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Genomic analyses reveal low mitochondrial and high nuclear diversity in the cyclosporin-producing fungus Tolypocladium inflatum

  • Genomics, transcriptomics, proteomics
  • Published:
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Abstract

Mitochondrial DNA is generally regarded to evolve faster than nuclear DNA in animals, whereas if this is also true in fungi remains unclear. Herein, we annotate the first complete mitochondrial genome (mitogenome) of the cyclosporin-producing fungus Tolypocladium inflatum and report the genome-wide sequence variations among five isolates originating from distantly separated localities. We found that T. inflatum has among the most compact of fungal mitogenomes; its 25 kb DNA molecule encodes all standard fungal mitochondrial genes and harbors only one intron. Transcriptional analyses validated the expression of most conserved genes. We found several uncommon repetitive elements and evidence of gene transfer from the mitochondrion to the nucleus. Phylogenetic analyses confirmed the placement of T. inflatum in the fungal order Hypocreales although there was uncertainty on its family-level affiliation. Comparative genomic analyses among the five isolates identified an overall lower level of intraspecific variation in mitogenomes than in nuclear genomes; however, both the nuclear and mitochondrial genomes revealed similar isolate relationships, not correlating with geographic sources of these isolates. Our study shed new insights into the evolution of the medicinally important ascomycete T. inflatum.

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References

  • Abyzov A, Urban AE, Snyder M, Gerstein M (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21:974–984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Balakrishnan K, Pandey A (1996) The panorama of cyclosporin research. J Basic Microb 36:121

    Article  CAS  Google Scholar 

  • Bartelli TF, Ferreira RC, Colombo AL, Briones MRS (2013) Intraspecific comparative genomics of Candida albicans mitochondria reveals non-coding regions under neutral evolution. Infect Genet Evol 14:302–312

    Article  CAS  PubMed  Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bissett J (1983) Notes on Tolypocladium and related genera. Can J Bot 61:1311–1329

    Article  Google Scholar 

  • Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotech 18:630–634

    Article  CAS  Google Scholar 

  • Brown WM, George M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A 76:1967–1971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burger TD, Shao R, Labruna MB, Barker SC (2014) Molecular phylogeny of soft ticks (Ixodida: Argasidae) inferred from mitochondrial genome and nuclear rRNA sequences. Ticks Tick-borne Dis 5:195–207

    Article  PubMed  Google Scholar 

  • Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW (2013) The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet 9:e1003496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chan DC (2006) Mitochondria: dynamic organelles in disease, aging, and development. Cell 125:1241–1252

    Article  CAS  PubMed  Google Scholar 

  • Chen XJ, Butow RA (2005) The organization and inheritance of the mitochondrial genome. Nat Rev Genet 6:815–825

    Article  CAS  PubMed  Google Scholar 

  • Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cummings DJ, McNally KL, Domenico JM, Matsuura ET (1990) The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr Genet 17:375–402

    Article  CAS  PubMed  Google Scholar 

  • Dai YC, Cui BK, Si J, He SH, Hyde KD, Yuan HS, Liu XY, Zhou LW (2015) Dynamics of the worldwide number of fungi with emphasis on fungal diversity in China. Mycol Prog 14(8):62

    Article  Google Scholar 

  • Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230

    Article  CAS  PubMed  Google Scholar 

  • Formey D, Moles M, Haouy A, Savelli B, Bouchez O, Becard G, Roux C (2012) Comparative analysis of mitochondrial genomes of Rhizophagus irregularis—syn. Glomus irregulare—reveals a polymorphism induced by variability generating elements. New Phytol 196:1217–1227

    Article  CAS  PubMed  Google Scholar 

  • Freel KC, Friedrich A, Hou J, Schacherer J (2014) Population genomic analysis reveals highly conserved mitochondrial genomes in the yeast species Lachancea thermotolerans. Genome Biol Evol 6:2586–2594

    Article  PubMed  PubMed Central  Google Scholar 

  • Fucikova K, Lahr DJ (2016) Uncovering cryptic diversity in two amoebozoan species using complete mitochondrial genome sequences. J Eukaryot Microbiol 63:112–122

    Article  CAS  PubMed  Google Scholar 

  • Gams W (1971) Tolypocladium, eine Hyphomycetengattung mit geschwollenen Phialiden. Persoonia 6:185–191

    Google Scholar 

  • Ghikas D, Kouvelis V, Typas M (2006) The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes, while intergenic regions show variation. Arch Microbiol 185:393–401

    Article  CAS  PubMed  Google Scholar 

  • Ghikas D, Kouvelis V, Typas M (2010) Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii. BMC Microbiol 10:174

    Article  PubMed  PubMed Central  Google Scholar 

  • Gräfe U, Ihn W, Schlegel B, Höfle G, Augustiniak H, Sandor P (1991) Structure of ergokonin C, a new carboxysterol antifungal antibiotic from a Tolypocladium inflatum mutant. Pharmazie 46:613–614

    PubMed  Google Scholar 

  • Gupta S, Krasnoff SB, Roberts DW, Renwick JAA, Brinen LS, Clardy J (1992) Structure of efrapeptins from the fungus Tolypocladium niveum: peptide inhibitors of mitochondrial ATPase. J Org Chem 57:2306–2313

    Article  CAS  Google Scholar 

  • Hawksworth D (2011) A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. MycoKeys 1:7–20

    Article  Google Scholar 

  • Hodge KT, Krasnoff SB, Humber RA (1996) Tolypocladium inflatum is the anamorph of Cordyceps subsessilis. Mycologia 88:715–719

    Article  Google Scholar 

  • Huang H, Manton KG (2004) The role of oxidative damage in mitochondria during aging: a review. Front Biosci 9:1100–1117

    Article  CAS  PubMed  Google Scholar 

  • Huang Y, Niu B, Gao Y, Fu L, Li W (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics 26:680–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang F, Li Y, Chen X (2017) The complete mitochondrial genome of a medicinal fungus, Tolypocladium ophioglossoides. Mitochondr DNA Part B 2:95–96

    Article  Google Scholar 

  • Jung PP, Friedrich A, Reisser C, Hou J, Schacherer J (2012) Mitochondrial genome evolution in a single protoploid yeast species. G3-Genes Genom. G E N 2:1103–1111

    CAS  Google Scholar 

  • Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kouvelis VN, Ghikas DV, Typas MA (2004) The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications. Fungal Genet Biol 41:930–940

    Article  CAS  PubMed  Google Scholar 

  • Kurtz S, Schleiermacher C (1999) REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15:426–427

    Article  CAS  PubMed  Google Scholar 

  • Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B (2016) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol 34:772–773

    Google Scholar 

  • Laslett D, Canbäck B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laslett D, Canbäck B (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24:172–175

    Article  CAS  PubMed  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin J, Chen XY, Cai XY, Yu XF, Liu XZ, Cao Y, Che YS (2011) Isolation and characterization of aphidicolin and chlamydosporol derivatives from Tolypocladium inflatum. J Nat Prod 74:1798–1804

    Article  CAS  PubMed  Google Scholar 

  • Lin RM, Liu CC, Shen BM, Bai M, Ling J, Chen GH, Mao ZC, Cheng XY, Xie BY (2015) Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales. BMC Microbiol 15:15

    Article  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:0955–0964

    Article  CAS  Google Scholar 

  • Lynch M, Koskella B, Schaack S (2006) Mutation pressure and the evolution of organelle genomic architecture. Science 311:1727

    Article  CAS  PubMed  Google Scholar 

  • Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci USA 105:9272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCluskey K (2012) Variation in mitochondrial genome primary sequence among whole-genome-sequenced strains of Neurospora crassa. IMA Fungus 3:93–98

    Article  PubMed  PubMed Central  Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nadimi M, Daubois L, Hijri M (2016) Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi. Mol Phylogenet Evol 98:74–83

    Article  CAS  PubMed  Google Scholar 

  • Oh J, Kong WS, Sung GH (2014) Complete mitochondrial genome of the entomopathogenic fungus Beauveria pseudobassiana (Ascomycota, Cordycipitaceae). Mitochondr DNA 26:777–778

  • Quandt CA, Kepler RM, Gams W, Araujo JP, Ban S, Evans HC, Hughes D, Humber R, Hywel-Jones N, Li Z, Luangsa-Ard JJ, Rehner SA, Sanjuan T, Sato H, Shrestha B, Sung GH, Yao YJ, Zare R, Spatafora JW (2014) Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium. IMA Fungus 5:121–134

    Article  PubMed  PubMed Central  Google Scholar 

  • Quinlan AR (2014) BEDTools: the Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics 47:11.12.1–11.12.34

    Article  Google Scholar 

  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    Article  PubMed  PubMed Central  Google Scholar 

  • Stamatakis A (2014) RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Summerbell RC, Gueidan C, Schroers H-J, de Hoog GS, Starink M, Rosete YA, Guarro J, Scott JA (2011) Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium. Stud Mycol 68:139–162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sung GH (2015) Complete mitochondrial DNA genome of the medicinal mushroom Cordyceps militaris (Ascomycota, Cordycipitaceae). Mitochondr DNA 26:789–790

    Article  CAS  Google Scholar 

  • Sung GH, Hywel-Jones NL, Sung JM, Luangsa-ard JJ, Shrestha B, Spatafora JW (2007) Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud Mycol 57:5–59

    Article  PubMed  PubMed Central  Google Scholar 

  • Survase SA, Kagliwal LD, Annapure US, Singhal RS (2011) Cyclosporin A—a review on fermentative production, downstream processing and pharmacological applications. Biotechnol Adv 29:418–435

    Article  CAS  PubMed  Google Scholar 

  • Svarstad H, Bugge HC, Dhillion SS (2000) From Norway to Novartis: cyclosporin from Tolypocladium inflatum in an open access bioprospecting regime. Biodivers Conserv 9:1521–1541

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Torriani SFF, Goodwin SB, Kema GHJ, Pangilinan JL, McDonald BA (2008) Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola. Fungal Genet Biol 45:628–637

    Article  CAS  PubMed  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Xu J, Li H, Song L, Yu Y, Zhang W, Liu G, Feng C (2016) The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes). Mitochondr DNA Part A 27:916–917

    Article  CAS  Google Scholar 

  • Weiser J, Matha V (1988) Tolypin, a new insecticidal metabolite of fungi of the genus Tolypocladium. J Invertebr Pathol 51:94–96

    Article  CAS  PubMed  Google Scholar 

  • Xin B, Lin R, Shen B, Mao Z, Cheng X, Xie B (2017) The complete mitochondrial genome of the nematophagous fungus Lecanicillium saksenae. Mitochondr DNA 28:52–53

    Article  CAS  Google Scholar 

  • Yang H, Wang K (2015) Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc 10:1556–1566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhan J, Pettway RE, McDonald BA (2003) The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow. Fungal Genet Biol 38:286–297

    Article  CAS  PubMed  Google Scholar 

  • Zhang YJ, Zhang S, Liu XZ, Wen HA, Wang M (2010) A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains. Lett Appl Microbiol 51:114–118

    PubMed  Google Scholar 

  • Zhang YJ, Zhang S, Zhang GZ, Liu XZ, Wang CS, Xu JP (2015) Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris. Fungal Genet Biol 77:95–107

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Hao AJ, Zhao YX, Zhang XY, Zhang YJ (2017a) Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris. Sci Rep 7:40219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang YJ, Zhang HY, Liu XZ, Zhang S (2017b) Mitochondrial genome of the nematode endoparasitic fungus Hirsutella vermicola reveals a high level of synteny in the family Ophiocordycipitaceae. Appl Microbiol Biotechnol 101:3295–3304

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors thank USDA-ARS Collection of Entomopathogenic Fungal Cultures for providing T. inflatum isolates.

Funding

This study was funded by the National Natural Science Foundation of China (81102759), the Natural Science Foundation of Shanxi Province (2014021030-2, 201601D011065), the Fund Program for the Scientific Activities of Selected Returned Overseas Professionals in Shanxi Province, and the Research Project Supported by Shanxi Scholarship Council of China (2017-015).

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Authors and Affiliations

  1. School of Life Sciences, Shanxi University, Taiyuan, 030006, China

    Yong-Jie Zhang & Xiao-Qing Yang

  2. Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China

    Xiao-Qing Yang

  3. Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, China

    Shu Zhang

  4. USDA, ARS Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853-2901, USA

    Richard A. Humber

  5. Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada

    Jianping Xu

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  1. Yong-Jie Zhang
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Zhang, YJ., Yang, XQ., Zhang, S. et al. Genomic analyses reveal low mitochondrial and high nuclear diversity in the cyclosporin-producing fungus Tolypocladium inflatum . Appl Microbiol Biotechnol 101, 8517–8531 (2017). https://doi.org/10.1007/s00253-017-8574-0

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