Genome-Wide Transcriptome Analysis Reveals Degeneration Progress of Subculture Cordyceps Militaris

The high frequency strain degeneration during subculture seriously restrict the large-scale production of Cordyceps militaris and industrialized process. In the current study, the high-throughput Illumina sequencing was performed on 6 passages subculture C. militaris strains to obtain the divergence of transciptomes in degeneration progress. Then various statistical comparison analysis was further conducted based on the HQ reads to better understand their difference. Over 9015 unigenes and 731 new genes were formed by initial sequence splicing and showed a perfect coverage;3737 ends in 3695 genes were optimized, 2010 at 5’ end (1847 genes ≥ 50 bps) and 1727 at 3’ end (1485 genes ≥ 50 bps); 134783 variants including 126923 SNP variants and 7860 InDelvariants were detected;more than 11304 RNA editing events occurred in total, which yielded 2950 nonsynonymous SNV, 6 stoploss, 5 stopgain and 8343 synonymous SNV; Compared with the first passage strain, the third passage strain exhibited 2498 differentially expressed genes (DEGs) including 1729 up-regulated genes and 769 down-regulated genes, which was higher than other samples. Seventeen enriched gene ontology (GO) terms were identified by GO enrichment analysis and twenty seven enriched pathways were identified by KEGG enrichment analysis, which might be mainly associated with the processing of degeneration. The findings revealed the DEGs involved into the degeneration progress of C. militaris and yielded insights into molecular mechanism of degeneration, which provide the reference for efficiently and artificially producing C. militaris. To obtain the divergence of tranisciptomes in degeneration progress of Cordyceps militaris