Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements

Autoři: Byoungnam Min aff001;  Hyeokjun Yoon aff002;  Julius Park aff001;  Youn-Lee Oh aff003;  Won-Sik Kong aff003;  Jong-Guk Kim aff002;  In-Geol Choi aff001
Působiště autorů: Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea aff001;  School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu, Korea aff002;  Mushroom Research Division, National Institute of Horticulture and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, Korea aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0227923


Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over “CpG” dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in the hyphae, where symbiotic interactions occur with the hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domains (PF01695) were conserved across taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in the hyphae. Similar to other ectomycorrhizal genomes, the CAZyme gene set was reduced in T. matsutake, including losses in the glycoside hydrolase genes. The T. matsutake genome sequence provides insight into the causes and consequences of genome size inflation.

Klíčová slova:

Comparative genomics – Fungal genetics – Fungal genomics – Gene prediction – Genomic libraries – Protein domains – Transcription factors – Transposable elements


1. Park H, Ka K-H. Spore Dispersion of Tricholoma matsutake at a Pinus densiflora Stand in Korea. Mycobiology. 2010;38: 203–205. doi: 10.4489/MYCO.2010.38.3.203 23956655

2. Kuo A, Kohler A, Martin FM, Grigoriev IV. Expanding genomics of mycorrhizal symbiosis. Front Microbiol. 2014;5: 582. doi: 10.3389/fmicb.2014.00582 25408690

3. Molloy S. ECM fungi and all that JAZz. Nat Rev Microbiol. 2014;12: 459. Available: https://doi.org/10.1038/nrmicro3305 24931037

4. Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS. Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol. 2016;14: 760–773. doi: 10.1038/nrmicro.2016.149 27795567

5. Trudell SA, Xu J, Saar I, Justo A, Cifuentes J. North American matsutake: names clarified and a new species described. Mycologia. 2017;109: 379–390. doi: 10.1080/00275514.2017.1326780 28609221

6. Miles PG, Chang ST. Mushrooms: Cultivation, Nutritional Value, Medicinal Effect, and Environmental Impact. CRC Press; 2004. Available: https://books.google.com/books?id=XO4EGzpp1M0C

7. Ohm RA, de Jong JF, de Bekker C, Wosten HAB, Lugones LG. Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation. Mol Microbiol. 2011;81: 1433–1445. doi: 10.1111/j.1365-2958.2011.07776.x 21815946

8. Wessels JGH, De Vries OMH, Asgeirsdottir SA, Schuren FHJ. Hydrophobin Genes Involved in Formation of Aerial Hyphae and Fruit Bodies in Schizophyllum. Plant Cell. 1991;3: 793–799. doi: 10.1105/tpc.3.8.793 12324614

9. Ohm RA, Aerts D, Wosten HAB, Lugones LG. The blue light receptor complex WC-1/2 of Schizophyllum commune is involved in mushroom formation and protection against phototoxicity. Environ Microbiol. 2013;15: 943–955. doi: 10.1111/j.1462-2920.2012.02878.x 22998561

10. Nowrousian M. Fungal Genomics. Fungal Genomics, 2nd Edition. 2014. pp. 149–172. doi: 10.1007/978-3-642-45218-5_7

11. Kidwell MG, Lisch DR. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution. 2001;55: 1–24. doi: 10.1111/j.0014-3820.2001.tb01268.x 11263730

12. Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 2008;9: 397–405. doi: 10.1038/nrg2337 18368054

13. Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, et al. Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun. 2016;7: 12662. doi: 10.1038/ncomms12662 27601008

14. Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, et al. Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. Genome Biol Evol. 2014;6: 1564–1578. doi: 10.1093/gbe/evu121 24923322

15. Castanera R, López-Varas L, Borgognone A, LaButti K, Lapidus A, Schmutz J, et al. Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles. PLOS Genet. 2016;12: e1006108. Available: https://doi.org/10.1371/journal.pgen.1006108 27294409

16. Min B, Grigoriev IV, Choi I-G. FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation. Bioinformatics. 2017;33: 2936–2937. doi: 10.1093/bioinformatics/btx353 28582481

17. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31: 3210–3212. doi: 10.1093/bioinformatics/btv351 26059717

18. Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J. An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol. 2005;350: 200–214. doi: 10.1016/j.jmb.2005.03.058 15922354

19. Nakayashiki H. RNA silencing in fungi: Mechanisms and applications. FEBS Lett. 2005;579: 5950–5957. doi: 10.1016/j.febslet.2005.08.016 16137680

20. Horns F, Petit E, Yockteng R, Hood ME. Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi. Genome Biol Evol. 2012;4: 240–247. doi: 10.1093/gbe/evs005 22250128

21. Freitag M, Williams RL, Kothe GO, Selker EU. A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci. 2002;99: 8802–8807. doi: 10.1073/pnas.132212899 12072568

22. Amselem J, Lebrun M-H, Quesneville H. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics. 2015;16: 141. doi: 10.1186/s12864-015-1347-1 25766680

23. Coste F, Kemp C, Bobezeau V, Hetru C, Kellenberger C, Imler J-L, et al. Crystal Structure of Diedel, a Marker of the Immune Response of Drosophila melanogaster. PLoS One. 2012;7: 1–8. doi: 10.1371/journal.pone.0033416 22442689

24. Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, et al. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol. 2010;28: 957–963. doi: 10.1038/nbt.1643 20622885

25. Bayry J, Aimanianda V, Guijarro JI, Sunde M, Latgé J-P. Hydrophobins—Unique Fungal Proteins. PLOS Pathog. 2012;8: e1002700. Available: https://doi.org/10.1371/journal.ppat.1002700 22693445

26. Martin F, Aerts A, Ahrén D, Brun A, Danchin EGJ, Duchaussoy F, et al. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature. 2008;452: 88–92. doi: 10.1038/nature06556 18322534

27. Kulkarni RD, Kelkar HS, Dean RA. An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins. Trends Biochem Sci. 2003;28: 118–121. doi: 10.1016/S0968-0004(03)00025-2 12633989

28. Beck MR, Dekoster GT, Cistola DP, Goldman WE. NMR structure of a fungal virulence factor reveals structural homology with mammalian saposin B. Mol Microbiol. 2009;72: 344–353. doi: 10.1111/j.1365-2958.2009.06647.x 19298372

29. Yeo CC, Poh CL. Characterization of IS1474, an insertion sequence of the IS21 family isolated from Pseudomonas alcaligenes NCIB 9867. FEMS Microbiol Lett. 1997;149: 257–263. doi: 10.1111/j.1574-6968.1997.tb10338.x 9141667

30. Schrader CU, Lee L, Rey M, Sarpe V, Man P, Sharma S, et al. Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping. Mol Cell Proteomics. 2017;16: 1162–1171. doi: 10.1074/mcp.M116.066803 28404794

31. Martin-Cuadrado AB, Encinar del Dedo J, de Medina-Redondo M, Fontaine T, del Rey F, Latge JP, et al. The Schizosaccharomyces pombe endo-1,3-beta-glucanase Eng1 contains a novel carbohydrate binding module required for septum localization. Mol Microbiol. 2008;69: 188–200. doi: 10.1111/j.1365-2958.2008.06275.x 18466295

32. Zhao Z, Liu H, Wang C, Xu J-R. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics. 2013;14: 274. doi: 10.1186/1471-2164-14-274 23617724

33. Bae B, Ohene-Adjei S, Kocherginskaya S, Mackie RI, Spies MA, Cann IKO, et al. Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA. J Biol Chem. 2008;283: 12415–12425. doi: 10.1074/jbc.M706513200 18025086

34. Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 2013;6: 41. doi: 10.1186/1754-6834-6-41 23514094

35. Fulton TM, Chunwongse J, Tanksley SD. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Report. 1995;13: 207–209. doi: 10.1007/BF02670897

36. Yoon H, Kong W-S, Kim YJ, Kim J-G. Complete mitochondrial genome of the ectomycorrhizal fungus Tricholoma matsutake. Mitochondrial DNA Part A, DNA mapping, Seq Anal. 2016;27: 3855–3857. doi: 10.3109/19401736.2014.958699 25208172

37. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357. Available: https://doi.org/10.1038/nmeth.1923 22388286

38. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 2008;18: 810–820. doi: 10.1101/gr.7337908 18340039

39. Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Front Genet. 2013;4: 237. doi: 10.3389/fgene.2013.00237 24348509

40. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30: 1236–1240. doi: 10.1093/bioinformatics/btu031 24451626

41. Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11: 1650–1667. doi: 10.1038/nprot.2016.095 27560171

42. Mandric I, Temate-Tiagueu Y, Shcheglova T, Al Seesi S, Zelikovsky A, Mandoiu II. Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. Bioinformatics. 2017;33: 3302–3304. doi: 10.1093/bioinformatics/btx365 28605502

43. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16: 157. doi: 10.1186/s13059-015-0721-2 26243257

44. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30: 1312–1313. doi: 10.1093/bioinformatics/btu033 24451623

45. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30: 772–780. doi: 10.1093/molbev/mst010 23329690

46. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56: 564–577. doi: 10.1080/10635150701472164 17654362

47. Kummerfeld SK, Teichmann SA. DBD: a transcription factor prediction database. Nucleic Acids Res. 2006;34: D74–81. doi: 10.1093/nar/gkj131 16381970

48. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44: D279–85. doi: 10.1093/nar/gkv1344 26673716

49. Price MN, Dehal PS, Arkin AP. FastTree 2–Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5: e9490. Available: https://doi.org/10.1371/journal.pone.0009490 20224823

50. Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40: W445–51. doi: 10.1093/nar/gks479 22645317

51. Kim K-T, Jeon J, Choi J, Cheong K, Song H, Choi G, et al. Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association. Front Plant Sci. 2016;7: 186. doi: 10.3389/fpls.2016.00186 26925088

52. Lum G, Min XJ. FunSecKB: the Fungal Secretome KnowledgeBase. Database. 2011;2011. doi: 10.1093/database/bar001 21300622

53. Garcia K, Ané J-M. Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins. Front Microbiol. 2016;7: 1734. doi: 10.3389/fmicb.2016.01734 27853454

54. Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8: 785. Available: https://doi.org/10.1038/nmeth.1701 21959131

55. Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, et al. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35: W585–7. doi: 10.1093/nar/gkm259 17517783

56. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007;2: 953–971. doi: 10.1038/nprot.2007.131 17446895

57. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305: 567–580. doi: 10.1006/jmbi.2000.4315 11152613

58. Min XJ. Evaluation of computational methods for secreted protein prediction in different eukaryotes. J Proteomics Bioinform. 2010;3: 143–147.

59. de Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, et al. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 2006;34: W362–5. doi: 10.1093/nar/gkl124 16845026

60. Fankhauser N, Maser P. Identification of GPI anchor attachment signals by a Kohonen self-organizing map. Bioinformatics. 2005;21: 1846–1852. doi: 10.1093/bioinformatics/bti299 15691858

61. Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics. 2016;32: 767–769. doi: 10.1093/bioinformatics/btv661 26559507

62. Hane JK, Oliver RP. RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics. 2008;9: 478. doi: 10.1186/1471-2105-9-478 19014496

Článek vyšel v časopise


2020 Číslo 1
Nejčtenější tento týden