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Naidu G, Tripathi DK, Nagar N, Mishra A, Poluri KM. Targeting chemokine-receptor mediated molecular signaling by ethnopharmacological approaches. JOURNAL OF ETHNOPHARMACOLOGY 2024; 325:117837. [PMID: 38310985 DOI: 10.1016/j.jep.2024.117837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/07/2023] [Accepted: 01/26/2024] [Indexed: 02/06/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Infection and inflammation are critical to global human health status and the goal of current pharmacological interventions intends formulating medications/preventives as a measure to deal with this situation. Chemokines and their cognate receptors are major regulatory molecules in many of these ailments. Natural products have been a keen source to the drug development industry, every year contributing significantly to the growing list of FDA approved drugs. A multiverse of natural resource is employed as a part of curative regimen in folk/traditional/ethnomedicine which can be employed to discover, repurpose, and design potent medications for the diseases of clinical concern. AIM OF THE STUDY This review aims to systematically document the ethnopharmacologically active agents targeting the infectious-inflammatory diseases through the chemokine-receptor nexus. MATERIALS AND METHODS Articles related to chemokine/receptor modulating ethnopharmacological anti-inflammatory, anti-infectious natural sources, bioactive compounds, and formulations have been examined with special emphasis on women related diseases. The available literature has been thoroughly scrutinized for the application of traditional medicines in chemokine associated experimental methods, their regulatory outcomes, and pertinence to women's health wherever applicable. Moreover, the potential traditional regimens under clinical trials have been critically assessed. RESULTS A systematic and comprehensive review on the chemokine-receptor targeting ethnopharmaceutics from the available literature has been provided. The article discusses the implication of traditional medicine in the chemokine system dynamics in diverse infectious-inflammatory disorders such as cardiovascular diseases, allergic diseases, inflammatory diseases, neuroinflammation, and cancer. On this note, critical evaluation of the available data surfaced multiple diseases prevalent in women such as osteoporosis, rheumatoid arthritis, breast cancer, cervical cancer and urinary tract infection. Currently there is no available literature highlighting chemokine-receptor targeting using traditional medicinal approach from women's health perspective. Moreover, despite being potent in vitro and in vivo setups there remains a gap in clinical translation of these formulations, which needs to be strategically and scientifically addressed to pave the way for their successful industrial translation. CONCLUSIONS The review provides an optimistic global perspective towards the applicability of ethnopharmacology in chemokine-receptor regulated infectious and inflammatory diseases with special emphasis on ailments prevalent in women, consecutively addressing their current status of clinical translation and future directions.
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Affiliation(s)
- Goutami Naidu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
| | - Deepak Kumar Tripathi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, 342011, Rajasthan, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India.
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Li X, Wang F, Liu Q, Li Q, Qian Z, Zhang X, Li K, Li W, Dong C. Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes. BMC Genomics 2019; 20:337. [PMID: 31054562 PMCID: PMC6500587 DOI: 10.1186/s12864-019-5708-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese cordyceps, also known as Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis), is of particular interest for its cryptic life cycle and economic and ecological importance. The large-scale artificial cultivation was succeeded recently after several decades of efforts and attempts. However, the induction of primordium, sexual development of O. sinensis and the molecular basis of its lifestyle still remain cryptic. RESULTS The developmental transcriptomes were analyzed for six stages covering the whole developmental process, including hyphae (HY), sclerotium (ST), primordium (PR), young fruiting body (YF), developed fruiting body (DF) and mature fruiting body (MF), with a focus on the expression of sexual development-related genes. Principal component analysis revealed that the gene expression profiles at the stages of primordium formation and fruiting body development are more similar than those of the undifferentiated HY stage. The PR and MF stages grouped together, suggesting that primordium differentiation and sexual maturation have similar expression patterns. Many more DEGs were identified between the ST and HY stages, covering 47.5% of the O. sinensis genome, followed by the comparisons between the ST and PR stages. Using pairwise comparisons and weighted gene coexpression network analysis, modules of coexpressed genes and candidate hub genes for each developmental stage were identified. The four mating type loci genes expressed during primordium differentiation and sexual maturation; however, spatiotemporal specificity of gene expression indicated that they also expressed during the anamorphic HY stage. The four mating type genes were not coordinately expressed, suggesting they may have divergent roles. The expression of the four mating type genes was highest in the fertile part and lowest in the sclerotium of the MF stage, indicating that there is tissue specificity. Half of genes related to mating signaling showed as the highest expression in the ST stage, indicating fruiting was initiated in the ST stage. CONCLUSIONS These results provide a new perspective to understanding of the key pathways and hub genes, and sexual development-related gene profile in the development of Chinese cordyceps. It will be helpful for underlying sexual reproduction, and add new information to existing models of fruiting body development in edible fungi.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Fen Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Quanping Li
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Zhengming Qian
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
| | - Wenjia Li
- Key Laboratory of State Administration of Traditional Chinese Medicine, Sunshine Lake Pharma Co., LTD, Dongguan, 523850 Guangdong China
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO. 3 Park 1, Beichen West Road, Chaoyang District, Beijing, 100101 China
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Zou J, Zeng TT, He ZM, Zhang P, Chen ZH. Cloning and analysis of Ophiocordyceps xuefengensis mating type (MAT) loci. FEMS Microbiol Lett 2019; 366:5437676. [PMID: 31062026 DOI: 10.1093/femsle/fnz070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/06/2019] [Indexed: 11/12/2022] Open
Abstract
The entomopathogenic fungus Ophiocordyceps xuefengensis, a recently described species and identified as the sister taxon of Ophiocordyceps sinensis, is a desirable alternative to O. sinensis. The mating systems of fungi play a vitally important role in the regulation of sexual reproduction and evolution, but the mating type loci of O. xuefengensis were completely unknown. In this study, the mating systems of O. xuefengensis were analyzed. The conserved α-box region of the MAT1-1-1 and HMG-box of MAT1-2-1 were successfully obtained by PCR amplification. The distribution of both mating types in different tissues of wild and cultivated O. xuefengensis growth was detected and analyzed. The results showed that the asci always harbored both mating types, whereas the sclerotium, the stipe and each isolated strain of wild O. xuefengensis always had only one idiomorph, either MAT1-1 or MAT1-2, which confirmed that O. xuefengensis is heterothallic. The MAT1-1 locus of O. xuefengensis harbors MAT1-1-1, MAT1-1-2 and MAT1-1-3, and MAT1-2 contains the MAT1-2-1 gene. Southern blot analysis showed the MAT-1-1-1 and MAT-1-2-1 genes were single-copy in O. xuefengensis. These results will help to understand its life cycle and support artificial cultivation of O. xuefengensis.
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Affiliation(s)
- Juan Zou
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China.,Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua 418000, China
| | - Ting-Ting Zeng
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zheng-Mi He
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Ping Zhang
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zuo-Hong Chen
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, College of Life Science, Hunan Normal University, Changsha 410081, China
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Li X, Liu Q, Li W, Li Q, Qian Z, Liu X, Dong C. A breakthrough in the artificial cultivation of Chinese cordyceps on a large-scale and its impact on science, the economy, and industry. Crit Rev Biotechnol 2018; 39:181-191. [PMID: 30394122 DOI: 10.1080/07388551.2018.1531820] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chinese cordyceps, an entity of the Chinese caterpillar fungus (Ophiocordyceps sinensis, syn. Cordyceps sinensis) that parasitizes ghost moth larvae, is one of the best known traditional Chinese medicines and is found exclusively on the Tibetan Plateau with limited natural resources. Although the fungus O. sinensis can grow on artificial substrates and the ghost moth has been successfully reared, the large-scale artificial cultivation of Chinese cordyceps has only recently been accomplished after several decades of efforts and attempts. In this article, research progress related to this breakthrough from living habitats, the life history of the fungus, its host insect, fungal isolation and culture, host larvae rearing, infection cycle of the fungus to the host, primordium induction, and fruiting body development have been reviewed. An understanding of the basic biology of O. sinensis, its host insect and the simulation of the Tibetan alpine environment resulted in the success of artificial cultivation on a large scale. Practical workshop production has reached annual yields of 2.5, 5, and 10 tons in 2014, 2015, and 2016, respectively. There was no difference in the chemical components detected between the cultivated and natural Chinese cordyceps. However, the artificial cultivation system can be controlled to avoid heavy metal contamination and results in high-quality products. Although omics studies, including genomic, transcriptomic, proteomic, and metabolomic studies, have helped to understand the biology of the fungus, the success of the artificial cultivation of the Chinese cordyceps is clearly a milestone and provides the possibility for research on the in-depth mechanisms of the interaction between the fungus and host insects and their adaptation to the harsh habitats. This cultivation will not only result in a large industry to alleviate the pressure of human demand but also protect the limited natural resources for sustainable utilization.
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Affiliation(s)
- Xiao Li
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Qing Liu
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Wenjia Li
- c Key Laboratory of State Administration of Traditional Chinese Medicine , Sunshine Lake Pharma Co., LTD , Dongguan , China
| | - Quanping Li
- c Key Laboratory of State Administration of Traditional Chinese Medicine , Sunshine Lake Pharma Co., LTD , Dongguan , China
| | - Zhengming Qian
- c Key Laboratory of State Administration of Traditional Chinese Medicine , Sunshine Lake Pharma Co., LTD , Dongguan , China
| | - Xingzhong Liu
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Caihong Dong
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing , China
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5
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Zhong X, Gu L, Wang H, Lian D, Zheng Y, 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. [DOI: 10.1016/j.funbio.2018.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/03/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
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The caterpillar fungus, Ophiocordyceps sinensis, genome provides insights into highland adaptation of fungal pathogenicity. Sci Rep 2017; 7:1806. [PMID: 28496210 PMCID: PMC5432009 DOI: 10.1038/s41598-017-01869-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/31/2017] [Indexed: 12/21/2022] Open
Abstract
To understand the potential genetic basis of highland adaptation of fungal pathogenicity, we present here the ~116 Mb de novo assembled high-quality genome of Ophiocordyceps sinensis endemic to the Qinghai-Tibetan Plateau. Compared with other plain-dwelling fungi, we find about 3.4-fold inflation of the O. sinensis genome due to a rapid amplification of long terminal repeat retrotransposons that occurred ~38 million years ago in concert with the uplift of the plateau. We also observe massive removal of thousands of genes related to the transport process and energy metabolism. O. sinensis displays considerable lineage-specific expansion of gene families functionally enriched in the adaptability of low-temperature of cold tolerance, fungal pathogenicity and specialized host infection. We detect signals of positive selection for genes involved in peroxidase and hypoxia to enable its highland adaptation. Resequencing and analyzing 31 whole genomes of O. sinensis, representing nearly all of its geographic range, exhibits latitude-based population divergence and nature selection for population inhabitation towards higher altitudes on the Qinghai-Tibetan Plateau.
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Transcriptome analysis of Ophiocordyceps sinensis before and after infection of Thitarodes larvae. Fungal Biol 2016; 120:819-26. [DOI: 10.1016/j.funbio.2016.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 12/19/2022]
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Zhong X, Li SS, Peng QY, Zhang JS, Kan XT, Zhang GR, Liu X. A Polycephalomyces hyperparasite of Ophiocordyceps sinensis leads to shortened duration of production and reduced numbers of host ascospores. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Tang X, Mi F, Zhang Y, He X, Cao Y, Wang P, Liu C, Yang D, Dong J, Zhang K, Xu J. Diversity, population genetics, and evolution of macrofungi associated with animals. Mycology 2015; 6:94-109. [PMID: 30151318 PMCID: PMC6106070 DOI: 10.1080/21501203.2015.1043968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/15/2015] [Indexed: 11/28/2022] Open
Abstract
Macrofungi refers to all fungi that produce visible fruiting bodies. These fungi are evolutionarily and ecologically very divergent. Evolutionarily, they belong to two main phyla, Ascomycota and Basidiomycota, and many of them have relatives that cannot form visible fruiting bodies. Ecologically, macrofungi can be associated with dead organic matter, plants, and animals. Here we review our current understanding of population structure and biogeography of macrofungi associated with animals. Their interactions, functions, and patterns of coevolution are described and discussed. Our focus is on studies using molecular markers. Our analyses suggest that the types of fungi-animal associations play an important role in the structure of these animal-associated fungal populations.
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Affiliation(s)
- Xiaozhao Tang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Fei Mi
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Ying Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Xiaoxia He
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Yang Cao
- Yunnan Institute for Tropical Crop Research, Jinghong, Yunnan, China
| | - Pengfei Wang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Chunli Liu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Dan Yang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Jianyong Dong
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Keqing Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
| | - Jianping Xu
- Laboratory for Conservation and Utilization of Bio-Resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming650091, Yunnan, PR China
- Department of Biology, McMaster University, Hamilton, Ontario, CanadaL8S 4K1
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Zhang Y, Zhang S, Li Y, Ma S, Wang C, Xiang M, Liu X, An Z, Xu J, Liu X. Phylogeography and evolution of a fungal-insect association on the Tibetan Plateau. Mol Ecol 2014; 23:5337-55. [DOI: 10.1111/mec.12940] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 09/18/2014] [Accepted: 09/22/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Yongjie Zhang
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
- School of Life Sciences; Shanxi University; Taiyuan 030006 China
- Department of Biology; McMaster University; Hamilton Ontario Canada L8S 4K1
| | - Shu Zhang
- School of Life Sciences; Shanxi University; Taiyuan 030006 China
| | - Yuling Li
- Institute of Grassland; Qinghai Academy of Animal & Veterinary Sciences; Xining 810016 China
| | - Shaoli Ma
- Institute of Grassland; Qinghai Academy of Animal & Veterinary Sciences; Xining 810016 China
| | - Chengshu Wang
- Institute of Plant Physiology and Ecology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai 200032 China
| | - Meichun Xiang
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xin Liu
- Institute of Grassland; Qinghai Academy of Animal & Veterinary Sciences; Xining 810016 China
| | - Zhiqiang An
- Institute of Molecular Medicine; University of Texas Health Science Center at Houston; Houston TX 77030 USA
| | - Jianping Xu
- Department of Biology; McMaster University; Hamilton Ontario Canada L8S 4K1
- Laboratory for Conservation and Utilization of Bio-Resources; Yunnan University; Kunming 650091 China
| | - Xingzhong Liu
- State Key Laboratory of Mycology; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
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Geng Y, Li Z, Xia LY, Wang Q, Hu XM, Zhang XG. Characterization and phylogenetic analysis of the mating-type loci in the asexual ascomycete genus Ulocladium. Mycologia 2014; 106:649-65. [PMID: 24891417 DOI: 10.3852/13-383] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genus Ulocladium is thought to be strictly asexual. Mating-type (MAT) loci regulate sexual reproduction in fungi and their study may help to explain the apparent lack of sexual reproduction in Ulocladium. We sequenced the full length of two MAT genes in 26 Ulocladium species and characterized the entire MAT idiomorphs plus flanking regions of Ulocladium botrytis. The MAT1-1 ORF encodes a protein with an alpha-box motif by the MAT1-1-1 gene and the MAT1-2 ORF encodes a protein with an HMG box motif by the MAT1-2-1 gene. Both MAT1-1-1 and MAT1-2-1 genes were detected in a single strain of every species. Moreover, the results of RT-PCR revealed that both MAT genes are expressed in all 26 Ulocladium species. This demonstrates that MAT genes of Ulocladium species might be functional and that they have the potential for sexual reproduction. Phylogenies based on MAT genes were compared with GAPDH and Alt a 1 phylograms in Ulocladium using maximum parsimony (MP) and Bayesian analysis. The MAT genealogies and the non-MAT trees displayed different topologies, indicating that MAT genes are unsuitable phylogenetic markers at the species level in Ulocladium. Furthermore, the conflicting topologies between MAT1-1-1 and MAT1-2-1 phylogeny indicate separate evolutionary events for the two MAT genes. However, the intergeneric phylogeny of four closely allied genera (Ulocladium, Alternaria, Cochliobolus, Stemphylium) based on MAT alignments demonstrated that MAT genes are suitable for phylogenetic analysis among allied genera.
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Affiliation(s)
- Yun Geng
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Zhuang Li
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Li-Yun Xia
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Qun Wang
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Xian-Mei Hu
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Xiu-Guo Zhang
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
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Chen ZH, Dai YD, Yu H, Yang K, Yang ZL, Yuan F, Zeng WB. Systematic analyses of Ophiocordyceps lanpingensis sp. nov., a new species of Ophiocordyceps in China. Microbiol Res 2013; 168:525-32. [DOI: 10.1016/j.micres.2013.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/22/2013] [Accepted: 02/23/2013] [Indexed: 10/27/2022]
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13
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Hu X, Zhang Y, Xiao G, Zheng P, Xia Y, Zhang X, St Leger RJ, Liu X, Wang C. Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5929-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Zhang S, Zhang YJ, Liu XZ, Zhang H, Liu DS. On the reliability of DNA sequences of Ophiocordyceps sinensis in public databases. J Ind Microbiol Biotechnol 2013; 40:365-78. [PMID: 23397071 DOI: 10.1007/s10295-012-1228-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 12/24/2012] [Indexed: 10/27/2022]
Abstract
Some DNA sequences in the International Nucleotide Sequence Databases (INSD) are erroneously annotated, which has lead to misleading conclusions in publications. Ophiocordyceps sinensis (syn. Cordyceps sinensis) is a fungus endemic to the Tibetan Plateau, and more than 100 populations covering almost its distribution area have been examined by us over recent years. In this study, using the data from authentic materials, we have evaluated the reliability of nucleotide sequences annotated as O. sinensis in the INSD. As of October 15, 2012, the INSD contained 874 records annotated as O. sinensis, including 555 records representing nuclear ribosomal DNA (63.5 %), 197 representing protein-coding genes (22.5 %), 92 representing random markers with unknown functions (10.5 %), and 30 representing microsatellite loci (3.5 %). Our analysis indicated that 39 of the 397 internal transcribed spacer entries, 27 of the 105 small subunit entries, and five of the 53 large subunit entries were incorrectly annotated as belonging to O. sinensis. For protein-coding sequences, all records of serine protease genes, the mating-type gene MAT1-2-1, the DNA lyase gene, the two largest subunits of RNA polymerase II, and elongation factor-1α gene were correct, while 14 of the 73 β-tubulin entries were indeterminate. Genetic diversity analyses using those sequences correctly identified as O. sinensis revealed significant genetic differentiation in the fungus although the extent of genetic differentiation varied with the gene. The relationship between O. sinensis and some other related fungal taxa is also discussed.
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Affiliation(s)
- Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
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Zhang YJ, Bai FR, Zhang S, Liu XZ. Determining novel molecular markers in the Chinese caterpillar fungus Ophiocordyceps sinensis by screening a shotgun genomic library. Appl Microbiol Biotechnol 2012; 95:1243-51. [PMID: 22466955 DOI: 10.1007/s00253-012-4028-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 11/24/2022]
Abstract
The Chinese caterpillar fungus Ophiocordyceps sinensis, endemic to alpine regions on the Tibetan Plateau, is one of the most valuable medicinal fungi in the world. Genetic differentiation within this fungus was observed; however, due to lack of highly efficient molecular markers, the overall genetic structure of this fungus has not been clarified. In this study, a shotgun genomic library of O. sinensis was constructed, and >181,848 nt were analyzed from >250 random clones. Primers from 33 sequenced fragments were then designed to amplify O. sinensis samples collected from widely separated regions on the Tibetan Plateau. Ten of the 33 fragments had no amplification or poor sequencing quality from all or certain samples. Sequence variations of the remaining 23 fragments among different samples were investigated in detail. Three fragments (OSRC14, OSRC19, and OSRC32) were the most variable with 7-43 single-nucleotide polymorphism (SNP) sites, representing the SNP frequency of 1.2-6.7 % per nucleotide site. These three fragments have the potential to be useful molecular markers for studying the population genetics of O. sinensis. These results also showed that constructing and screening a shotgun genomic library was an efficient approach to identify novel molecular markers from non-model organisms.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, China
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