Phylogenetic relationship and species delimitation of matsutake and allied species based on multilocus phylogeny and haplotype analyses

Mycologia

Volumn 104, Issue 6, 2012, Pages 1369-1380

  Ota, Yuko ^a   Yamanaka, Takashi ^a   Murata, Hitoshi ^a   Neda, Hitoshi ^a   Ohta, Akira ^b   Kawai, Masataka ^c   Yamada, Akiyoshi ^d   Konno, Miki ^e   Tanaka, Chihiro ^f  

^a FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^b Shiga Forest Research Center   (Japan)

^c Nara Forest Research Institute   (Japan)

^d SHINSHU UNIVERSITY   (Japan)

^e Miyagi Prefectural Forestry Technology Institute   (Japan)

^f KYOTO UNIVERSITY   (Japan)

Author keywords

Ectomycorrhizal fungi; Median joining haplotype network

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN; RIBOSOMAL SPACER DNA;

BROAD-LEAVED FOREST; CONIFEROUS TREE; DATA SET; ECTOMYCORRHIZA; EDIBLE SPECIES; GENOTYPE; GEOGRAPHICAL DISTRIBUTION; MUSHROOM; NORTHERN HEMISPHERE; PHYLOGENETICS; RELATEDNESS;

ARTICLE; CHEMISTRY; CLASSIFICATION; CONIFER; DNA SEQUENCE; FRUITING BODY; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; ISOLATION AND PURIFICATION; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; MULTILOCUS SEQUENCE TYPING; MYCORRHIZA; NUCLEOTIDE SEQUENCE; PHYLOGENY; TREE; TRICHOLOMA;

BASE SEQUENCE; CONIFEROPHYTA; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; FRUITING BODIES, FUNGAL; FUNGAL PROTEINS; GENETIC VARIATION; HAPLOTYPES; MOLECULAR SEQUENCE DATA; MULTILOCUS SEQUENCE TYPING; MYCOLOGICAL TYPING TECHNIQUES; MYCORRHIZAE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TREES; TRICHOLOMA;

BASIDIOMYCOTA; CONIFEROPHYTA; FUNGI; TRICHOLOMA; TRICHOLOMA BAKAMATSUTAKE; TRICHOLOMA CALIGATUM; TRICHOLOMA FULVOCASTANEUM; TRICHOLOMA MAGNIVELARE; TRICHOLOMA MATSUTAKE;

EID: 84871801291     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/12-068     Document Type: Article

References (48)

1. Amend A, Garbelotto M, Fang Z, Keeley S. 2010. Isolation by landscape in populations of a prized edible mushroom Tricholoma matsutake. Conserv Genet 11:795-802
2. Babasaki K, Neda H, Murata H. 2007. megB1, a novel macroevolutionary genomic marker of the fungal phylum Basidiomycota. Biosci Biotechnol Biochem 71:1927- 1939
3. Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48
4. Bao D, Koike A, Yao F, Yamanaka K, Aimi T, Kitamoto Y. 2007. Analyses of the genetic diversity of matsutake isolates collected from different ecological environments in Asia. J Wood Sci 53:344-350
5. Bergius N, Danell E. 2000. The Swedish matsutake (Tricholoma nauseosum syn. T. matsutake): distribution, abundance and ecology. Scand J For Res 15:318-325
6. Bon M. 1984. Les tricholomes de France, et d'Europe occidentale. É dition Lechevalier SARL, Paris. 324 p.
7. Chapela IH, Garbelotto M. 2004. Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs. Mycologia 96: 730-741
8. Dobinson KF, Harris RE, Hamer JE. 1993. Grasshopper, a long terminal repeat (LTR) retroelement in the phytopathogenic fungus Magnaporthe grisea. Mol Plant Microbe Interact 6:114-126
9. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
10. Gardes M, Bruns T. 1993. ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2:113-118
11. Hall TA. 1999. BioEdit: author-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
12. Hongo T. 1960. Notes on Japanese larger fungi 15. J Japan Bot 35:83-90.
13. Hongo T. 1974. Notes on Japanese larger fungi 21. J Japan Bot 49:295-305.
14. Hosford D, Pilz D, Molina R, Amaranthus M. 1997. Ecology and management of the commercially harvested American Matsutake mushrooms. USDA Forest service PNW-GTR-412. 68 p.
15. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755
16. Intini M, Dogan HH, Riva A. 2003. Tricholoma anatolicum spec. nov.: un nuovo membro del gruppo matsutake. Micol Veg Mediterr 18:135-142.
17. Ito S. 1959. Mycological flora of Japan. Vol 2, No 5. Tokyo: Yokendo. 658 p. (in Japanese).
18. Japan Tariff Association. 2010. Japan exports and imports (commodity by country). Tokyo: Japan Tariff Ass. 1504 p.
19. Jargeat P, Martos F, Carriconde F, Gryta H, Moreau P-A, Gardes M. 2010. Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota). Mol Ecol 19:5216-5230
20. Johannesson H, Johannesson H, Stenlid J. 2000. Development of primer sets to amplify fragments of conserved genes for systematic and population studies in the genus Daldinia. Mol Ecol 9:375-378
21. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066
22. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Bioinformatics 9:286-298.
23. Kauserud H, Schumacher T. 2001. Outcrossing or inbreeding: DNA markers provide evidence for type of reproductive mode in Phellinus nigrolimitatus (Basidiomycota). Mycol Res 105:676-683
24. Kytövuori I. 1988. The Tricholoma caligatum group in Europe and north Africa. Karstenia 28:65-77.
25. Lim SR, Fischer A, Berbee M, Berch SM. 2003. Is the booted Tricholoma in British Columbia really Japanese matsutake? BC J Ecosyst Manage 3:1-7.
26. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452
27. Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo J-M, Ge Z-W, Yang Z-L, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982-995
28. Matsushita N, Kikuchi K, Sasaki Y, Guerin-Laguette A, Lapeyrie F, Vaario L-M, Intini M, Suzuki K. 2005. Genetic relationship of Tricholoma matsutake and T. nauseosum from the northern hemisphere based on analyses of ribosomal DNA spacer regions. Mycoscience 46:90-96
29. Moncalvo JM, Vilgalys R, Readhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni T, Thorn RG, Jacobsson S, Clémençon H, Miller OK Jr. 2002. One hundred seventeen clades of euagarics. Mol Phyl Evol 23:357-400
30. Murata H, Babasaki K. 2005. Intra- and interspecific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycorrhiza 15:505-512
31. Murata H, Babasaki K, Miyazaki Y, Yamada A. 2002. Genetic evidence that two types of retroelements evolved through different pathways in ectomycorrhizal homobasidiomycetes Tricholoma spp. Biosci Biotechnol Biochem 66:1880-1886
32. Murata H, Babasaki K, Yamada A. 2005. Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on σmarY1, the long terminal repeat of gypsy-type retroelement marY1. Mycorrhiza 15:179-186
33. Murata H, Babasaki K, Saegusa T, Takemoto K, Yamada A, Ohta A. 2008. Traceability of Asian matsutake, specialty mushrooms produced by the ectomycorrhizal basidiomycete Tricholoma matsutake, on the basis of retroelementbased DNA markers. Appl Environ Microbiol 74:2023- 2031
34. Murata H, Yamada A, Babasaki K. 1999. Identification of repetitive sequences containing motifs of retrotransposons in the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycologia 91:766-775
35. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia Univ. Press. 512 p.
36. Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Uppsala, Sweden: Evolutionary Biology Centre, Uppsala University.
37. Ogawa M. 1978. The biology of matsutake. Tsukiji-shokan, Tokyo, Japan. (In Japanese)
38. Peck CH. 1878. Report of the botanist. Ann. Rep N.Y. State Mus Nat Hist 29:29-82.
39. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574
40. Sanmee R, Dell B, Lumyong P, Lumyong S. 2007. First record of Tricholoma fulvocastaneum from Thailand. Mycoscience 48:131-133
41. Swofford DL. 2002. PAUPz.ast; 4.0b10: phylogenetic analysis using parsimony (z.ast;and other methods). Sunderland, Massachusetts: Sinauer Associates.
42. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
43. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28:2731-2739
44. Yamada A, Kobayashi H, Maeda K, Murata H, Kalmiş E, Kalyoncu F, Fukuda M. 2010. In vitro ectomycorrhizal specificity between the Asian red pine Pinus densiflora and Tricholoma matsutake and allied species from worldwide Pinaceae and Fagaceae forests. Mycorrhiza 20:333-339
45. Yamanaka K, Aimi T, Wan J, Cao Hui, Chen M. 2011. Species of host trees associated with Tricholoma matsutake and close allies in Asia. Mushroom Sci Biotechnol 19:79-87.
46. Viviani D. 1834. I funghi d'Italia e principalmente le loro specie mangerecce, velenose o sospette discritte ed illustrate con tavole disegnate, e colorite dal vero. Genova. 64 p.
47. Wan J, Koike A, Yamanaka K, Sotome K, Morinaga T, Tanaka C, Terashima Y, Aimi T. 2012. Genetic diversity of Tricholoma matsutake and close allies associated with broad- leaved trees in Asia. Mushroom Sci Biotechol 19: 167-174.
48. Xu J, Sha T, Li YC, Zhao ZW, Yang ZL. 2008. Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China. Mol Ecol 17:1238-1247