Transcriptome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis

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.

Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis

“…However, the transcriptome analyses using EST library sequencing of stroma of O. sinensis revealed more expressed genes (9,641) (Xiang et al, 2014) than the genome prediction by Hu et al (2013). Even more surprisingly, a total of 12,980 unigenes were found to be expressed in cultured mycelia of the species in a recent study (Liu et al, 2015). The secondary metabolism clusters were largely conserved between O. sinensis and other insect pathogens (Hu et al, 2013) and enzymes associated with carbohydrate metabolism were found to be expressed (Xiang et al, 2014).…”

“…The estimated genome size (120 Mb) is approximately three times larger than other insect ascomycete pathogens due to repeat driven expansion. Their number of predicted genes (6,972) was much fewer than that of a closely related fungus, Cordyceps militaris (9,684), with a much smaller genome size (32.2 Mb) (Zheng et al, 2011), and also fewer than the number of expressed genes detected from transcriptome analysis of O. sinensis (Xiang et al, 2014;Liu et al, 2015). This first draft genome assembly of O. sinensis is likely far from complete.…”

Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

“…e analysis rstly maps all DEGs to GO terms in the database (http://www.geneontology. org/), calculating gene numbers for every term, then using ultra-geometric test to nd signi cantly enriched GO terms in DEGs comparing to the genome background [31]. e calculating formula is shown as follows:…”

Comparative Transcriptomics of Metabolites in Wild and Cultivated Pinellia ternata

“…These technologies also promote research progress in the eld of traditional Chinese medicine. Since 2010, RNA-seq technology has been used in Chinese herbal medicines (Chen et al 2011;Liu et al 2015;Fukushima et al 2016).…”