Multigene phylogeny of Endogonales, an early diverging lineage of fungi associated with plants

IMA Fungus

Volumn 8, Issue 2, 2017, Pages 245-257

  Desirò, Alessandro ^a   Rimington, William R ^b   Jacob, Alison ^b   Pol, Natalie Vande ^a   Smith, Matthew E ^c   Trappe, James M ^d   Bidartondo, Martin I ^b,e   Bonito, Gregory ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c UNIVERSITY OF FLORIDA   (United States)

^d OREGON STATE UNIVERSITY   (United States)

^e JODRELL LABORATORY   (United Kingdom)

Author keywords

Densosporaceae Endogone; Endophytes Jimgerdemannia; Multigene phylogeny

Indexed keywords

EID: 85039753796     PISSN: 22106340     EISSN: 22106359     Source Type: Journal    
DOI: 10.5598/imafungus.2017.08.02.03     Document Type: Article

References (69)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402
2. Berch SM, Castellano MA (1986) Sporulation of Endogone pisiformis in axenic and monoxenic culture. Mycologia 78: 292-295
3. Berch SM, Fortin JA (1983) Endogone pisiformis: axenic culture and associations with Sphagnum, Pinus sylvestris, Allium cepa, and Allium porrum. Canadian Journal of Botany 61: 899-905
4. Berch SM, Fortin JA (1982) Germination of zygospores of Endogone incrassata. Mycologia 74: 861-864
5. Berkeley MJ, Broome CE (1874) Enumeration of the fungi of Ceylon. Part II. Botanical Journal of the Linnean Society 14: 29-141
6. Berkeley MJ, Broome CE (1846) Notices of British hypogaeous fungi. Annals and Magazine of Natural History 18: 73-82
7. Bidartondo MI, Read DJ, Trappe JM, Merckx V, Ligrone R, et al. (2011) The dawn of symbiosis between plants and fungi. Biology Letters 7: 574-577
8. Bonfante P, Desirò A (2017) Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota. The ISME Journal 11: 1727-1735
9. Chu-Chou M, Grace LJ (1984) Endogone flammicorona and Tuber sp. as mycorrhizal fungi of Pinus radiata in New Zealand. New Zealand Journal of Botany 22: 525-531
10. Chu-Chou M, Grace LJ (1979) Endogone flammicorona as a mycorrhizal symbiont of Douglas fir in New Zealand. New Zealand Journal of Forest Science 9: 344-347
11. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552
12. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772
13. Desirò A, Faccio A, Kaech A, Bidartondo MI, Bonfante P (2015) Endogone, one of the oldest plant-associated fungi, host unique Mollicutes-related endobacteria. New Phytologist 205: 1464-1472
14. Desirò A, Duckett JG, Pressel S, Villarreal JC, Bidartondo MI (2013) Fungal symbioses in hornworts: a chequered history. Proceedings of the Royal Society of London, B: Biological Sciences 280: 20130207
15. Doyle J (1991) DNA protocols for plants. In: Molecular techniques in taxonomy (GM Hewitt, AWB Johnston & JPW Young, eds): 283-293. Berlin: Springer
16. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797
17. Fassi B, Fontana A, Trappe JM (1969) Ectomycorrhizae formed by Endogone lactiflua with species of Pinus and Pseudotsuga. Mycologia 5: 412-414
18. Fassi B, Palenzona M (1969) Mycorrhizal synthesis between Pinus strobus, Pseudotsuga menziesii and Endogone lactiflua. Allionia 15: 105-114
19. Fassi B (1965) Ectotrophic mycorrhizae produced by Endogone lactiflua Berk, on Pinus strobus L. Allionia 11: 7-15
20. Field KJ, Rimington WR, Bidartondo MI, Allinson KE, Beerling DJ, et al. (2016) Functional analysis of liverworts in dual symbiosis with Glomeromycota and Mucoromycotina fungi under a simulated Palaeozoic CO2 decline. The ISME Journal 10: 1514-1526
21. Field KJ, Pressel S, Duckett JG, Rimington WR, Bidartondo MI (2015) Symbiotic options for the conquest of land. Trends in Ecology and Evolution 30: 477-486
22. Field KJ, Rimington WR, Bidartondo MI, Allinson KE, Beerling DJ, et al. (2015) First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO2. New Phytologist 205: 743-756
23. Gerdemann JW, Trappe JM (1974) Endogonaceae in the Pacific Northwest. Mycological Memoirs 5: 1-76
24. Hirose D, Degawa Y, Yamamoto K, Yamada A (2014) Sphaerocreas pubescens is a member of the Mucoromycotina closely related to fungi associated with liverworts and hornworts. Mycoscience 55: 221-226
25. Ihrmark K, Bödeker IT, Cruz-Martinez K, Friberg H, Kubartova A, et al. (2012) New primers to amplify the fungal ITS2 region-evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 82: 666-677
26. Jabaji-Hare SH, Charest PM (1987) Ultrastructural and cytochemical observations on the somatic phase of Endogone pisiformis (Endogonaceae). Mycologia 79: 433-444
27. James TY, KauffF, Schoch CL, Matheny PB, Hofstetter V, et al. (2006) Reconstructing the early evolution of Fungi using a sixgene phylogeny. Nature 443: 818-822
28. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780
29. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649
30. Krings, M, Taylor TN, Dotzler N, Persichini G (2012) Fossil fungi with suggested affinities to the Endogonaceae from the Middle Triassic of Antarctica. Mycologia 104: 835-844
31. Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DG, et al. (2014) Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genetics 10: p.e1004078
32. Link HF (1809) Observationes in ordines plantarum naturales. Dissertatio I. Magazin der Gesellschaft Naturforschenden Freunde Berlin 3: 3-42
33. Lloyd CG (1918) Mycological Notes 56. Mycological Writings 5: 797-812
34. Maser C, Trappe JM, Nussbaum RA (1978) Fungal-small mammal interrelationships with emphasis on Oregon coniferous forests. Ecology 59: 799-809
35. McGee PA, Trappe JM (2002) The Australian zygomycetous mycorrhizal fungi. II. Further Australian sporocarpic Glomaceae. Australian Systematic Botany 15: 115-124
36. McGee PA (1996) The Australian zygomycetous mycorrhizal fungi: the genus Densospora gen. nov. Australian Systematic Botany 9: 329-336
37. Orchard S, Hilton S, Bending GD, Dickie IA, Standish RJ, et al. (2017) Fine endophytes (Glomus tenue) are related to Mucoromycotina, not Glomeromycota. New Phytologist 213: 481-486
38. Orchard S, Standish RJ, Dickie IA, Renton M, Walker C, et al. (2017) Fine root endophytes under scrutiny: a review of the literature on arbuscule-producing fungi recently suggested to belong to the Mucoromycotina. Mycorrhiza 27: 619-638
39. Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, et al. (2013) Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One 8: E62419
40. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A (2010) How many bootstrap replicates are necessary? Journal of Computational Biology 17: 337-354
41. Rehner SA, Buckley E (2005) A Beauveria phylogeny inferred from nuclear ITS and EF1-a sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97: 84-98
42. Rimington WR, Pressel S, Duckett JG, Bidartondo MI (2015) Fungal associations of basal vascular plants: reopening a closed book? New Phytologist 205: 1394-1398
43. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542
44. Saccardo PA (1882) Fungi boreali-Americani. Michelia 2: 564-582
45. Smit E, Leeflang P, Glandorf B, Van Elsas JD, Wernars K (1999) Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Applied and Environmental Microbiology 65: 2614-2621
46. Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, et al. (2016) Zygomycete genealogy of life (ZyGoLife): a phylumlevel phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108: 1028-1046
47. Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313
48. Stürmer SL (2012) A history of the taxonomy and systematics of arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota. Mycorrhiza 22: 247-258
49. Tandy PA (1975) Sporocarpic species of Endogonaceae in Australia. Australian Journal of Botany 23: 849-866
50. Tedersoo L, Smith ME (2017) Ectomycorrhizal fungal lineages: detection of four new groups and notes on consistent recognition of ectomycorrhizal taxa in high-throughput sequencing studies. In: Biogeography of Mycorrhizal Symbiosis (Tedersoo L, ed.): 125-142. Springer International Publishing
51. Tedersoo L, Liiv I, Kivistik PA, Anslan S, Kõljalg U, et al. (2016) Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens. MycoKeys 13: 1
52. Tedersoo L, Smith ME (2013) Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground. Fungal Biology Reviews 27: 83-99
53. Tedersoo L, Jairus T, Horton BM, Abarenkov K, Suvi T, et al. (2008) Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxonspecific primers. New Phytologist 180: 479-490
54. Thaxter R (1922) A revision of the Endogoneae. Proceedings of the American Academy of Arts and Sciences 57: 289-350
55. Torres-Cruz TJ, Tobias TL, Almatruk M, Hesse CN, Kuske CR et al. (2017) Bifiguratus adelaidae gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats. Mycologia 109: 363-378
56. Trappe JM, Gerdemann JW (1972) Endogone flammicorona sp. nov., a distinctive segregate from Endogone lactiflua. Transactions of the British Mycological Society 59: 403-407
57. Truong C, Mujic AB, Healy R, Kuhar F, Furci G, et al. (2017) How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. New Phytologist 214: 913-919
58. Vetrovský T, Kolarík M, Žifcáková L, Zelenka T, Baldrian P (2015) The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities. Molecular Ecology Resources 16: 388-401
59. Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238-4246
60. Walker C (1985) Endogone lactiflua forming ectomycorrhizas with Pinus contorta. Transactions of the British Mycological Society 84: 353-355
61. Warcup JH (1990) Taxonomy, culture and mycorrhizal associations of zygosporic Endogonaceae. Mycological Research 94: 173-178
62. Warcup JH (1985) Ectomycorrhizal formation by Glomus tubiforme. New Phytologist 99: 267-272
63. Warcup JH (1975) A culturable Endogone associated with eucalyptus. In: Endomycorrhizas (Sanders FE, Mosse B, Tinker PB, eds): 53-63. London: Academic Press
64. White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications (Innis MA, Gelfand DH, Sninsky JJ & White TJ, eds): 315-322. San Diego: Academic Press
65. Wu CG, Lin SJ (1997) Endogonales in Taiwan: a new genus with unizygosporic sporocarps and a hyphal mantle. Mycotaxon 64: 179-188
66. Yamamoto K, Endo N, Degawa Y, Fukuda M, Yamada A (2017) First detection of Endogone ectomycorrhizas in natural oak forests. Mycorrhiza 27: 295-301
67. Yamamoto K, Degawa Y, Takashima Y, Fukuda M, Yamada A (2017) Endogone corticioides sp. nov. from subalpine conifer forests in Japan and China, and its multi-locus phylogeny. Mycoscience 58: 23-29
68. Yamamoto K, Degawa Y, Hirose D, Fukuda M, Yamada A (2015) Morphology and phylogeny of four Endogone species and Sphaerocreas pubescens collected in Japan. Mycological Progress 14: 86
69. Yao YJ, Pegler DN, Young TWK (1995) Youngiomyces, a new genus in Endogonales (Zygomycotina). Kew Bulletin 50: 349-357