo strategy to obtain 78,729 Unigenes with an N50 of 4,463 bp. Compared with public databases, about 11,435, 6,947, and 5,994 Unigenes were annotated to the Non-Redundant (NR), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genome (KEGG), respectively. The comprehensive analysis of the mycelium terpene biosynthesis-related genes in A. cinnamomea revealed that the expression of acetyl-CoA acetyltransferase (AACT), acyl-CoA dehydrogenase (MCAD), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), mevalonate pyrophosphate decarboxylase (MVD), and isopentenyl diphosphate isomerase (IDI) was significantly higher on NZM compared to the other two wood substrates. Similarly, the expression of geranylgeranyltransferase (GGT) was significantly higher on YZM compared to NZM and XZM, and the expression of farnesyl transferase (FTase) was significantly higher on XZM. Furthermore, the expressions of 2,3-oxidized squalene cyclase (OCS), squalene synthase (SQS), and squalene epoxidase (SE) were significantly higher on NZM. Overall, this study provides a potential approach to explore the molecular regulation mechanism of terpenoid biosynthesis in A. cinnamomea.

Keywords: Antrodia cinnamomea; biosynthesis; de novo transcriptome; qRT-PCR; terpenoid.

Figure 1.

Growth of mycelia on different wood substrates of Antrodia cinnamomea. (A) NZM 90 d; (B) XZM 90 d; (C) YZM 90 d.

Figure 2.

Triterpene content of Antrodia cinnamomea. Data are expressed as the average of three biological replicates.Different letters indicate significant differences at p < 0.05 (Duncan’s multiple range test).

Figure 3.

The KEGG metabolic pathway map of Antrodia cinnamomea Unigene transcriptome.

Figure 4.

Venn diagram of differentially expressed genes in the transcriptome of Antrodia cinnamomea. The sum of the numbers in each circle represents the total number of differential genes in the comparison combination, and the overlap of the circles represents the common differential genes between the two comparison groups. (A)Venn diagrams showing the up-regulated DEGs; (B)Venn diagrams showing the down-regulated DEGs.

Figure 5.

Interactive heat map of transcriptome expression of terpenoid biosynthetases encoded by Antrodia cinnamomea transcriptome. Each column represents an experimental sample (NZM, XZM, and YZM) and each row represents a gene. High expression levels are shown in red. Low expression levels are shown in blue.

Figure 6.

Relative expression of differentially expressed genes by qRT-PCR. (A) ACS13; (B) AACT2; (C) ACC1; (D) AOC; (E) HMG-CoA; (F) MVD; (G) OCS; (H) SQS; (I) SE; (J) HMGS2; qRT-PCR: real-time quantitative reverse transcription PCR. Error bars indicate the standard deviation of three independent biological replicates. Different letters indicate significant differences at p < 0.05.