Transcriptome-wide analysis reveals the progress of Cordyceps militaris subculture degeneration

• Published in: PloS one Vol. 12; no. 10; p. e0186279
• Main Authors: Yin, Juan, Xin, Xiangdong, Weng, Yujie, Gui, Zhongzheng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26.10.2017; Public Library of Science (PLoS)
• Subjects: Alcohol; Alternative splicing; Biology and Life Sciences; Biosynthesis; Biotechnology; Chinese medicine; Chromatin remodeling; Cluster analysis; Cordyceps; Cordyceps - genetics; Cordyceps militaris; Degeneration; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA methylation; Energy metabolism; Fruit bodies; Gene expression; Gene Expression Regulation, Fungal; Genes; Genes, Fungal; Genetic aspects; Genomes; Growth; Medicine and Health Sciences; Metabolism; Pharmacology; Physiological aspects; Real-Time Polymerase Chain Reaction; Research and analysis methods; Ribonucleic acid; RNA; Sterols; Subculture; Transcription (Genetics); Transcriptome; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0186279

The entomopathogenic mushroom Cordyceps militaris is an important medicinal and food resource owing to its various medicinal components and pharmacological effects. However, the high frequency of strain degeneration during subculture seriously restricts the large-scale production of C. militaris, and the mechanism underlying strain degeneration remains unclear. In this study, we artificially cultured C. militaris for six generations and compared changes during fruiting body growth. The transcriptome of six generations of C. militaris strains were sequenced with the Illumine Hiseq4000. The subcultured C. militaris strains degenerated beginning at the third generation, with incomplete fruiting body growth beginning at the fourth generation. Over 9,015 unigenes and 731 new genes were identified. In addition, 35,323 alternative splicing (AS) events were detected in all samples, and more AS events occurred in the second, fourth and sixth generations. Compared with the first generation, the third generation (degenerated strain) included 2,498 differentially expressed genes (DEGs) including 1,729 up-regulated and 769 down-regulated genes. This number was higher than the number of DEGs in the second (1,892 DEGs), fourth (2,006 DEGs), fifth (2,273 DEGs) and sixth (2,188 DEGs) generations. Validation of RNA-seq by qRT-PCR showed that the expression patterns of 51 DEGs were in accordance with the transcriptome data. Our results suggest that the mechanism of C. militaris strain degeneration is associated with gene involved in toxin biosynthesis, energy metabolism, and DNA methylation and chromosome remodeling.