Mutations and Differential Transcription of Mating-Type and Pheromone Receptor Genes in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungi Complex
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Gene and Genome Sequences of H. sinensis Strains and Natural C. sinensis
2.2. Transcriptome and Metatranscriptome Assemblies and Transcripts of the Mating-Type Genes of H. sinensis Strains and Natural C. sinensis
2.3. Sequence Alignment Analysis
2.4. Amino Acid Property and Scale Analyses
3. Results
3.1. Mating-Type Genes and Encoded Proteins in H. sinensis Strains
3.2. Differential Transcription and Alternative Splicing of Mating-Type Genes in the Transcriptome of H. sinensis Strains
3.3. Differential Occurrence of Mating-Type Genes in Natural and Cultivated C. sinensis Insect-Fungi Complexes
3.4. Differential Transcription of Mating-Type Genes in Natural and Cultivated C. sinensis Insect-Fungi Complexes
3.4.1. Transcription of Mating-Type Genes in the Metatranscriptome Assemblies of Natural C. sinensis
3.4.2. Transcription of Mating-Type Genes in Unassembled Metatranscriptome Sequencing Read Archives of Natural and Cultivated C. sinensis
3.5. Variations in Mating Proteins
3.6. Occurrence and Transcription of Pheromone Receptor Genes and Variations in Pheromone Receptor Proteins in H. sinensis and Natural C. sinensis
3.6.1. a-Factor-like Pheromone Receptor in H. sinensis and Natural C. sinensis
3.6.2. α-Factor-like Pheromone Receptor in H. sinensis and Natural C. sinensis
3.7. Other Pheromone-Related Genes in H. sinensis and Natural C. sinensis
4. Discussion
4.1. Reproductive Behavior of H. sinensis, Genotype #1 of O. sinensis
4.2. Sexual Reproduction Strategy during the Lifecycle of Natural C. sinensis
- Li et al. [13] detected GC-biased H. sinensis (Genotype #1) and AT-biased Genotype #5 of O. sinensis in eight of 15 heterogeneous cultures (1206, 1208, 1209, 1214, 1220, 1224, 1227, and 1228) from mono-ascospores of natural C. sinensis, in addition to 7 other cultures that contained homogenous GC-biased H. sinensis (1207, 1218, 1219, 1221, 1222, 1225, and 1229). In addition to the nondisclosure of 9 other possible ascosporic clones (namely, clones 1210, 1211, 1212, 1213, 1215, 1216, 1217, 1223, and 1226), the authors misinterpreted all the AT-biased genotypes as the “ITS pseudogene” components of the H. sinensis genome, whereas AT-biased Genotypes #4, #6, and #15–17 were not detected by Li et al. [13] in the cultures of the mono-ascospores or the sequences of all the AT-biased genotypes residing not in the genomes of the GC-biased H. sinensis strains 1229, CC1406-203, Co18, IOZ07, and ZJB12195 but instead in the genomes of independent O. sinensis fungi [5,6,9,14,15,36,43,44,45,46]. These results suggest the possibility that GC-biased H. sinensis (Genotype #1) and AT-biased Genotype #5 of O. sinensis may become sexual partners to accomplish the sexual reproduction of O. sinensis.
- Zhu et al. [11] demonstrated the co-occurrence of GC-biased Genotypes #1 and #2 of O. sinensis in the stromata of natural C. sinensis during maturation. The ITS sequences of these two genotypes share 94.7% sequence similarity [5,6,15]. The Genotype #2 sequences were located outside the phylogenetic clade of Genotype #1 in the Bayesian trees (cf. Figure 7 of [15] and Figure 2 of [5]) and did not reside in the genome of Genotype #1 H. sinensis [5,15]. The abundances of the two genotypes undergo dynamic alterations in a disproportional, asynchronous manner in the stromata of natural C. sinensis during maturation [5], indicating the genomic independence of the two genotypes as evidence of independent O. sinensis fungi. These results suggest the possibility that GC-biased Genotypes #1 and #2 of O. sinensis may become sexual partners to accomplish the sexual reproduction of O. sinensis.
- Chen et al. [12] reported the detection of the Genotype #1 H. sinensis sequence AJ488255 from the caterpillar body of a natural C. sinensis specimen (#H1023) collected from Qinghai Province in China and the Genotype #7 sequence AJ488254 with multiple transversions and transition point mutations from the stroma of the same specimen [5,6,15]. The GC-biased Genotype #7 sequence is located within the phylogenetic clade of GC-biased Genotype #1 in the Bayesian trees but does not reside in the genome of H. sinensis (GC-biased Genotype #1 of O. sinensis) [5,15]. These results suggest the possibility that GC-biased Genotypes #1 and #7 of O. sinensis may become sexual partners to accomplish the sexual reproduction of O. sinensis.
- The co-occurrence of multiple GC- and AT-biased genotypes of O. sinensis in different combinations has been observed in the stroma, caterpillar body, ascocarps, and ascospores of natural C. sinensis [5,6,9,11,14,15]. The sequences of the O. sinensis genotypes do not reside in the genome of the GC-biased H. sinensis but instead belong to the genomes of independent fungi [5,6,9,11,14,15,36,43,44,45,46]. The abundances of the GC- and AT-biased genotypes of O. sinensis undergo dynamic alterations in a disproportional, asynchronous manner in the caterpillar bodies and stromata of C. sinensis during maturation, with a consistent predominance of the AT-biased genotypes of O. sinensis, not the GC-biased H. sinensis, in the stromata [5,6,11]. These results suggest the possibility that GC-biased H. sinensis (Genotype #1) and one of AT-biased genotypes of O. sinensis may become sexual partners to accomplish the sexual reproduction of O. sinensis.
- Mao et al. [16] identified AT-biased Genotype #4 or #5 of O. sinensis fungi without the co-occurrence of GC-biased H. sinensis in natural C. sinensis specimens collected from geographically remote production areas. They also reported that AT-biased mutant genotypes presented indistinguishable H. sinensis-like morphologic and growth characteristics and were able to form “H”-shaped hyphal crossings and anastomoses during germination, which are related to the sexual reproduction of O. sinensis. Similarly, Kinjo and Zang [7] reported the detection of AT-biased Genotype #4 or #5 of O. sinensis in several natural C. sinensis samples collected from remote production areas and of GC-biased Genotype #1 H. sinensis in other C. sinensis specimens collected from different production areas. These results suggest the possibility that different AT-biased genotypes of O. sinensis may become sexual partners without the participation of GC-biased Genotype #1 H. sinensis to accomplish the sexual reproduction of O. sinensis.
- Hu et al. [36] reported the use of a mixture of two pure H. sinensis strains, Co18 and QH195-240, to inoculate 40 larvae of Hepialidae sp. Fungal inoculation induced death and mummification of the larvae but failed to induce the development of fruiting bodies and ascospores, indicating biological separation of the larval death/mummification process and the fungal fruiting body development process. The authors cited two other studies [61,62] and reported that inoculation of ghost moth larvae of the Hepialidae family with pure H. sinensis consistently failed to produce fruiting bodies and ascospores. Zhang et al. [49] (coauthors of [36]) summarized 40 years of experience in artificial cultivation of C. sinensis and concluded that “it is very difficult in our laboratory to induce development of the C. sinensis fruiting bodies, either on culture medium or on insects.” Our findings presented in this paper provide evidence at the genetic, transcriptional, and protein levels to explain the self-sterility of H. sinensis and the failure of the inoculation experiments using pure cultures of H. sinensis as the sole inoculant.
- Wei et al. [63] reported a species contradiction between anamorphic inoculants (3 strains of the GC-biased Genotype #1 H. sinensis: 130508-KD-2B, 20110514, and H01-20140924-03) and the only teleomorph of the AT-biased Genotype #4 of O. sinensis in the fruiting body of cultivated C. sinensis. In addition, Figure 6 of [63] shows two phylogenetically distinct teleomorphs of O. sinensis: the AT-biased Genotype #4 of O. sinensis in cultivated C. sinensis and the GC-biased Genotype #1 in the natural C. sinensis specimen G3, which was used as the teleomorphic reference in the phylogenetic analysis. Because the sequences of the AT- and GC-biased genotypes of O. sinensis reside in independent genomes of different fungi [5,9,11,36,43,44,45,46], Wei et al. [63] demonstrated two distinct teleomorphs of O. sinensis and questioned the true causal fungus/fungi and anamorph-teleomorph connections of O. sinensis according to Koch’s postulates and the sole anamorph and sole teleomorph hypotheses proposed 10 years ago by the same group of key authors [40]. Under the self-sterility hypothesis for H. sinensis presented in this bioinformatic paper, the AT-biased genotypes of O. sinensis may play a possible hybridization role as the mating partner(s) of the GC-biased H. sinensis if they belong to different fungal species, “even at higher taxonomic levels (genera and family)”.
- Tolypocladium sinense in natural C. sinensis was first identified and reported by Li [17]. It was subsequently isolated from natural C. sinensis and characterized morphologically and genetically [20,21]. Engh [41] reported the molecular identification of the Cordyceps-Tolypocladium complex in natural C. sinensis. The “Cordyceps” sequence AJ786590 obtained by Engh [41] was published and uploaded to GenBank by Stensrud et al. [42] and phylogenetically clustered into AT-biased Group B (Genotype #4) of O. sinensis, along with other C. sinensis sequences, by Stensrud et al. [8]. Barseghyan et al. [24] performed a macro/micromycology study and concluded that H. sinensis, which is presumed to be psychrophilic, and T. sinensis, which is presumed to be mesophilic, are dual anamorphs of O. sinensis. Notably, the O. sinensis fungus, which has H. sinensis-like morphology and growth characteristics, was not genotyped molecularly in that study. According to the self-sterility hypothesis for H. sinensis presented in this bioinformatic paper, the close association of T. sinense with H. sinensis may help mycological physiologists plan future studies to explore the possibility of O. sinensis hybridization reproduction.
- Genotypes #13 (KT339190) and #14 (KT339178) of O. sinensis have been identified in either semiejected or fully ejected multicellular heterokaryotic ascospores, respectively, collected from the same specimen of natural C. sinensis [5,6,15]. The two genotypes feature precise reciprocal substitutions of large DNA segments due to chromosomal intertwining interactions and genetic material recombination between two parental fungi, Genotype #1 H. sinensis (Group A by Stensrud et al. [8]) and an AB067719-type Group E fungus (Table S3) [5,6,15]. A pure culture of the AB067719-type fungus has not been obtained, and its taxonomic position is unclear. More than 900 sequences highly homologous to AB067719, including those of Alternaria sp., Ascomycota sp., Aspergillus sp., Avena sp., Berberis sp., Colletotrichum sp., Cordyceps sp., Cyanonectria sp., Dikarya sp., Fusarium sp., Gibberella sp., Hypocreales sp., Juglans sp., Lachnum sp., Nectria sp., Nectriaceae sp., Neonectria sp., and Penicillium sp., have been uploaded to GenBank [15]. Chromosomal intertwining and genetic material recombination may occur after plasmogamy and karyogamy of heterospecific parental fungi under sexual reproduction hybridization or parasexuality, which is characterized by the prevalence of heterokaryosis and results in concerted chromosome loss for transferring/substituting genetic materials without conventional meiosis [37,75,76,77]. The phenomena of precise vertical transfer and reciprocal substitution of genetic materials between the chromosomes of heterospecific parental fungi that occurred differently between the two types of ascospores collected from the same specimen of natural C. sinensis are distinct from the randomness and arbitrariness of horizontal environmental gene drift.
- P. hepiali was first isolated from natural C. sinensis by Dai et al. [19,20]. A close association between psychrophilic O. sinensis (GC- and AT-biased genotypes) and mesophilic P. hepiali has been found in the caterpillar body, stroma, and stromal fertile portion, which are densely covered with ascocarps and ascospores of natural C. sinensis, and even in the formation of a fungal complex in “pure” H. sinensis strains that were isolated from natural C. sinensis and provided as gifts by a distinguished mycology taxonomist [6,11,15,20,22]. Whether certain strains of these fungal species would select each other as sexual partners will depend on their mating choices for hybridization and their ability to break interspecific isolation barriers to adapt to extremely harsh ecological environments on the Qinghai-Tibet Plateau and the seasonal change from the extremely cold winter when C. sinensis is in its asexual growth phase to the spring and early summer when C. sinensis switches to the sexual reproduction phase [70,71,72,73,74]. According to the self-sterility hypothesis for H. sinensis presented in this bioinformatic paper, P. hepiali may possibly play a hybridization role as the mating partner(s) of the GC- and AT-biased genotypes of O. sinensis.
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Zhu, J.-S.; Halpern, G.M.; Jones, K. The scientific rediscovery of an ancient Chinese herbal medicine: Cordyceps sinensis: Part I. J. Altern. Complement. Med. 1998, 4, 289–303. [Google Scholar] [CrossRef] [PubMed]
- Zhu, J.-S.; Halpern, G.M.; Jones, K. The scientific rediscovery of a precious ancient Chinese herbal regimen: Cordyceps sinensis: Part II. J. Altern. Complement. Med. 1998, 4, 429–457. [Google Scholar] [CrossRef] [PubMed]
- Zhu, J.-S.; Li, C.-L.; Tan, N.-Z.; Berger, J.L.; Prolla, T.A. Combined use of whole-gene expression profiling technology and mouse lifespan test in anti-aging herbal product study. In Proceedings of the 2011 New TCM Products Innovation and Industrial Development Summit, Hangzhou, China, 27 November 2011; pp. 443–448. [Google Scholar]
- Ren, Y.; Wan, D.-G.; Lu, X.-M.; Guo, J.-L. The study of scientific name discussion for TCM Cordyceps. LisShenzhen Med. Mater. Med. Res. 2013, 24, 2211–2212. [Google Scholar]
- Li, Y.-L.; Li, X.-Z.; Yao, Y.-S.; Xie, W.-D.; Zhu, J.-S. Molecular identification of Ophiocordyceps sinensis genotypes and the indiscriminate use of the Latin name for the multiple genotypes and the natural insect-fungi complex. Am. J. Biomed. Sci. 2022, 14, 115–135. [Google Scholar] [CrossRef]
- Zhu, J.-S.; Li, Y.-L. A Precious Transitional Chinese Medicine, Cordyceps sinensis: Multiple Heterogeneous Ophiocordyceps sinensis in the Insect-Fungi Complex; Lambert Academic Publishing: Saarbrüchen, Germany, 2017. [Google Scholar]
- Kinjo, N.; Zang, M. Morphological and phylogenetic studies on Cordyceps sinensis distributed in southwestern China. Mycoscience 2001, 42, 567–574. [Google Scholar] [CrossRef]
- Stensrud, Ø.; Schumacher, T.; Shalchian-Tabrizi, K.; Svegardenib, I.B.; Kauserud, H. Accelerated nrDNA evolution and profound AT bias in the medicinal fungus Cordyceps sinensis. Mycol. Res. 2007, 111, 409–415. [Google Scholar] [CrossRef]
- Xiao, W.; Yang, J.-P.; Zhu, P.; Cheng, K.-D.; He, H.-X.; Zhu, H.-X.; Wang, Q. Non-support of species complex hypothesis of Cordyceps sinensis by targeted rDNA-ITS sequence analysis. Mycosystema 2009, 28, 724–730. [Google Scholar]
- Zhang, Y.-J.; Xu, L.-L.; Zhang, S.; Liu, X.-Z.; An, Z.-Q.; Wàngmŭ; Guo, Y.-L. Genetic diversity of Ophiocordyceps sinensis, a medicinal fungus endemic to the Tibetan Plateau: Implications for its evolution and conservation. BMC Evol. Biol. 2009, 9, 290. [Google Scholar] [CrossRef]
- Zhu, J.-S.; Gao, L.; Li, X.-H.; Yao, Y.-S.; Zhou, Y.-J.; Zhao, J.-Q.; Zhou, Y.-J. Maturational alterations of oppositely orientated rDNA and differential proliferations of CG:AT-biased genotypes of Cordyceps sinensis fungi and Paecilomyces hepiali in natural C. sinensis. Am. J. Biomed. Sci. 2010, 2, 217–238. [Google Scholar] [CrossRef]
- Chen, C.-S.; Hseu, R.-S.; Huang, C.-T. Quality control of Cordyceps sinensis teleomorph, anamorph, and Its products. Chapter 12. In Quality Control of Herbal Medicines and Related Areas; Shoyama, Y., Ed.; InTech: Rijeka, Croatia, 2011; pp. 223–238. Available online: www.intechopen.com (accessed on 2 March 2024).
- Li, Y.; Jiao, L.; Yao, Y.-J. Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis. Mol. Phylogenet. Evol. 2013, 68, 373–379. [Google Scholar] [CrossRef]
- Li, Y.-L.; Gao, L.; Yao, Y.-S.; Wu, Z.-M.; Lou, Z.-Q.; Xie, W.-D.; Wu, J.-Y.; Zhu, J.-S. Altered GC- and AT-biased genotypes of Ophiocordyceps sinensis in the stromal fertile portions and ascospores of natural Cordyceps sinensis. PLoS ONE 2023, 18, e0286865. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.-L.; Li, X.-Z.; Yao, Y.-S.; Wu, Z.-M.; Gao, L.; Tan, N.-Z.; Lou, Z.-Q.; Xie, W.-D.; Wu, J.-Y.; Zhu, J.-S. Differential cooccurrence of multiple genotypes of Ophiocordyceps sinensis in the stromata, stromal fertile portion (ascocarps) and ascospores of natural Cordyceps sinensis. PLoS ONE 2023, 18, e0270776. [Google Scholar] [CrossRef]
- Mao, X.-M.; Zhao, S.-M.; Cao, L.; Yan, X.; Han, R.-C. The morphology observation of Ophiocordyceps sinensis from different origins. J. Environ. Entomol. 2013, 35, 343–353. [Google Scholar]
- Li, C.-L. A study of Tolypocladium sinense C.L. Li. sp. nov. and cyclosporin production. Acta Mycol. Sin. 1988, 7, 93–98. [Google Scholar]
- Li, X.; Wang, F.; Liu, Q.; Li, Q.-P.; Qian, Z.-M.; Zhang, X.-L.; Li, K.; Li, W.-J.; Dong, C.-H. Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes. BMC Genom. 2019, 20, 337. [Google Scholar] [CrossRef]
- Dai, R.-Q.; Lan, J.-L.; Chen, W.-H.; Li, X.-M.; Chen, Q.-T.; Shen, C.-Y. Discovery of a new fungus Paecilomyces hepiali Chen & Dai. Acta Agric. Univ. Pekin. 1989, 15, 221–224. [Google Scholar]
- Jiang, Y.; Yao, Y.-J. A review for the debating studies on the anamorph of Cordyceps sinensis. Mycosistema 2003, 22, 161–176. [Google Scholar]
- Leung, P.-H.; Zhang, Q.-X.; Wu, J.-Y. Mycelium cultivation, chemical composition and antitumour activity of a Tolypocladium sp. fungus isolated from wild Cordyceps sinensis. J. Appl. Microbiol. 2006, 101, 275–283. [Google Scholar] [CrossRef]
- Zhu, J.-S.; Guo, Y.-L.; Yao, Y.-S.; Zhou, Y.-J.; Lu, J.-H.; Qi, Y.; Chen, W.; Zheng, T.-Y.; Zhang, L.; Wu, Z.-M.; et al. Maturation of Cordyceps sinensis associates with co-existence of Hirsutella sinensis and Paecilomyces hepiali DNA and dynamic changes in fungal competitive proliferation predominance and chemical profiles. J. Fungal Res. 2007, 5, 214–224. [Google Scholar]
- Zhang, Y.-J.; Sun, B.-D.; Zhang, S.; Wàngmŭ; Liu, X.-Z.; Gong, W.-F. Mycobiotal investigation of natural Ophiocordyceps sinensis based on culture-dependent investigation. Mycosistema 2010, 29, 518–527. [Google Scholar]
- Barseghyan, G.S.; Holliday, J.C.; Price, T.C.; Madison, L.M.; Wasser, S.P. Growth and cultural-morphological characteristics of vegetative mycelia of medicinal caterpillar fungus Ophiocordyceps sinensis G.H. Sung et al. (Ascomycetes) Isolates from Tibetan Plateau (P.R.China). Int. J. Med. Mushrooms 2011, 13, 565–581. [Google Scholar] [CrossRef]
- Xia, F.; Liu, Y.; Shen, G.-L.; Guo, L.-X.; Zhou, X.-W. Investigation and analysis of microbiological communities in natural Ophiocordyceps sinensis. Can. J. Microbiol. 2015, 61, 104–111. [Google Scholar] [CrossRef]
- Wang, J.B.; St. Leger, R.J.; Wang, C. Advances in Genomics of Entomopathogenic Fungi. Adv. Genet. 2016, 94, 67–105. [Google Scholar] [CrossRef]
- Meng, Q.; Yu, H.-Y.; Zhang, H.; Zhu, W.; Wang, M.-L.; Zhang, J.-H.; Zhou, G.-L.; Li, X.; Qin, Q.-L.; Hu, S.-N.; et al. Transcriptomic insight into the immune defenses in the ghost moth, Hepialus xiaojinensis, during an Ophiocordyceps sinensis fungal infection. Insect Biochem. Mol. Biol. 2015, 64, 1–15. [Google Scholar] [CrossRef]
- Lu, H.-L.; St. Leger, R.J. Chapter Seven—Insect Immunity to Entomopathogenic Fungi. In Advances in Genetics; Lovett, B., St. Leger, R.J., Eds.; Academic Press: Cambridge, MA, USA, 2016; Volume 94, pp. 251–285. [Google Scholar]
- Wang, Y.; Stata, M.; Wang, W.; Stajich, J.E.; White, M.M.; Moncalvo, J.M. Comparative genomics reveals the core gene toolbox for the fungus-insect symbiosis. mBio 2018, 9, e00636-18. [Google Scholar] [CrossRef]
- Sung, G.-H.; Hywel-Jones, N.L.; Sung, J.-M.; Luangsa-ard, J.J.; Shrestha, B.; Spatafora, J.W. Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud. Mycol. 2007, 57, 5–59. [Google Scholar] [CrossRef]
- Zhang, Y.-J.; Li, E.-W.; Wang, C.-S.; Li, Y.-L.; Liu, X.-Z. Ophiocordyceps sinensis, the flagship fungus of China: Terminology, life strategy and ecology. Mycology 2012, 3, 2–10. [Google Scholar] [CrossRef]
- Debuchy, R.; Turgeo, B.G. Mating-Type Structure, Evolution, and Function in Euascomycetes. In Growth, Differentiation and Sexuality; Kües, U., Fischer, R., Eds.; Springer: Berlin/Heidelberg, Germany, 2006; pp. 293–323. [Google Scholar]
- Jones, S.K.; Bennett, R.J. Fungal mating pheromones: Choreographing the dating game. Fungal Genet. Biol. 2011, 48, 668–676. [Google Scholar] [CrossRef]
- Zheng, P.; Wang, C.-S. Sexuality Control and Sex Evolution in Fungi. Sci. Sin. Vitae 2013, 43, 1090–1097. [Google Scholar]
- Wilson, A.M.; Wilken, P.M.; van der Nest, M.A.; Steenkamp, E.T.; Wingfield, M.J.; Wingfield, B.D. Homothallism: An umbrella term for describing diverse sexual behaviours. IMA Fungus 2015, 6, 207–214. [Google Scholar] [CrossRef]
- Hu, X.; Zhang, Y.-J.; Xiao, G.-H.; Zheng, P.; Xia, Y.-L.; Zhang, X.-Y.; St Leger, R.J.; Liu, X.-Z.; Wang, C.-S. Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus. Chin. Sci. Bull. 2013, 58, 2846–2854. [Google Scholar] [CrossRef]
- Bushley, K.E.; Li, Y.; Wang, W.-J.; Wang, X.-L.; Jiao, L.; Spatafora, J.W.; Yao, Y.-J. Isolation of the MAT1-1 mating type idiomorph and evidence for selfing in the Chinese medicinal fungus Ophiocordyceps sinensis. Fungal Biol. 2013, 117, 599–610. [Google Scholar] [CrossRef]
- Zhang, S.; Zhang, Y.-J.; Liu, X.-Z.; Wen, H.-A.; Wàngmŭ; Liu, D.-S. Cloning and analysis of the MAT1-2-1 gene from the traditional Chinese medicinal fungus Ophiocordyceps sinensis. Fungal Biol. 2011, 115, 708–714. [Google Scholar] [CrossRef]
- Zhang, S.; Zhang, Y.-J. Molecular evolution of three protein-coding genes in the Chinese caterpillar fungus Ophiocordyceps sinensis. Microbiol. China 2015, 42, 1549–1560. [Google Scholar]
- Wei, X.-L.; Yin, X.-C.; Guo, Y.-L.; Shen, N.-Y.; Wei, J.-C. Analyses of molecular systematics on Cordyceps sinensis and its related taxa. Mycosystema 2006, 25, 192–202. [Google Scholar]
- Engh, I.B. Molecular Phylogeny of the Cordyceps-Tolypocladium Complex. Candidate. Scientific Thesis, Department of Biology, University of Oslo, Oslo, Norway, 1999. [Google Scholar]
- Stensrud, Ø.; Hywel-Jones, N.L.; Schumacher, T. Towards a phylogenetic classification of Cordyceps: ITS nrDNA sequence data confirm divergent lineages and paraphyly. Mycol. Res. 2005, 109, 41–56. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.; Hsiang, T.; Yang, R.-H.; Hu, X.-D.; Wang, K.; Wang, W.-J.; Wang, X.-L.; Jiao, L.; Yao, Y.-J. Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis. J. Microbiol. Methods 2016, 128, 1–6. [Google Scholar] [CrossRef] [PubMed]
- Jin, L.-Q.; Xu, Z.-W.; Zhang, B.; Yi, M.; Weng, C.-Y.; Lin, S.; Wu, H.; Qin, X.-T.; Xu, F.; Teng, Y.; et al. Genome sequencing and analysis of fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis. AMB Express 2020, 10, 105. [Google Scholar] [CrossRef]
- Liu, J.; Guo, L.-N.; Li, Z.-W.; Zhou, Z.; Li, Z.; Li, Q.; Bo, X.-C.; Wang, S.-Q.; Wang, J.-L.; Ma, S.-C.; et al. Genomic analyses reveal evolutionary and geologic context for the plateau fungus Ophiocordyceps sinensis. Clin. Med. 2020, 15, 107–119. [Google Scholar] [CrossRef]
- Shu, R.-H.; Zhang, J.-H.; Meng, Q.; Zhang, H.; Zhou, G.-L.; Li, M.-M.; Wu, P.-P.; Zhao, Y.-N.; Chen, C.; Qin, Q.-L. A new high-quality draft genome assembly of the Chinese cordyceps Ophiocordyceps sinensis. Genome Biol. Evol. 2020, 12, 1074–1079. [Google Scholar] [CrossRef]
- Li, X.-Z.; Li, Y.-L.; Yao, Y.-S.; Xie, W.-D.; Zhu, J.-S. Further discussion with Li et al. (2013, 2019) regarding the “ITS pseudogene hypothesis” for Ophiocordyceps sinensis. Mol. Phylogenet. Evol. 2020, 146, 106728. [Google Scholar] [CrossRef] [PubMed]
- Li, X.-Z.; Li, Y.-L.; Zhu, J.-S. Differential transcription of mating-type genes during sexual reproduction of natural Cordyceps sinensis. Chin. J. Chin. Mater. Med. 2023, 48, 2829–2840. [Google Scholar] [CrossRef]
- Zhang, S.; Zhang, Y.-J.; Shrestha, B.; Xu, J.-P.; Wang, C.-S.; Liu, X.-Z. Ophiocordyceps sinensis and Cordyceps militaris: Research advances, issues and perspectives. Mycosystema 2013, 32, 577–597. [Google Scholar]
- Yao, Y.-S.; Gao, L.; Li, Y.-L.; Ma, S.-L.; Wu, Z.-M.; Tan, N.-Z.; Wu, J.-Y.; Ni, L.-Q.; Zhu, J.-S. Amplicon density-weighted algorithms for analyzing dissimilarity and dynamic alterations of RAPD polymorphisms of Cordyceps sinensis. Beijing Da Xue Xue Bao Yi Xue Bao 2014, 46, 618–628. [Google Scholar]
- Liang, Z.-Q.; Han, Y.-F.; Liang, J.-D.; Dong, X.; Du, W. Issues of concern in the studies of Ophiocordyceps sinensis. Microbiol. Chin. 2010, 37, 1692–1697. [Google Scholar]
- Liu, Z.-Q.; Lin, S.; Baker, P.J.; Wu, L.-F.; Wang, X.-R.; Wu, H.; Xu, F.; Wang, H.-Y.; Brathwaite, M.E.; Zheng, Y.-G. Transcriptome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis. BMC Genom. 2015, 16, 106–123. [Google Scholar] [CrossRef]
- Xiang, L.; Li, Y.; Zhu, Y.; Luo, H.; Li, C.; Xu, X.; Sun, C.; Song, J.-Y.; Shi, L.-H.; He, L.; et al. Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis. Genomics 2014, 103, 154–159. [Google Scholar] [CrossRef]
- Xia, E.-H.; Yang, D.-R.; Jiang, J.-J.; Zhang, Q.-J.; Liu, Y.; Liu, Y.-L.; Zhang, Y.; Zhang, H.-B.; Shi, C.; Tong, Y.; et al. The caterpillar fungus, Ophiocordyceps sinensis, genome provides insights into highland adaptation of fungal pathogenicity. Sci. Rep. 2017, 7, 1806. [Google Scholar] [CrossRef] [PubMed]
- Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644–652. [Google Scholar] [CrossRef] [PubMed]
- Chou, P.Y.; Fasman, G.D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. Relat. Areas. Mol. Biol. 1978, 47, 45–148. [Google Scholar] [CrossRef]
- Deleage, G.; Roux, B. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng. Des. Sel. 1987, 1, 289–294. [Google Scholar] [CrossRef]
- Nakamura, N.; Tanaka, C.; Takeuchi-Kaneko, Y. Transmission of antibiotic-resistance markers by hyphal fusion suggests partial presence of parasexuality in the root endophytic fungus Glutinomyces brunneus. Mycol. Prog. 2019, 18, 453–462. [Google Scholar] [CrossRef]
- Zhang, Y.-J.; Zhang, S.; Li, Y.-L.; Ma, S.-L.; Wang, C.-S.; Xiang, M.-C.; Liu, X.; An, Z.-Q.; Xu, J.-P.; Liu, X.-Z. Phylogeography and evolution of a fungal–insect association on the Tibetan Plateau. Mol. Ecol. 2014, 23, 5337–5355. [Google Scholar] [CrossRef] [PubMed]
- Turgeon, B.G.; Yoder, O.C. Proposed nomenclature for mating type genes of filamentous ascomycetes. Fungal Genet. Biol. 2000, 31, 1–5. [Google Scholar] [CrossRef] [PubMed]
- Holliday, J.; Cleaver, M. Medicinal value of the caterpillar fungi species of the genus Cordyceps (Fr.) Link (Ascomycetes). A review. Int. J. Med. Mushrooms 2008, 10, 219–234. [Google Scholar] [CrossRef]
- Stone, R. Improbable partners aim to bring biotechnology to a Himalayan kingdom. Science 2010, 327, 940–941. [Google Scholar] [CrossRef] [PubMed]
- Wei, J.-C.; Wei, X.-L.; Zheng, W.-F.; Guo, W.; Liu, R.-D. Species identification and component detection of Ophiocordyceps sinensis cultivated by modern industry. Mycosystema 2016, 35, 404–410. [Google Scholar]
- Zhang, S.-W.; Cen, K.; Liu, Y.; Zhou, X.-W.; Wang, C.-S. Metatranscriptomics analysis of the fruiting caterpillar fungus collected from the Qinghai-Tibetan plateau. Sci. Sin. Vitae 2018, 48, 562–570. [Google Scholar]
- Zhong, X.; Gu, L.; Wang, H.-Z.; Lian, D.-H.; Zheng, Y.-M.; Zhou, S.; Zhou, W.; Gu, J.; Zhang, G.; Liu, X. Profile of Ophiocordyceps sinensis transcriptome and differentially expressed genes in three different mycelia, sclerotium and fruiting body developmental stages. Fungal Biol. 2018, 122, 943–951. [Google Scholar] [CrossRef]
- Zhao, Y.-N.; Zhang, J.-H.; Meng, Q.; Zhang, H.; Zhou, G.-L.; Li, M.-M.; Wu, P.-P.; Shu, R.-H.; Gao, X.-X.; Guo, L.; et al. Transcriptomic analysis of the orchestrated molecular mechanisms underlying fruiting body initiation in Chinese cordyceps. Gene 2020, 763, 145061. [Google Scholar] [CrossRef]
- Yang, J.-Y.; Tong, X.-X.; He, C.-Y.; Bai, J.; Wang, F.; Guo, J.-L. Comparison of endogenetic microbial community diversity between wild Cordyceps sinensis, artificial C. sinensis and habitat soil. Chin. J. Chin. Mater. Med. 2021, 46, 3106–3115. [Google Scholar]
- Peters, C.; Elofsson, A. Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? Proteins 2014, 82, 2190–2198. [Google Scholar] [CrossRef] [PubMed]
- Simm, S.; Einloft, J.; Mirus, O.; Schleiff, E. 50 years of amino acid hydrophobicity scales: Revisiting the capacity for peptide classification. Biol. Res. 2016, 49, 31. [Google Scholar] [CrossRef]
- Pfennig, K.S. Facultative Mate Choice Drives Adaptive Hybridization. Science 2007, 318, 965–967. [Google Scholar] [CrossRef] [PubMed]
- Du, X.-H.; Wu, D.-M.; Kang, H.; Wang, H.-C.; Xu, N.; Li, T.-T.; Chen, K.-L. Heterothallism and potential hybridization events inferred for twenty-two yellow morel species. IMA Fungus 2020, 11, 4. [Google Scholar] [CrossRef]
- Hėnault, M.; Marsit, S.; Charron, G.; Landry, C.R. The effect of hybridization on transposable element accumulation in an undomesticated fungal species. eLife 2020, 9, e60474. [Google Scholar] [CrossRef]
- Samarasinghe, H.; You, M.; Jenkinson, T.S.; Xu, J.-P.; James, T.Y. Hybridization Facilitates Adaptive Evolution in Two Major Fungal Pathogens. Genes 2020, 11, 101. [Google Scholar] [CrossRef]
- Steensels, J.; Gallone, B.; Verstrepen, K.J. Interspecific hybridization as a driver of fungal evolution and Adaptation. Nat. Rev. Microbiol. 2021, 19, 485–500. [Google Scholar] [CrossRef]
- Bennett, R.J.; Johnson, A.D. Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains. EMBO J. 2003, 22, 2505–2515. [Google Scholar] [CrossRef]
- Sherwood, R.K.; Bennett, R.J. Fungal meiosis and parasexual reproduction--lessons from pathogenic yeast. Curr. Opin. Microbiol. 2009, 12, 599–607. [Google Scholar] [CrossRef]
- Seervai, R.N.H.; Jones, S.K.; Hirakawa, M.P.; Porman, A.M.; Bennett, R.J. Parasexuality and ploidy change in Candida tropicalis. Eukaryot. Cell 2013, 12, 1629–1640. [Google Scholar] [CrossRef] [PubMed]
GenBank Accession | H. sinensis Strain | Sequencing Method | Assembly Method | Ref. |
---|---|---|---|---|
ANOV00000000 | Co18 | Roche 454 GS FLX system (Illumina HiSeq: 454) | SOAPdenovo v.1.05 and Newbler v.2.3 | [36] |
JAAVMX000000000 | IOZ07 | PacBio Sequel sequencing technology | Canu v.1.7 | [46] |
LKHE00000000 | 1229 | Illumina HiSeq sequencing technology | ABySS v.1.2.3 | [43] |
LWBQ00000000 | ZJB12195 | Illumina sequencing technology (HiSeq 2000 Sequencing System) | SOAPdenovo v.2.0 | [44] |
NGJJ00000000 | CC1406-20395 | Hierarchical Genome Assembly Process (HGAP) workflow (PacBioDevNet; Pacific Biosciences) | CA software (v.7.0) and the PacBio Rs_PreAssembler.1 module | [45] |
GCQL00000000 | L0106 | Illumina HiSeq sequencing technology | SOAPdenovo v.2.0 | [52] |
GAGW00000000 | Natural C. sinensis (Kangding, Sichuan, China) | 454 technology | GS De Novo Assembler software v 2.6 or Newbler 2.6 | [53] |
(Metatranscriptome sequence not uploaded in GenBank) | Natural C. sinensis (Deqin, Yunnan, China) | Illumina HiSeq2000 platform | Trinity (version r20140717) | [54] |
MAT1-1-1 | MAT1-1-2 | MAT1-1-3 | MAT1-2-1 | |
---|---|---|---|---|
(vs. KC437356 of Strain CS68-2-1229) | (vs. JQ325153 of Strain GS09_121) | |||
% similarity of the genome sequences | ||||
H. sinensis strain 1229 | 100% | 100% | 100% | 99.9% |
H. sinensis strain Co18 | 99.9% | 100% | 100% | 99.7% |
H. sinensis strain IOZ07 | 100% | 100% | 100% | ― |
H. sinensis strain CC1406-203 | ― | ― | ― | 99.9% |
H. sinensis strain ZJB12195 | ― | ― | ― | 99.9% |
% similarity of the coding sequences of the genes (excluding introns) and the transcriptome sequences | ||||
H. sinensis strain L0106 | ― | ― | ― | 99.0% |
H. sinensis strain 1229 | 100% | 100% | 100% | 100% |
Natural C. sinensis (Deqin, Yunnan) | 100% | ― | ― | 100% |
Natural C. sinensis (Kangding, Sichuan) | 100% | ― | ― | ― |
% Amino Acids of Mating-Type Protein | |||||
---|---|---|---|---|---|
Hydrophobic | Acidic | Basic | Neutral | ||
MAT1-1-1 protein | |||||
AGW27560 | H. sinensis strain CS68-2-1229 | 41.4% | 13.2% | 11.0% | 34.4% |
GAGW01008880 | Natural C. sinensis | 41.3% | 14.1% | 9.8% | 34.8% |
OSIN7648 | Natural C. sinensis | 41.9% | 13.1% | 11.1% | 33.7% |
MAT1-2-1 protein | |||||
AFX66389 | H. sinensis strain GS09_121 | 41.2% | 10.0% | 16.5% | 33.3% |
OSIN7649 | Natural C. sinensis | 41.2% | 10.0% | 16.5% | 33.3% |
Percent Similarity | ||
---|---|---|
a-Factor-like Pheromone Receptor | α-Factor-like Pheromone Receptor | |
Between the sequences of pheromone receptor genes and the H. sinensis genomes | ||
H. sinensis strain 1229 | 100% | 99.8% |
H. sinensis strain CC1406-203 | 100% | 99.8% |
H. sinensis strain Co18 | 100% | 100% |
H. sinensis strain IOZ07 | 100% | 99.9% |
H. sinensis strain ZJB12195 | 95.2% | 97.5% |
Between the coding sequences of the pheromone receptor genes (excluding introns) and the transcriptome sequences of H. sinensis and natural C. sinensis | ||
H. sinensis strain L0106 | ― | 99.3% |
Natural C. sinensis (Deqin, Yunnan) | 100% | 99.7% |
Natural C. sinensis (Kangding, Sichuan) | 98.5–100% | ― |
Between the pheromone receptor protein sequences translated from the gene sequences and the transcript sequences of H. sinensis and natural C. sinensis | ||
H. sinensis strain L0106 | ― | 86.4–100% |
Natural C. sinensis (Deqin, Yunnan) | 100% | 82.9% |
Natural C. sinensis (Kangding, Sichuan) | 97.8–100% | ― |
% Amino Acids of Pheromone Receptor Proteins | |||||
---|---|---|---|---|---|
Hydrophobic | Acidic | Basic | Neutral | ||
a-pheromone receptor protein | |||||
EQK97482 | H. sinensis strain Co18 | 50.7% | 6.5% | 11.6% | 31.4% |
GAGW01004735-GAGW01004736 | Natural C. sinensis | 50.4% | 6.2% | 11.2% | 31.2% |
OSIN6252 | Natural C. sinensis | 50.7% | 6.5% | 11.6% | 31.4% |
α-pheromone receptor protein | |||||
EQK99119 | H. sinensis strain Co18 | 55.1% | 5.6% | 7.4% | 31.8% |
GCQL01017756 | H. sinensis strain L0106 | 50.8% | 6.0% | 9.0% | 34.2% |
GCQL01015779 | H. sinensis strain L0106 | 51.8% | 6.0% | 9.0% | 33.2% |
OSIN6424 | Natural C. sinensis | 52.7% | 5.8% | 8.6% | 32.8% |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Li, X.-Z.; Xiao, M.-J.; Li, Y.-L.; Gao, L.; Zhu, J.-S. Mutations and Differential Transcription of Mating-Type and Pheromone Receptor Genes in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungi Complex. Biology 2024, 13, 632. https://doi.org/10.3390/biology13080632
Li X-Z, Xiao M-J, Li Y-L, Gao L, Zhu J-S. Mutations and Differential Transcription of Mating-Type and Pheromone Receptor Genes in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungi Complex. Biology. 2024; 13(8):632. https://doi.org/10.3390/biology13080632
Chicago/Turabian StyleLi, Xiu-Zhang, Meng-Jun Xiao, Yu-Ling Li, Ling Gao, and Jia-Shi Zhu. 2024. "Mutations and Differential Transcription of Mating-Type and Pheromone Receptor Genes in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungi Complex" Biology 13, no. 8: 632. https://doi.org/10.3390/biology13080632