Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis

Abstract

Ophiocordyceps sinensis is a highly valuable and popular medicinal fungus used as a tonic and roborant for thousands of years in traditional Asian medicine. However, unsustainable harvesting practices have endangered this species and very little is known about its developmental programming, its biochemistry and genetics. To begin to address this, the transcriptome of the medicinal O. sinensis fruiting body was analyzed by high-throughput. In this O. sinensis 454-EST dataset, four mating type genes and 121 genes that may be involved in fruiting body development, especially in signal transduction and transcription regulation, were discovered. Moreover, a model was developed for the synthesis of the primary medicinal compound, cordycepin, and the putative biosynthetic enzymes identified. This transcriptome dataset provides a significant new resource for gene discovery in O. sinensis and dissection of its valuable biosynthetic and developmental pathways.

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

“…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 identified pseudogenes should be re-evaluated to check whether the fungus has really lost the relevant function or whether functional paralogs can be found in the genome.…”

“…Obligate biotrophs may have lost some metabolic pathways, including the metabolism of inorganic nitrogen, inorganic sulfur and thiamine, and genes encoding carbohydrate active enzymes and secondary metabolism enzyme (Baxter et al, 2010;Spanu, 2012). 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).…”

“…Hu et al (2013) published a 87.7 Mb draft genome of O. sinensis and stated that the genome size should be closer to ~120 Mb based on K-mer calculations. Almost 7,000 genes were predicted from this draft assembly, however, EST library sequencing revealed many more expressed genes (9,641) (Xiang et al, 2014). The results of the present study gave a draft genome size for a haploid single ascospore isolate of O. sinensis at between 114 and 139 Mb (with highly repetitive regions absent from the assembly since Illumina HiSeq short read data does not give these regions), which is larger than the previous estimate of ~120 Mb by Hu et al (2013).…”

“…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.…”

Simple Genetic Tools to Study Fruiting Body Development in Fungi

“…Fruiting body mutants are now available for many fungi other than P. anserina, including Sordaria macrospora [27], N. crassa [28], A. nidulans [29] and Coprinopsis cinerea (formely Coprinus cinereus) [30,31] and could be analyzed using similar methods. They are complementary to the now more widespread large scale analyses of transcriptomes during fruiting body development as performed in the ascomycetes Fusarium graminearum and Fusarium verticilloides [32][33][34], N. crassa [35,36], S. macrospora [37], Pyronema confluens [38], Tuber melanosporum [39][40][41], Cordyceps militaris [42] and Ophiocordyceps sinensis [43], as well as in the basidiomycetes C. cinerea [44], Moniliophthora perniciosa [45], Agrocybe aegerita [46], Lentinula edodes [47,48], Auricularia polytricha [49] and Ganoderma lucidum [50].…”