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. 2017 Oct 26;12(10):e0186279.
doi: 10.1371/journal.pone.0186279. eCollection 2017.

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

Juan Yin  1 , Xiangdong Xin  1 , Yujie Weng  1 , Zhongzheng Gui  1   2
Affiliations

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

Juan Yin et al. PLoS One. .

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Changes in the C. militaris fruiting body at different generations.
Fig 2
Fig 2. Differentially expressed genes (DEGs) analyses.
Note: (A) DEGs statistics of different samples. (B) Scatter plot of YCCZ1-YCCZ2. (C) Scatter plot of YCCZ1-YCCZ3. (D) Scatter plot of YCCZ1-YCCZ4. (E) Scatter plot of YCCZ1-YCCZ5. (F) Scatter plot of YCCZ1-YCCZ6.
Fig 3
Fig 3. DEG-based correlation heat map (CHM) and sample cluster analysis.
Fig 4
Fig 4. GO classification map of YCCZ1 vs. YCCZ5.
Fig 5
Fig 5. Validation of DEGs expression by qRT-PCR.
(A) Genes related to DNA methylation, chromosome remodeling, mitosis, and meiosis. (B) Genes related to fruiting body formation, sexual development, light-induced brown film formation, and secondary metabolites biosynthesis. (C) Genes related to toxin biosynthesis and detoxification, and transmembrane transport. (D) Genes related to cell growth and development, cell apoptosis and autophagy, and macro molecular metabolism.
See this image and copyright information in PMC

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