Abstract
BackgroundOphiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years. H. sinensis is reported as the only correct anamorph of O. sinensis and its main active ingredients are similar to the natural O. sinensis.ResultsH. sinensis L0106, asexual strain of O. sinensis, was isolated and identified in this study. Three transcriptomes of H. sinensis at different cultivation periods (growth period 3d, pre-stable period 6d and stable period 9d) were sequenced for the first time by RNA-Seq method, and 25,511 unigenes (3d), 25,214 unigenes (6d) and 16,245 unigenes (9d) were assembled and obtained, respectively. These unigenes of the three samples were further assembled into 20,822 unigenes (All), and 62.3 percent of unigenes (All) could be annotated based on protein databases. Subsequently, the genes and enzymes involved in the biosynthesis of the active ingredients according to the sequencing and annotation results were predicted. Based on the predictions, we further investigated the interaction of different pathway networks and the corresponding enzymes. Furthermore, the differentially expressed genes (DEGs) of H. sinensis grown during different developmental stages (3d-VS-6d, 3d-VS-9d and 6d-VS-9d) were globally detected and analyzed based on the data from RNA-Seq, and 764 DEGs between 3d and 6d, 1,869 DEGs between 3d and 9d, and 770 DEGs between 6d and 9d were found, respectively.ConclusionsThis work presented here would aid in understanding and carrying out future studies on the genetic basis of H. sinensis and contribute to the further artificial production and application of this organism. This study provided a substantial contribution and basis to further characterize the gene expression profiles of H. sinensis in the metabolic pathways of active ingredients.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1269-y) contains supplementary material, which is available to authorized users.
Highlights
Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years
We investigated and globally detected the differentially expressed genes of H. sinensis grown during different developmental stages based on RNA-Seq, and found 764 DEGs between 3d and 6d, including 549 and 215 genes up- and down-regulated from 3d to 6d (FDR ≤0.001), 1,869 DEGs between 3d and 9d, including 1,410 and 459 genes up- and down-regulated from 3d to 9d, and 770 DEGs between 6d and 9d, including 215 and 555 genes up- and down-regulated from 6d to 9d, respectively
Summary of RNA-Seq data sets To obtain an overview of the H. sinensis transcriptome at different developmental stages, the RNA samples were prepared from the mycelium in different cultivation phases (3d, 6d and 9d), and poly(A)-enriched mRNA samples were subjected to high-throughput Illumina GA IIx sequencing
Summary
Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years. The use of next-generation sequencing technology of transcriptome could systematically provide a complete view of expressed genes and their expression levels for the organisms at a given cultivation time, find genes and proteins involved in secondary metabolism and clarify functions of the corresponding metabolic pathways. Some methods such as serial analysis of gene expression (SAGE) [15], reassociation kinetics (Rot) [16], microarrays [17], sequencing of expressed sequence tags (ESTs) and full length transcripts [18] have been used to extensively study the transcriptomes. Zhang et al [27] used the paired-end RNA-Seq technology to sequence eight organs of cultivated rice, and detected 7,232 new transcription areas which have not yet been determined
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