Background: Ophiocordyceps sinensis, which is only naturally found in the high-elevation extreme environment of the Tibetan Plateau, has been used in traditional Chinese medicine. Information concerning the evolutionary and geologic context of O. sinensis remains limited, however. Methods: We constructed the high-quality genome of O. sinensis and provided insight into the evolution and ecology of O. sinensis using comparative genomics. Results: We mapped the whole genome of the anamorph/asexual form Hirsutella of O. sinensis using Illumina and PacBio sequencing technologies and obtained a well assembled genome of 119.2 Mbp size. Long-read Single Molecule Real Time (SMRT) sequencing technology generated an assembly with more accurate representation of repeat sequence abundances and placement. Evolutionary analyses indicated that O. sinensis diverged from other fungi 65.9 Mya in the Upper Cretaceous, during the uplift of the Tibetan Plateau. Gene family expansions and contractions in addition to genome inflation via long terminal repeat (LTR) retrotransposon insertions were implicated as an important driver of O. sinensis divergence. The insertion rate of LTR sequences into the O. sinensis genome peaked ~ 30–40 Mya, when the Tibetan Plateau rose rapidly. Gene Ontology (GO) enrichment analysis suggested that O. sinensis contained more genes related to ice binding compared to other closely related fungi, which may aid in their adaptability to the cold Tibetan Plateau. Further, heavy metal resistance genes were in low abundance in the O. sinensis genome, which may help to explain previous observations that O. sinensis tissues contain high levels of heavy metals. Conclusions: Our results reveal the evolutionary, geological, and ecological context for the evolution of the O. sinensis genome and the factors that have contributed to the environmental adaptability of this valuable fungus. These findings suggest that genome inflation via LTR retrotransposon insertions in O. sinensis coincided with the uplift of the Tibetan Plateau. LTRs and the specific genetic mechanisms of O. sinensis contributed to its adaptation to the environment on the plateau.

Traditional Chinese medicine is characterized by numerous chemical constituents, complex components, and unpredictable interactions among constituents. Therefore, a single analytical technique is usually unable to obtain comprehensive chemical information. Data fusion is an information processing technology that can improve the accuracy of test results by fusing data from multiple devices, which has a broad application prospect by utilizing chemometrics methods, adopting low-level, mid-level, and high-level data fusion techniques, and establishing final classification or prediction models. This paper summarizes the current status of the application of data fusion strategies based on spectroscopy, mass spectrometry, chromatography, and sensor technologies in traditional Chinese medicine (TCM) in light of the latest research progress of data fusion technology at home and abroad. It also gives an outlook on the development of data fusion technology in TCM analysis to provide references for the research and development of TCM.

The material basis of Cordyceps sinensis (Berk.) Sacc has not yet been well understood and natural C. sinensis resources are very rare. The present study aimed to clarify the substance basis and compare the protective effect of natural and artificially-cultivated C. sinensis against cyclophosphamide (CTX)-induced myelosuppression. Both natural and artificially-cultivated C. sinensis effectively improved CTX-induced decrease of peripheral blood counts and hemopoietic growth factors, pathological changes, and apoptosis of bone marrow. Importantly, artificially-cultivated C. sinensis showed similar capacity compared with natural C. sinensis. Uridine (1), adenosine (2), L-pyroglutamic acid (3), lysinonorleucine (4), 1,3,5-trimethoxybenzene (5), D-mannitol (6), L-pyroglutamic acid methyl ester (7), tryptophan (8), and phenylalanine (9) were isolated from bioactivity-guided fraction and identified to attenuate CTX-induced myelosuppression in mice. In conclusions, nucleosides and amino acids represented the effective chemical components in C. sinensis. Artificial cultivation can be used as an effective substitute for natural C. sinensis. Graphical Abstract