Application of High-Throughput Internal Transcribed Spacer rRNA Metagenomics Analysis in Deciphering Endophytic Fungi Diversity of Dendrobium Officinale

High-throughput sequencing (HTS) was applied to compare the fungal species richness, diversity and community composition among 21 samples from Dendrobium officinale in seven different geographic areas in China. Genomic DNA was extracted and amplified using internal transcribed spacer (ITS) region sequences of rRNA. Illumina sequencing of Dendrobium officinale samples yielded 398 065 reads with an average read length of 316 nucleotides. Taxonomic analysis of metagenomic reads indicated that the fungal communities were diverse and strongly dominated by Ascomycota with Fusarium (32.73%), Glomerella (7.58%) and Cladosporium (6.48%) as the most abundant genera. Besides, the fungal community in some areas of Dendrobium officinale showed relatively high abundance of profitable strain, such as Mycena, Colletotrichum and Alternaria, some of which commonly have the function of growth promotion and may play potentially important roles in Dendrobium officinale. In addition, the richness and diversity of fungal community of Dendrobium officinale samples differed in geographic areas and plant tissues. Therefore, the HTS method provides a good alternative for investigating the fungal communities and roles of endophytes in Dendrobium officinale.