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Xu N, Zhang S, Zhang YJ. Complete mitochondrial genome of the edible mushroom Singerocybe alboinfundibuliformis (Clitocybaceae, Agaricales). Mitochondrial DNA B Resour 2024; 9:960-964. [PMID: 39091511 PMCID: PMC11293268 DOI: 10.1080/23802359.2024.2385608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Singerocybe alboinfundibuliformis (Seok et al.) Yang, Qin & Takah 2014 is an edible mushroom distributed in several East or Southeast Asian countries. Herein, we report the mitochondrial genome of S. alboinfundibuliformis based on Illumina sequencing data. The overall length of the mitochondrial genome is 64,279 bp, with a GC content of 29.0%. It contains 14 typical protein-coding genes, 27 tRNA genes, two rRNA genes, and 13 intergenic ORFs. Most of these genes (39 out of 56) are transcribed at the forward strand, and few (17 out of 56) are transcribed at the reverse strand. Among these genes, only the rnl gene is invaded by an intron, and all other genes are intron-free. Phylogenetic analysis based on mitochondrial amino acid sequences supports the phylogenetic position of S. alboinfundibuliformis in Clitocybaceae, being close to Lepista sordida (Schumach.) Singer 1951. This study serves as a springboard for future investigation on fungal evolution in Clitocybaceae.
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Affiliation(s)
- Nuo Xu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, Taiyuan, China
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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Qu Q, Zhang S, Zhang YJ. Complete mitochondrial genome of the bird's nest fungus Nidula shingbaensis (Nidulariaceae, Agaricales). Mitochondrial DNA B Resour 2024; 9:954-959. [PMID: 39091513 PMCID: PMC11290291 DOI: 10.1080/23802359.2024.2385595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Bird's nest fungi involve six different genera, but only one of these genera (i.e. Cyathus) have available mitochondrial genomes (mitogenomes) to date. In this study, we report the first mitogenome in the genus Nidula with Nidula shingbaensis K. Das & R.L. Zhao 2013 as a representative. The mitogenome is a circular molecule of 65,793 bp with a GC content of 26.2%. There are a total of 43 genes, including 14 typical protein-coding genes, 26 tRNA genes, two rRNA genes, and one free-standing intergenic open reading frame (ORF). Three introns (two in cox1 and one in cob) are present in the mitogenome, with each containing an ORF encoding for a LAGLIDADG endonuclease. Phylogenetic analysis based on mitochondrial amino acid sequences confirms the phylogenetic placement of N. shingbaensis in Nidulariaceae in Agaricales. This study serves as a springboard for future investigation on fungal evolution in Nidulariaceae.
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Affiliation(s)
- Qi Qu
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, Taiyuan, China
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
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Lu H, Nie Y, Huang B. The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales. Mitochondrial DNA B Resour 2024; 9:332-337. [PMID: 38476836 PMCID: PMC10930110 DOI: 10.1080/23802359.2024.2324938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.
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Affiliation(s)
- Hanwen Lu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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Komaba K, Kimura S, Kumai R, Goto H. Optically Electroactive Polymer Synthesized in a Liquid Crystal with Cyclosporin A─Circularly Polarized Electron Spin Resonance. J Phys Chem B 2024; 128:2000-2009. [PMID: 38377516 DOI: 10.1021/acs.jpcb.3c07375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Cyclosporine A (CsA), a naturally derived biomaterial and physiologically active substance, is commonly used as an immunosuppressant. In this study, CsA was revealed to function as a chiral inducer of cholesteric liquid crystals (CLCs) with a high helical twisting power. CsA induced helical structures in 4-cyano-4'-pentylbiphenyl, a synthetic liquid crystal (LC) used for general purposes. Electrochemical polymerization in CLC with CsA was also performed. The polymer prepared in CLC showed electro-optical activity via chiral induction by CsA. Synchrotron X-ray diffraction measurements indicated that the polymer film prepared in the CLC formed in the manner of LC molecular arrangement through molecular form imprinting from the LC order, although the polymer exhibited no liquid crystallinity. The polymer showed structural color and laser light oscillation diffraction derived from its periodic structure. The anisotropy of the circularly polarized electron spin resonance signals for the resulting polymer with respect to the magnetic field was observed.
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Affiliation(s)
- Kyoka Komaba
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
| | - Shojiro Kimura
- Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 Japan
| | - Reiji Kumai
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Hiromasa Goto
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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Wang J, Liu M, Mao C, Li S, Zhou J, Fan Y, Guo L, Yu H, Yang X. Comparative proteomics reveals the mechanism of cyclosporine production and mycelial growth in Tolypocladium inflatum affected by different carbon sources. Front Microbiol 2023; 14:1259101. [PMID: 38163081 PMCID: PMC10757567 DOI: 10.3389/fmicb.2023.1259101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Cyclosporine A (CsA) is a secondary cyclopeptide metabolite produced by Tolypocladium inflatum that is widely used clinically as an immunosuppressant. CsA production and mycelial growth differed when T. inflatum was cultured in different carbon source media. During early fermentation, CsA was preferred to be produced in fructose medium, while the mycelium preferred to accumulate in sucrose medium. On the sixth day, the difference was most pronounced. In this study, high-throughput comparative proteomics methods were applied to analyze differences in protein expression of mycelial samples on day 6, revealing the proteins and mechanisms that positively regulate CsA production related to carbon metabolism. The differences included small molecule acid metabolism, lipid metabolism, organic catabolism, exocrine secretion, CsA substrate Bmt synthesis, and transcriptional regulation processes. The proteins involved in the regulation of mycelial growth related to carbon metabolism were also revealed and were associated with waste reoxidation processes or coenzyme metabolism, small molecule synthesis or metabolism, the stress response, genetic information or epigenetic changes, cell component assembly, cell wall integrity, membrane metabolism, vesicle transport, intramembrane localization, and the regulation of filamentous growth. This study provides a reliable reference for CsA production from high-efficiency fermentation. This study provides key information for obtaining more CsA high-yielding strains through metabolic engineering strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuqing Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Zhang YJ, Fan XP, Li JN, Zhang S. Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps. IMA Fungus 2023; 14:13. [PMID: 37415259 DOI: 10.1186/s43008-023-00118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
Cordyceps is a diverse genus of insect pathogenic fungi, with about 180 accepted species, including some well-known ones used as ethnic medicine and/or functional food. Nevertheless, mitogenomes are only available for four members of the genus. The current study reports the mitogenome of Cordyceps blackwelliae, a newly described entomopathogenic fungus. The 42,257-bp mitogenome of the fungus encoded genes typically found in fungal mitogenomes, and a total of 14 introns inserted into seven genes, including cob (1 intron), cox1 (4), cox3 (3), nad1 (1), nad4 (1), nad5 (1), and rnl (3). RNA-Seq analysis revealed differential expression of mitochondrial genes and supported annotations resulting from in silico analysis. There was clear evidence for polycistronic transcription and alternative splicing of mitochondrial genes. Comparison among mitogenomes of five different Cordyceps species (i.e., C. blackwelliae, C. chanhua, C. militaris, C. pruinosa, and C. tenuipes) revealed a high synteny, with mitogenome size expansion correlating with intron insertions. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. This study promotes our understanding of fungal evolution in Cordyceps.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China.
| | - Xiang-Ping Fan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia-Ni Li
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Wu XQ, Li J, Zhou X, Wang J, Tan YF, Mo JS, Liu S, Xu KP, Tan GS, Zhang W, Wang WX. Liver-cell protective pyridones from the fungi Tolypocladium album dws120. PHYTOCHEMISTRY 2023; 212:113730. [PMID: 37220864 DOI: 10.1016/j.phytochem.2023.113730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023]
Abstract
Five previously undescribed pyridone derivatives, tolypyridones I-M, were identified from the solid rice medium fermented by Tolypocladium album dws120, along with two known compounds tolypyridone A (or trichodin A) and pyridoxatin. Their planar structures and partial relative configurations have been determined by careful interpretation of their spectroscopic data. The full assignment of the relative and absolute configurations of tolypyridones I-M was achieved by gauge-independent atomic orbital 13C NMR calculation, quantitative nuclear Overhauser effects based interatomic distance calculation, and electronic circular dichroism calculation. In addition, we have fully determined the configuration of tolypyridone A by X-ray diffraction analysis. In bioassay, tolypyridones I was able to restore cell viability and inhibit the release of alanine aminotransferase and aspartate aminotransferase for ethanol-induced LO2 cell, suggesting its potential as a liver protective agent.
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Affiliation(s)
- Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Li
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China; Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Xi Zhou
- School of Life Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Ji-Song Mo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Shao Liu
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Wei Zhang
- Hunan Institute for Drug Control, Changsha, Hunan, 410001, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan, 410008, PR China.
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Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å. Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Front Microbiol 2023; 14:1159811. [PMID: 37275157 PMCID: PMC10234125 DOI: 10.3389/fmicb.2023.1159811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/16/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species. Methods In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers. Results and Discussion Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
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Affiliation(s)
| | | | | | | | - Åke Olson
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Silan E, Ozkilinc H. Phylogenetic divergences in brown rot fungal pathogens of Monilinia species from a worldwide collection: inferences based on the nuclear versus mitochondrial genes. BMC Ecol Evol 2022; 22:119. [PMID: 36271324 PMCID: PMC9585774 DOI: 10.1186/s12862-022-02079-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Phylogenetic analyses for plant pathogenic fungi explore many questions on diversities, relationships, origins, and divergences of populations from different sources such as species, host, and geography. This information is highly valuable, especially from a large global sampling, to understand the evolutionary paths of the pathogens worldwide. Monilinia fructicola and M. laxa are two important fungal pathogens of stone fruits that cause the widespread disease commonly known as brown rot. Three nuclear genes (Calmodulin, SDHA, TEF1α) and three mitochondrial genes (Cytochrome_b, NAD2, and NAD5) of the two pathogen species from a worldwide collection including five different countries from four different continents were studied in this work. RESULTS Both Maximum Likelihood and Bayesian approaches were applied to the data sets, and in addition, Maximum Parsimony based approaches were used for the regions having indel polymorphisms. Calmodulin, SDHA, NAD2, and NAD5 regions were found phylogenetically informative and utilized for phylogenetics of Monilinia species for the first time. Each gene region presented a set of haplotypes except Cytochrome_b, which was monomorphic. According to this large collection of two Monilinia species around the world, M. fructicola showed more diversity than M. laxa, a result that should be carefully considered, as M. fructicola is known to be a quarantine pathogen. Moreover, the other two mitochondrial genes (NAD2 and NAD5) did not have any substitution type mutations but presented an intron indel polymorphism indicating the contribution of introns as well as mobile introns to the fungal diversity and evolution. Based on the concatenated gene sets, nuclear DNA carries higher mutations and uncovers more phylogenetic clusters in comparison to the mitochondrial DNA-based data for these fungal species. CONCLUSIONS This study provides the most comprehensive knowledge on the phylogenetics of both nuclear and mitochondrial genes of two prominent brown rot pathogens, M. fructicola and M. laxa. Based on the regions used in this study, the nuclear genes resolved phylogenetic branching better than the mitochondrial genes and discovered new phylogenetic lineages for these species.
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Affiliation(s)
- Ece Silan
- School of Graduate Studies, MSc Program in Biomolecular Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Hilal Ozkilinc
- School of Graduate Studies, MSc Program in Biomolecular Sciences, Çanakkale Onsekiz Mart University, Çanakkale, Turkey.
- Dept. of Molecular Biology and Genetics, Faculty of Science, Çanakkale Onsekiz Mart University, Çanakkale, Turkey.
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Li Q, Zhang T, Li L, Bao Z, Tu W, Xiang P, Wu Q, Li P, Cao M, Huang W. Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma. J Fungi (Basel) 2022; 8:781. [PMID: 35893149 PMCID: PMC9394262 DOI: 10.3390/jof8080781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
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Yang Y, Liu XY, Huang B. The complete mitochondrial genome of Linnemannia amoeboidea (W. Gams) Vandepol & Bonito ( Mortierellales: Mortierellaceae). Mitochondrial DNA B Resour 2022; 7:374-376. [PMID: 35187234 PMCID: PMC8856043 DOI: 10.1080/23802359.2022.2039080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The complete mitochondrial genome of Linnemannia amoeboidea (W. Gams) Vandepol & Bonito 2020 (Strain no.: CBS 889.72) was sequenced under the next-generation sequencing platform. It was the second one in the family Mortierellaceae Luerss. 1877. The circular genome was 49,702 bp in size, with a GC content of 20.86%. Gene prediction revealed 15 PCGs, two rRNA genes, 26 tRNA genes, one rnpB gene and seven ORFs. Phylogenetic analyses showed that L. amoeboidea was closely related to Podila verticillate (Linnem.) Vandepol & Bonito 2020.
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Affiliation(s)
- Yang Yang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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12
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Comparative Mitogenomics of Fungal Species in Stachybotryaceae Provides Evolutionary Insights into Hypocreales. Int J Mol Sci 2021; 22:ijms222413341. [PMID: 34948138 PMCID: PMC8706829 DOI: 10.3390/ijms222413341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 01/03/2023] Open
Abstract
Stachybotrys chartarum is one of the world’s ten most feared fungi within the family Stachybotryaceae, although to date, not a single mitogenome has been documented for Stachybotryaceae. Herein, six mitogenomes of four different species in Stachybotryaceae are newly reported. The S. chartarum mitogenome was 30.7 kb in length and contained two introns (one each in rnl and cox1). A comparison of the mitogenomes of three different individuals of S. chartarum showed few nucleotide variations and conservation of gene content/order and intron insertion. A comparison of the mitogenomes of four different Stachybotryaceae species (Memnoniella echinata, Myrothecium inundatum, S. chartarum, and S. chlorohalonata), however, revealed variations in intron insertion, gene order/content, and nad2/nad3 joining pattern. Further investigations on all Hypocreales species with available mitogenomes showed greater variabilities in gene order (six patterns) and nad2/nad3 joining pattern (five patterns) although a dominant pattern always existed in each case. Ancestral state estimation showed that in each case the dominant pattern was always more ancestral than those rare patterns. Phylogenetic analyses based on mitochondrion-encoded genes supported the placement of Stachybotryaceae in Hypocreales. The crown age of Stachybotryaceae was estimated to be approximately the Early Cretaceous (141–142 Mya). This study greatly promotes our understanding of the evolution of fungal species in Hypocreales.
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Nie Y, Zhao H, Wang Z, Zhou Z, Liu X, Huang B. The Gene Rearrangement, Loss, Transfer, and Deep Intronic Variation in Mitochondrial Genomes of Conidiobolus. Front Microbiol 2021; 12:765733. [PMID: 34858376 PMCID: PMC8632527 DOI: 10.3389/fmicb.2021.765733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/01/2021] [Indexed: 12/22/2022] Open
Abstract
The genus Conidiobolus s.s. was newly delimited from Conidiobolus s.l. In order to gain insight into its mitochondrial genetic background, this study sequenced six mitochondrial genomes of the genus Conidiobolus s.s. These mitogenomes were all composed of circular DNA molecules, ranging from 29,253 to 48,417 bp in size and from 26.61 to 27.90% in GC content. The order and direction for 14 core protein-coding genes (PCGs) were identical, except for the atp8 gene lost in Conidiobolus chlamydosporus, Conidiobolus polyspermus, and Conidiobolus polytocus, and rearranged in the other Conidiobolus s.s. species. Besides, the atp8 gene split the cox1 gene in Conidiobolus taihushanensis. Phylogenomic analysis based on the 14 core PCGs confirmed that all Conidiobolus s.s. species formed a monophyly in the Entomophthoromycotina lineage. The number and length of introns were the main factors contributing to mitogenomic size, and deep variations and potential transfer were detected in introns. In addition, gene transfer occurred between the mitochondrial and nuclear genomes. This study promoted the understanding of the evolution and phylogeny of the Conidiobolus s.s. genus.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Heng Zhao
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zimin Wang
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Zhengyu Zhou
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Xiaoyong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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14
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Abuduaini A, Wang YB, Zhou HY, Kang RP, Ding ML, Jiang Y, Suo FY, Huang LD. The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species. IMA Fungus 2021; 12:31. [PMID: 34670626 PMCID: PMC8527695 DOI: 10.1186/s43008-021-00081-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/10/2021] [Indexed: 01/06/2023] Open
Abstract
In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.
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Affiliation(s)
- Aifeire Abuduaini
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Yuan-Bing Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hui-Ying Zhou
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Rui-Ping Kang
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Ming-Liang Ding
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yu Jiang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Fei-Ya Suo
- College of Life Science and Technology, Xinjiang University, Urumchi, 830046, China
| | - Luo-Dong Huang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China. .,Guangxi Research Center for Microbial and Enzyme Engineering Technology, Guangxi University, Nanning, 530004, China.
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15
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Zhang S, Bai X, Ren LY, Sun HH, Tang HP, Vaario LM, Xu J, Zhang YJ. Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake. Environ Microbiol 2021; 23:7214-7230. [PMID: 34587365 DOI: 10.1111/1462-2920.15792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/25/2021] [Indexed: 01/26/2023]
Abstract
Fungi, as eukaryotic organisms, contain two genomes, the mitochondrial genome and the nuclear genome, in their cells. How the two genomes evolve and correlate to each other is debated. Herein, taking the gourmet pine mushroom Tricholoma matsutake as an example, we performed comparative mitogenomic analysis using samples collected from diverse locations and compared the evolution of the two genomes. The T. matsutake mitogenome encodes 49 genes and is rich of repetitive and non-coding DNAs. Six genes were invaded by up to 11 group I introns, with one cox1 intron cox1P372 showing presence/absence dynamics among different samples. Bioinformatic analyses suggested limited or no evidence of mitochondrial heteroplasmy. Interestingly, hundreds of mitochondrial DNA fragments were found in the nuclear genome, with several larger than 500 nt confirmed by PCR assays and read count comparisons, indicating clear evidence of transfer of mitochondrial DNA into the nuclear genome. Nuclear DNA of T. matsutake showed a higher mutation rate than mitochondrial DNA. Furthermore, we found evidence of incongruence between phylogenetic trees derived from mitogenome and nuclear DNA sequences. Together, our results reveal the dynamic genome evolution of the gourmet pine mushroom.
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Affiliation(s)
- Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Xue Bai
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Li-Yuan Ren
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Hui-Hui Sun
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Hui-Ping Tang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Lu-Min Vaario
- Department of Forest Science, University of Helsinki, Helsinki, FI-00014, Finland
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
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16
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A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers. Int J Genomics 2021; 2021:6652508. [PMID: 34212028 PMCID: PMC8208876 DOI: 10.1155/2021/6652508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.
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17
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Sun HH, Zhang YJ, Zhang S. Complete mitogenome of the entomopathogenic fungus Metarhizium album and phylogenetic analysis of Hypocreales. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1689-1690. [PMID: 34104739 PMCID: PMC8143629 DOI: 10.1080/23802359.2021.1914229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Metarhizium album, with a narrow host range, is an entomopathogenic fungus in the family Clavicipitaceae. Its nuclear genome has been sequenced, whereas its mitogenome is still unknown. In this study, the complete mitogenome of M. album was assembled and annotated. This circular mitogenome was 68,425 bp in length and encodes two rRNA genes, 26 tRNA genes, 14 standard protein-coding genes of the oxidative phosphorylation system, and seven intergenic ORFs. A total of 23 introns invaded ten genes, including atp9 (1 intron), cob (2), cox1 (9), cox2 (1), nad1 (1), nad2 (2), nad3 (1), nad4 (1), nad5 (2), and rnl (3). Except for one group II intron (i.e. mL2060), others were all group I introns and involved four subgroups (i.e. IA, IB, IC2 and ID). Phylogenetic analysis based on mitochondrial nucleotide sequences confirmed M. album in the family Clavicipitaceae, being closely related to its congeneric Metarhizium rileyi.
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Affiliation(s)
- Hui-Hui Sun
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
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18
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Zhang SL, Pu SC, Lin AT, Luan FG. The complete mitochondrial genome of Beauveria lii (Hypocreales: Cordycipitaceae). Mitochondrial DNA B Resour 2021; 6:586-588. [PMID: 33628939 PMCID: PMC7889086 DOI: 10.1080/23802359.2021.1875917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome of Beauveria lii, strain RCEF500, was sequenced on the NovaSeq 6000 and the Nanopore Sequencer, and annotated. The genome is 59,014 bp in length, encoding 15 conserved protein-coding genes (PCGs), 2 rRNA genes and 23 tRNA genes. The nucleotide composition of Beauveria lii mitochondrial genome was 38.23% of A, 35.81% of T, 11.61% of C, 14.36% of G, 25.97% of G + C content. Phylogenetic analysis confirmed B. lii as a member of Beauveria (Cordycipitaceae). The mitochondrial genome of B. lii will contribute to the understanding of phylogeny and evolution of the genus and family.
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Affiliation(s)
- Sheng-Li Zhang
- Institute of Biological Engineering, Bozhou College, Bozhou, China
| | - Shun-Chang Pu
- Institute of Biological Engineering, Bozhou College, Bozhou, China
| | - Ai-Ting Lin
- Shanghai Biozeron Biotechnology Co., Ltd, Shanghai, China
| | - Feng-Gang Luan
- College of Landscape and Art, Jiangxi Agricultural University, Nanchang, China
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19
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Mitogenome of Tolypocladium guangdongense. Appl Microbiol Biotechnol 2020; 104:9295-9308. [PMID: 32918580 DOI: 10.1007/s00253-020-10889-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 01/08/2023]
Abstract
Tolypocladium guangdongense is a high-value edible fungus with various medicinal and food safety properties. However, its evolutionary and genetic information is still limited. Mitochondrial genomes are potential models for molecular evolution and phylogenetic studies. In this study, we sequenced the complete mitogenome of T. guangdongense, demonstrating circular sequence of 46,102 bp, containing 14 standard protein-coding genes (PCGs), 2 ribosomal RNA subunit genes, and 28 tRNA genes. Phylogenetic analysis based on mitochondrial genes indicated that T. guangdongense was clustered into the Tolypocladium genus with high support value, based on the core PCG dataset. In addition, rps3 is also a suitable marker in the phylogenetic analysis in Hypocreales. Gene rearrangement analysis indicated that the gene order of PCGs was highly consistent in Hypocreales, and tRNA rearrangement events occurred in most species of Hypocreales; however, the rearrangement rates were not taxonomically correlated. Divergence time estimation based on the old fossil record and previous reports revealed that T. guangdongense originated approximately in the middle Cenozoic (42 Mya, 95% highest posterior density interval: 43-116) with the Tolypocladium genus differentiation. Our results provided more mitogenomic information of T. guangdongense and shed new insights into evolution of the Tolypocladium genus. KEY POINTS: • The general and unique features of T. guangdongense mitogenome are firstly reported. • Phylogenetic analysis further verified the taxonomic status of T. guangdongense. • Divergence time estimation provides more evolutionary information of T. guangdongense.
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20
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Wang WR, Chen YX, Yan Z, Wei XY, Qiu JZ, Zhang YJ. Complete mitogenome of the entomopathogenic fungus Orbiocrella petchii. Mitochondrial DNA B Resour 2020; 5:2695-2696. [PMID: 33457908 PMCID: PMC7781985 DOI: 10.1080/23802359.2020.1787258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the complete mitogenome of an entomopathogenic fungus Orbiocrella petchii (syn. Torrubiella petchii) was assembled and annotated. This circular mitogenome was 23,794 bp in length and consisted of 2 rRNA genes (rnl and rns), 25 tRNA genes, and 14 standard protein-coding genes of the oxidative phosphorylation system. Two group I introns were identified, and they encoded ribosomal protein S3 (in rnl) or a GIY-YIG endonuclease (in nad1). Phylogenetic analysis based on mitochondrial DNA sequences confirms O. petchii in the family of Clavicipitaceae.
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Affiliation(s)
- Wei-Rong Wang
- School of Life Science, Shanxi University, Taiyuan , PR China
| | - Yu-Xi Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zhong Yan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Xiu-Yan Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Jun-Zhi Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan , PR China
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21
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Medina R, Franco MEE, Bartel LC, Martinez Alcántara V, Saparrat MCN, Balatti PA. Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management. Front Microbiol 2020; 11:978. [PMID: 32547508 PMCID: PMC7272585 DOI: 10.3389/fmicb.2020.00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 01/18/2023] Open
Abstract
Mitochondrial genomes (mt-genomes) are characterized by a distinct codon usage and their autonomous replication. Mt-genomes encode highly conserved genes (mt-genes), like proteins involved in electron transport and oxidative phosphorylation but they also carry highly variable regions that are in part responsible for their high plasticity. The degree of conservation of their genes is such that they allow the establishment of phylogenetic relationships even across distantly related species. Here, we describe the mechanisms that generate changes along mt-genomes, which play key roles at enlarging the ability of fungi to adapt to changing environments. Within mt-genomes of fungal pathogens, there are dispensable as well as indispensable genes for survival, virulence and/or pathogenicity. We also describe the different complexes or mechanisms targeted by fungicides, thus addressing a relevant issue regarding disease management. Despite the controversial origin and evolution of fungal mt-genomes, the intrinsic mechanisms and molecular biology involved in their evolution will help to understand, at the molecular level, the strategies for fungal disease management.
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Affiliation(s)
- Rocio Medina
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Laura Cecilia Bartel
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Virginia Martinez Alcántara
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mario Carlos Nazareno Saparrat
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
- Instituto de Fisiología Vegetal (INFIVE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Pedro Alberto Balatti
- Centro de Investigaciones de Fitopatología, Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIDEFI-CICPBA), Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Argentina
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22
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Park J, Xi H, Park J, Lee W. The complete mitochondrial genome of fungal endosymbiont, Ophiocordycipitaceae sp., isolated from Ricania speculum (Hemiptera: Ricaniidae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1754141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Jongsun Park
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Hong Xi
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jonghyun Park
- Infoboss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Wonhoon Lee
- Department of Plant Medicine and Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Republic of Korea
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Zhang S, Ren LY, Zhang YJ. Complete mitogenome of the entomopathogenic fungus Metarhizium rileyi. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1742596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
| | - Li-Yuan Ren
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
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24
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Mogilnicka I, Ufnal M. Gut Mycobiota and Fungal Metabolites in Human Homeostasis. Curr Drug Targets 2020; 20:232-240. [PMID: 30047327 DOI: 10.2174/1389450119666180724125020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/13/2018] [Accepted: 07/19/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Accumulating evidence suggests that microbiota play an important role in host's homeostasis. Thus far, researchers have mostly focused on the role of bacterial microbiota. However, human gut is a habitat for several fungal species, which produce numerous metabolites. Furthermore, various types of food and beverages are rich in a wide spectrum of fungi and their metabolites. METHODS We searched PUBMED and Google Scholar databases to identify clinical and pre-clinical studies on fungal metabolites, composition of human mycobiota and fungal dysbiosis. RESULTS Fungal metabolites may serve as signaling molecules and exert significant biological effects including trophic, anti-inflammatory or antibacterial actions. Finally, research suggests an association between shifts in gut fungi composition and human health. Changes in mycobiota composition have been found in obesity, hepatitis and inflammatory bowel diseases. CONCLUSION The influence of mycobiota and dietary fungi on homeostasis in mammals suggests a pharmacotherapeutic potential of modulating the mycobiota which may include treatment with probiotics and fecal transplantation. Furthermore, antibacterial action of fungi-derived molecules may be considered as a substitution for currently used antibacterial agents and preservatives in food industry.
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Affiliation(s)
- Izabella Mogilnicka
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Ufnal
- Department of Experimental Physiology and Pathophysiology, Laboratory of the Centre for Preclinical Research, Medical University of Warsaw, Warsaw, Poland
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25
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Zhang YJ, Yang XB, Zhang S. Complete mitogenome of the entomopathogenic fungus Akanthomyces lecanii. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:1021-1022. [PMID: 33366856 PMCID: PMC7748497 DOI: 10.1080/23802359.2020.1721349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, the complete mitogenome of an entomopathogenic fungus Akanthomyces lecanii is assembled and annotated. This circular mitogenome is 24,643 bp in length and consists of 2 rRNA genes (rnl and rns), 26 tRNA genes and 14 standard protein-coding genes of the oxidative phosphorylation system. Only one intron (group IA) is identified, which invades rnl and carries an ORF coding for ribosomal protein S3. Phylogenetic analysis based on concatenated mitochondrial nucleotide sequences confirms A. lecanii in Cordycipitaceae, and A. lecanii clusters together with Akanthomyces muscarius.
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Affiliation(s)
- Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Xue-Bin Yang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
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26
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Zhang S, Zhang YJ. Complete mitogenome of the entomopathogenic fungus Tolypocladium cylindrosporum. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:680-682. [PMID: 33366701 PMCID: PMC7748670 DOI: 10.1080/23802359.2020.1714495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this study, the complete mitogenome of an entomopathogenic fungus Tolypocladium cylindrosporum is assembled and annotated. This circular mitogenome is 34,698 bp in length and consists of two rRNA genes (rnl and rns), 26 tRNA genes, 14 standard protein-coding genes of the oxidative phosphorylation system, and four intergenic free-standing ORFs. A total of six introns (all group I) were identified in atp9, cob, cox1, and rnl, and they may encode ribosomal protein S3, LAGLIDADG or GIY-YIG endonucleases. Phylogenetic analysis based on concatenated mitochondrial protein sequences confirms T. cylindrosporum in Ophiocordycipitaceae.
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Affiliation(s)
- Shu Zhang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
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27
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Zhang S, Zhang YJ. Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes. IMA Fungus 2019; 10:15. [PMID: 32647619 PMCID: PMC7325650 DOI: 10.1186/s43008-019-0015-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022] Open
Abstract
Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungus Tolypocladium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16 fungi of different phyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.
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Affiliation(s)
- Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006 China
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Zhang S, Zhang YJ, Li ZL. Complete mitogenome of the entomopathogenic fungus Sporothrix insectorum RCEF 264 and comparative mitogenomics in Ophiostomatales. Appl Microbiol Biotechnol 2019; 103:5797-5809. [PMID: 31089765 DOI: 10.1007/s00253-019-09855-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/05/2019] [Accepted: 04/14/2019] [Indexed: 01/14/2023]
Abstract
The fungal order Ophiostomatales contains numerous species important in medical fields, agriculture, and forestry, and several species have had available mitogenome information. The nuclear genome of the entomopathogenic fungus Sporothrix insectorum has been reported, while its mitogenome remains unknown. Herein, we firstly described the mitogenome of S. insectorum RCEF 264 and then compared Ophiostomatales mitogenomes from both interspecific and intraspecific perspectives. The mitogenome of S. insectorum RCEF 264 was 31,454 bp in length, containing typical fungal mitochondrial genes plus rnpB. Four group I introns interrupted rnl and cox1. Phylogenetic analyses confirmed the placement of S. insectorum RCEF 264 in Ophiostomatales. Comparison of mitogenomes among seven Ophiostomatales species revealed conserved gene contents and a high synteny, although there were also some differences among them. Their mitogenomes showed more than two-fold variations (26.6-65.1 kb) in size, with a total of 37 intron insertional loci from 11 genes (1-25 introns per species). The sole intron shared by all species was an rps3-encoding intron in rnl (mL2450), and this intron-based phylogeny was highly consistent with those constructed using mitochondrial/nuclear genes, suggesting convergent evolution of this intron with Ophiostomatales species. The dendrogram based on presence/absence patterns at all intron loci was quite different from those based on mitochondrial/nuclear genes. Comparison of mitogenomes among two to three intraspecific individuals in Ophiostoma novo-ulmi subsp. novo-ulmi and Sporothrix schenckii revealed mitogenome size variations due to single-nucleotide polymorphisms (SNPs) and indels but without fluctuation of intron numbers for each species. This study greatly enhanced our understanding of mitogenome evolution in Ophiostomatales.
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Affiliation(s)
- Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, China.
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Zhi-Liang Li
- School of Agriculture, Ludong University, Yantai, 264025, China
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29
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Fan WW, Zhang S, Zhang YJ. The complete mitochondrial genome of the Chan-hua fungus Isaria cicadae: a tale of intron evolution in Cordycipitaceae. Environ Microbiol 2019; 21:864-879. [PMID: 30623556 DOI: 10.1111/1462-2920.14522] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/04/2019] [Accepted: 01/05/2019] [Indexed: 11/30/2022]
Abstract
Isaria cicadae is an entomogenous fungus of great medicinal value. Its nuclear genome has been reported, while its mitogenome remains unknown. Herein, we first described its mitogenome and then inferred intron evolution from both intraspecific and interspecific perspectives. The fungus represented the largest mitogenome (56.6 kb in strain CCAD02) known in Cordycipitaceae due to the presence of 25 introns interrupting nine genes. Comparison of three I. cicadae strains revealed intron presence/absence dynamics at six intron loci plus a few indels and single nucleotide polymorphisms. Phylogenetic analyses confirmed the placement of I. cicadae in Cordycipitaceae. Comparison of 10 Cordycipitaceae species revealed a high degree of synteny and conserved genetic content. They, however, varied in intron numbers (1-25 per species) with overall 34 intron loci identified, which resulted in more than twofold variations in mitogenome sizes (24.5-56.6 kb). An rnl intron encoding ribosomal protein S3 was present in all species, suggesting its early invasion in Cordycipitaceae, while further divergence occurred for this intron. The other introns identified in this study were present in some, but not all of the species and have undergone multiple gains and losses in Cordycipitaceae. This study greatly enhanced our understanding of intron evolution in Cordycipitaceae.
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Affiliation(s)
- Wen-Wen Fan
- School of Life Science, Shanxi University, Taiyuan 030006, China.,Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan 030006, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan 030006, China
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30
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Zhang SL, wei L, Luan FG. The mitochondrial genome analysis of Isaria tenuipes (Hypocreales: Cordycipitaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Sheng-Li Zhang
- Institute of Biological Engineering, Bozhou College, Bozhou, China
| | - Lei wei
- Institute of Biological Engineering, Bozhou College, Bozhou, China
| | - Feng-Gang Luan
- College of Landscape and Art, Jiangxi Agricultural University, Nanchang, China
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31
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Zhang YJ, Zhang S. Complete mitogenome of the entomopathogenic fungus Isaria farinosa ARSEF 3. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1601515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, China
| | - Shu Zhang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
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32
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Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Liu Q, Huang W. Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol 2019; 121:249-260. [DOI: 10.1016/j.ijbiomac.2018.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
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33
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Nie Y, Wang L, Cai Y, Tao W, Zhang YJ, Huang B. Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi. Appl Microbiol Biotechnol 2018; 103:1379-1391. [PMID: 30569217 DOI: 10.1007/s00253-018-9549-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Entomophthoroid fungi represent an ecologically important group of fungal pathogens on insects. Here, the whole mitogenome of Conidiobolus heterosporus, one of the entomophthoroid fungi, was described and compared to those early branching fungi with available mitogenomes. The 53,364-bp circular mitogenome of C. heterosporus contained two rRNA genes, 14 standard protein-coding genes, 26 tRNA genes, and three free-standing ORFs. Thirty introns interrupted nine mitochondrial genes. Phylogenetic analysis based on mitochondrion-encoded proteins revealed that C. heterosporus was most close to Zancudomyces culisetae in the Zoopagomycota of basal fungi. Comparison on mitogenomes of 23 basal fungi revealed great variabilities in terms of mitogenome conformation (circular or linear), genetic code (codes 1, 4, or 16), AT contents (53.3-85.5%), etc. These mitogenomes varied from 12.0 to 97.3 kb in sizes, mainly due to different numbers of genes and introns. They showed frequent DNA rearrangement events and a high variability of gene order, although high synteny and conserved gene order were also present between closely related species. By reporting the first mitogenome in Entomophthoromycotina and the second in Zoopagomycota, this study greatly enhanced our understanding on evolution of basal fungi.
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Affiliation(s)
- Yong Nie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.,School of Civil Engineering and Architecture, Anhui University of Technology, Ma'anshan, 243002, China
| | - Lin Wang
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Yue Cai
- Department of Biological and Environmental Engineering, Hefei University, Hefei, 230601, China
| | - Wei Tao
- School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yong-Jie Zhang
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.
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Li Q, Liao M, Yang M, Xiong C, Jin X, Chen Z, Huang W. Characterization of the mitochondrial genomes of three species in the ectomycorrhizal genus Cantharellus and phylogeny of Agaricomycetes. Int J Biol Macromol 2018; 118:756-769. [DOI: 10.1016/j.ijbiomac.2018.06.129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022]
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35
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Wang L, Zhang S, Li JH, Zhang YJ. Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungusHirsutella thompsonii. Environ Microbiol 2018; 20:3393-3405. [DOI: 10.1111/1462-2920.14379] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Lin Wang
- School of Life Science; Shanxi University; Taiyuan 030006 China
- Institute of Biotechnology; Shanxi University; Taiyuan 030006 China
| | - Shu Zhang
- Institute of Applied Chemistry; Shanxi University; Taiyuan 030006 China
| | - Jian-Hui Li
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu 030801 China
| | - Yong-Jie Zhang
- School of Life Science; Shanxi University; Taiyuan 030006 China
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36
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Fungal mitochondrial genomes and genetic polymorphisms. Appl Microbiol Biotechnol 2018; 102:9433-9448. [PMID: 30209549 DOI: 10.1007/s00253-018-9350-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/24/2022]
Abstract
Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.
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