Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism

Abstract

Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Reconstructed gene family and expansion histories along a time-calibrated phylogeny.
Fig. 2: Identification of significantly over-represented GO terms among these significantly expanded gene families.
Fig. 3: Pan-genome components of eleven P. neosporulosa isolates.
Fig. 4: Incomplete saprotrophy-biotrophy transition and intraspecific physiological variations in P. neosporulosa.
Fig. 5: Summary of single nucleotide polymorphisms and indels in the P. neosporulosa population.
Fig. 6: Mating type structure, polymorphism in the P. neosporulosa genome and phylogeny of mat1-2-1.
Fig. 7: Selection signatures acting on the CAZomes and SMGCs.

Data availability

M44 genomic data are available at the NCBI (BioProject number PRJNA517416, BioSample number SAMN10830013). This Whole Genome Sequencing (WGS) Project has been deposited at DDBJ/ENA/GenBank under the accession number SELE00000000. The raw genome resequencing data obtained have been deposited at the NCBI in the Short Read Archive database under the accession numbers SRR8568788-SRR8568862. Raw VCF files (SNP and indel variants) are available via Data Dryad (https://doi.org/10.5061/dryad.zs7h44j6x). The alignment and ML tree of mat1-2-1 were deposited in TreeBase (http://purl.org/phylo/treebase/phylows/study/TB2:S27214).

References

  1. Tigano A, Colella JP, MacManes MD. Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent. Mol Ecol. 2020;29:1300–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, et al. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol. 2014;23:753–73.

    Article  PubMed  Google Scholar 

  3. Martin F, Aerts A, Ahrén D, Brun A, Danchin EG, Duchaussoy F, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008;452:88–92.

    Article  CAS  PubMed  Google Scholar 

  4. Weiß M, Waller F, Zuccaro A, Selosse MA. Sebacinales-one thousand and one interactions with land plants. New Phytol. 2016;211:20–40.

    Article  PubMed  Google Scholar 

  5. Knapp DG, Németh JB, Barry K, Hainaut M, Henrissat B, Johnson J, et al. Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep. 2018;8:6321.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Martino E, Morin E, Grelet GA, Kuo A, Kohler A, Daghino S, et al. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. New Phytol. 2018;217:1213–29.

    Article  CAS  PubMed  Google Scholar 

  7. Arnold AE. Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev. 2007;21:51–66.

    Article  Google Scholar 

  8. Carroll G. Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology. 1988;69:2–9.

    Article  Google Scholar 

  9. Miller JD, Sumarah MW, Adams GW. Effect of a rugulosin-producing endophyte in Picea glauca on Choristoneura fumiferana. J Chem Ecol. 2008;34:362–8.

    Article  CAS  PubMed  Google Scholar 

  10. White JF Jr, Torres MS. Is plant endophyte-mediated defensive mutualism the result of oxidative stress protection? Physiol Plant. 2010;138:440–6.

    Article  CAS  PubMed  Google Scholar 

  11. May G, Nelson P. Defensive mutualisms: do microbial interactions within hosts drive the evolution of defensive traits? Funct Ecol. 2014;28:356–63.

    Article  Google Scholar 

  12. Carroll G. The foraging ascomycete, in: Abstracts of the 16th International Botanical Congress. St Louis, Missouri, USA, 1999.

  13. Müller MM, Valjakka R, Suokko A, Hantula J. Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers. Mol Ecol. 2001;10:1801–10.

    Article  PubMed  Google Scholar 

  14. Thomas DC, Vandegrift R, Ludden A, Carroll GC, Roy BA. Spatial ecology of the fungal genus Xylaria in a tropical cloud forest. Biotropica. 2016;48:381–93.

    Article  Google Scholar 

  15. Naranjo-Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc. 2019;94:1443–76.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Oono R, Lutzoni F, Arnold AE, Kaye L, U’Ren JM, May G, et al. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species. Am J Bot. 2014;101:1362–74.

    Article  PubMed  Google Scholar 

  17. Shao S, Jin Z. In Species Diversity and Extinction (ed. Tepper, GH) Ch. 15. Nova Science Publishers. 2010.

  18. Yuan ZL, Rao LB, Chen YC, Zhang CL, Wu YG. From pattern to process: species and functional diversity in fungal endophytes of Abies beshanzuensis. Fungal Biol. 2011;115:197–213.

    Article  PubMed  Google Scholar 

  19. Yuan ZL, Verkley GJM. Pezicula neosporulosa sp. nov. (Helotiales, Ascomycota), an endophytic fungus associated with Abies spp. in China and Europe. Mycoscience. 2014;56:205–13.

    Article  Google Scholar 

  20. Sieber T. Endophytic fungi in forest trees: are they mutualists? Fungal Biol Rev. 2007;21:75–89.

    Article  Google Scholar 

  21. Levis NA, Martin RA, O’Donnell KA, Pfennig DW. Intraspecific adaptive radiation: competition, ecological opportunity, and phenotypic diversification within species. Evolution. 2017;71:2496–509.

    Article  PubMed  Google Scholar 

  22. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, et al. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014;42:D699–D704.

    Article  CAS  PubMed  Google Scholar 

  23. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495.

    Article  CAS  PubMed  Google Scholar 

  24. Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–W101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Blin K, Wolf T, Chevrette MG, Lu XW, Schwalen CJ, Kautsar SA, et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45:W36–W41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52.

    Article  CAS  PubMed  Google Scholar 

  29. Enright AJ, Dongen SV, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Han MV, Thomas GW, Lugo-Martinez J, Hahn MW. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013;30:1987–97.

    Article  CAS  PubMed  Google Scholar 

  31. Walkowiak S, Rowland O, Rodrigue N, Subramaniam R. Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum. BMC Genomics. 2016;17:1014.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1–11.10.33.

    Article  Google Scholar 

  35. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123:585–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133:693–709.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Hutter S, Vilella AJ, Rozas J. Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinform. 2006;7:409.

    Article  CAS  Google Scholar 

  38. Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, et al. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet. 2019;15:e1008223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254–67.

    Article  CAS  PubMed  Google Scholar 

  40. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.

    Article  PubMed  CAS  Google Scholar 

  41. Looney B, Miyauchi S, Morin E, Drula E, Courty PE, Kohler A, et al. Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement? bioRxiv. 2021. https://doi.org/10.1101/2021.02.23.432530.

  42. Wey T, Schlegel M, Stroheker S, Gross A. MAT-gene structure and mating behavior of Hymenoscyphus fraxineus and Hymenoscyphus albidus. Fungal Genet Biol. 2016;87:54–63.

    Article  CAS  PubMed  Google Scholar 

  43. Zijlstra JD, Van’t Hof P, Baar J, Verkley GJM, Summerbell RC, Paradi I, et al. Diversity of symbiotic root endophytes of the Helotiales in ericaceous plants and the grass, Deschampsia flexuosa. Stud Mycol. 2005;53:147–62.

    Article  Google Scholar 

  44. Almario J, Jeena G, Wunder J, Langen G, Zuccaro A, Zuccaro A, et al. Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. Proc Natl Acad Sci USA. 2017;114:E9403–E9412.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, et al. The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol. 2016;120:26–42.

    Article  CAS  PubMed  Google Scholar 

  46. Perotto S, Daghino S, Martino E. Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? New Phytol. 2018;220:1141–7.

    Article  PubMed  Google Scholar 

  47. Wrzosek M, Ruszkiewicz-Michalska M, Sikora K, Damszel M, Sierota Z. The plasticity of fungal interactions. Mycol Prog. 2017;16:101–8.

    Article  Google Scholar 

  48. Parrent JL, James TY, Vasaitis R, Taylor AF. Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evol Biol. 2009;9:148.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Zhang F, Anasontzis GE, Labourel A, Champion C, Haon M, Kemppainen M, et al. The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1,4 endoglucanase that plays a key role in symbiosis development. New Phytol. 2018;220:1309–21.

    Article  CAS  PubMed  Google Scholar 

  50. Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, et al. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun. 2021;12:7227.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Schulz B, Sucker J, Aust HJ. Biologically active secondary metabolites of endophytic Pezicula species. Mycol Res. 1995;99:1007–15.

    Article  CAS  Google Scholar 

  52. Tanney JB, McMullin DR, Miller JD. Toxigenic Foliar Endophytes from the Acadian Forest. In: Pirttilä A, Frank A (eds) Endophytes of Forest Trees. Forestry Sciences, vol 86. Springer, Cham. 2018;343–81.

  53. Yue Q, Li Y, Chen L, Zhang X, Liu X, An Z, et al. Genomics-driven discovery of a novel self-resistance mechanism in the echinocandin-producing fungus Pezicula radicicola. Environ Microbiol. 2018;20:3154–67.

    Article  CAS  PubMed  Google Scholar 

  54. Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, et al. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol. 2021;30:1155–73.

    Article  CAS  PubMed  Google Scholar 

  55. Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, et al. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics. 2019;20:430.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Yang Y, Liu X, Cai J, Chen Y, Li B, Guo Z, et al. Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae. BMC Genomics. 2019;20:782.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Franco MEE, Wisecaver JH, Arnold AE, Ju YM, Slot JC, Ahrendt S, et al. Secondary metabolism drives ecological breadth in the Xylariaceae. bioRxiv. 2021. https://doi.org/10.1101/2021.06.01.446356.

  58. Matsuda Y, Yamakawa M, Inaba T, Obase K, Ito S. Intraspecific variation in mycelial growth of Cenococcum geophilum isolates in response to salinity gradients. Mycoscience. 2017;58:369–77.

    Article  Google Scholar 

  59. Taylor JW, Branco S, Gao C, Hann-Soden C, Montoya L, Sylvain I, et al. Sources of fungal genetic variation and associating it with phenotypic diversity. Microbiol Spectr. 2017;5:1–21.

    Article  CAS  Google Scholar 

  60. Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, et al. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. New Phytol. 2018;220:1161–71.

    Article  CAS  PubMed  Google Scholar 

  61. McCutcheon TL, Carroll GC, Schwab S. Genotypic diversity in populations of a fungal endophyte from Douglas Fir. Mycologia. 1993;85:180–6.

    Article  Google Scholar 

  62. Perotto S, Girlanda M, Martino E. Ericoid mycorrhizal fungi: some new perspectives on old acquaintances. Plant Soil. 2002;244:41–53.

    Article  CAS  Google Scholar 

  63. Müller MM, Valjakka R, Hantula J. Genetic diversity of Lophodermium piceae in South Finland. For Pathol. 2007;37:329–37.

    Article  Google Scholar 

  64. Morgenstern K, Polster J-U, Krabel D. Genetic variation between and within two populations of Rhabdocline pseudotsugae in Germany. Can J Res. 2016;46:716–24.

    Article  CAS  Google Scholar 

  65. Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol. 2015;6:996.

    Article  PubMed  PubMed Central  Google Scholar 

  66. Gasca-Pineda J, Velez P, Hosoya T. Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan. MycoKeys. 2020;65:1–24.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Groenewald M, Linde CC, Groenewald JZ, Crous PW. Indirect evidence for sexual reproduction in Cercospora beticola populations from sugar beet. Plant Pathol. 2008;57:25–32.

    CAS  Google Scholar 

  68. Nordborg M, Charlesworth B, Charlesworth D. Increased levels of polymorphism surrounding selectively maintained sites in highly selfing species. Proc R Soc B. 1996;263:1033–9.

    Article  Google Scholar 

  69. Koenig D, Hagmann J, Li R, Bemm F, Slotte T, Neuffer B, et al. Long-term balancing selection drives evolution of immunity genes in Capsella. Elife. 2019;8:e43606.

    Article  PubMed  PubMed Central  Google Scholar 

  70. Carbone I, Jakobek JL, Ramirez-Prado JH, Horn BW. Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus. Mol Ecol. 2007;16:4401–17.

    Article  CAS  PubMed  Google Scholar 

  71. Drott MT, Debenport T, Higgins SA, Buckley DH, Milgroom MG. Fitness cost of aflatoxin production in Aspergillus flavus when competing with soil microbes could maintain balancing selection. mBio. 2019;10:e02782–18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Chen F, Goodwin PH, Khan A, Hsiang T. Population structure and mating-type genes of Colletotrichum graminicola from Agrostis palustris. Can J Microbiol. 2002;48:427–36.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

Research in Yuan’s lab is financially supported by the Fundamental Research Funds for the Central Non-profit Research of the Chinese Academy of Forestry (CAFYBB2019ZA001-3) and the National Natural Science Foundation of China (No. 31722014 and 31772032). Research in Martin’s lab is supported by the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01) and the Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. We extend our sincere gratitude to Dr. Primrose Boynton (Wheaton College, USA) and Dr. Fengyan Bai (State Key Laboratory of Mycology, Chinese Academy of Sciences) for useful discussions. We thank Dr Yougui Wu (Fengyangshan-Baishanzu National Nature Reserve, China) for providing basic information about the wild relict fir trees.

Author information

Authors and Affiliations

Authors

Contributions

ZLY and QW conceived and designed this study. XYW conducted molecular and microbiological work. LXX performed HPLC analysis. ZLY, ISD, GHS completed bioinformatics, evolutionary, and phylogenetic analyses and interpreted the results with guidance from QW, JYW, and ZJL. ISD and XLS helped ZLY and QW with figure preparation. ZLY wrote the manuscript, and BPS, FMM, ZHZ, ISD, and CPK contributed improvements to the text. ZLY and ISD prepared the revised version of the manuscript. LP contributed text to the supplementary file. FMM, QW, BPS, CPK, and CF aided in the discussion of results. All authors approved the final version of the manuscript.

Corresponding authors

Correspondence to Zhilin Yuan or Francis M. Martin.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yuan, Z., Wu, Q., Xu, L. et al. Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism. ISME J 16, 1294–1305 (2022). https://doi.org/10.1038/s41396-021-01176-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41396-021-01176-6

Search

Quick links