453
Views
46
CrossRef citations to date
0
Altmetric
Original Articles

Phylogeny and diversity of Japanese truffles (Tuber spp.) inferred from sequences of four nuclear loci

, &
Pages 779-794 | Received 05 May 2010, Accepted 27 Dec 2010, Published online: 20 Jan 2017

LITERATURE CITETD

  • Aanen DK, Kuyper TW. 1999. Intercompatibility tests in the Hebeloma crustuliniforme complex in northwestern Europe. Mycologia 91:783–795, doi:10.2307/3761532
  • Bonito G, Trappe JM, Vilgalys R. 2009. North American truffles in the Tuberaceae: molecular and morphological perspectives. Acta Bot Yunnanica 16:39–51.
  • ———, ———, Rawlinson P, Vilgalys R. 2010. Improved resolution of major clades within Tuber and taxonomy of species within Tuber gibbosum complex. Mycologia 102:1042–1057, doi:10.3852/09-213
  • Brock PM, Döring H, Bidartondo MI. 2009. How to know unknown fungi: the role of a herbarium. New Phytol 181:719–724, doi:10.1111/j.1469-8137.2008.02703.x
  • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552.
  • Ceruti A, Fontana A, Nosenzo C. 2003. Le specie europee del genere Tuber. Una revisione storica. Torino, Italy: Regione Piemonte, Museo Regionale di Scienze Naturali.
  • Chen J, Liu PG, Wang Y. 2005. Notes on Tuber aestivum Vittad. (Tuberaceae, Ascomycota) from China. Acta Bot Yunnanica 27:385–389.
  • ———, Wang Y, Liu PG. 2008. Two new records of Tuber (Pezizomycetes, Pezizales) from China. Mycotaxon 104: 65–71.
  • Colwell RK. 2006. Estimate S 8: Staistical estimation of species richness and shared species from samples.
  • Eckert AJ, Hall BD. 2006. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae)—phylogenetic tests of fossil-based hypotheses. Mol Phylogenet Evol 40:166–182, doi:10.1016/j.ympev.2006.03.009
  • García-Montero LG, Díaz P, Massimo GD, García-Abril A. 2010. A review of research on Chinese Tuber species. Mycol Prog 9:315–335, doi:10.1007/s11557-009-0647-8
  • Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118, doi:10.1111/j.1365-294X.1993.tb00005.x
  • Guadet J, Julien J, Lafay JF, Brygoo Y. 1989. Phylogeny of some Fusarium species, as determined by large-subunit ribosomal-RNA sequence comparison. Mol Biol Evol 6: 227–242.
  • Guindon S, Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704, doi:10.1080/10635150390235520
  • Halász K, Bratek Z, Szego D, Rudnóy S, Rácz I, Lásztity D, Trappe JM. 2005. Tests of concepts of the small, white, European group of Tuber spp. based on morphology and rDNA ITS sequences with special reference to Tuber rapeaodorum. Mycol Prog 4:281–290, doi:10.1007/s11557-006-0132-6
  • Huang JY, Hu HT, Shen WC. 2009. Phylogenetic study of two truffles, Tuber formosanum and Tuber furfuraceum, identified from Taiwan. FEMS Microbiol Lett 294:157–171, doi:10.1111/j.1574-6968.2009.01571.x
  • Jeandroz S, Murat C, Wang Y, Bonfante P, Le Tacon F. 2008. Molecular phylogeny and historical biogeography of the genus Tuber, the “true truffles”. J Biogeogr 35:815–829, doi:10.1111/j.1365-2699.2007.01851.x
  • Karkouri KE, Murat C, Zampieri E, Bonfante P. 2007. Identification of internal transcribed spacer sequence motifs in truffles: a first step toward their DNA bar cording. Appl Environ Microbiol 73:5320–5330, doi:10.1128/AEM.00530-07
  • Kimura M. 2000. Paleogeography of the Rykyu Islands. Tropics 10:5–24, doi:10.3759/tropics.10.5
  • Kirk PM, Cannon PF, Minter DW, Stalpers JA. 2008. Ainsworth & Bisby’s dictionary of the fungi. 10th ed. Oxon, UK: CAB International. 640 p.
  • Lœssøe T, Hansen K. 2007. Truffle trouble: What happened to the Tuberales? Mycol Res 111:1075– 1099, doi:10.1016/j.mycres.2007.08.004
  • Lanfranco L, Wyss C, Marzachi C, Bonfante P. 1993. DNA probes for identification of the ectomycorrhizal fungus Tuber magnatum Pico. FEMS Microbiol Lett 114:245–252, doi:10.1111/j.1574-6968.1993.tb06581.x
  • Liu B. 1985. New species and new records of hypogeous fungi from China I. Acta Mycol Sin 4:84–89.
  • Liu JL, Whelen S, Hall BD. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799–1808.
  • Maser C, Claridge AW, Trappe JM. 2008. Trees, truffles and beasts: how forests function. New Brunswick, New Jersey: Rutgers Univ Press. 304 p.
  • Matheny PB. 2005. Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). Mol Phyl Evol 35:1–20, doi:10.1016/j.ympev.2004.11.014
  • Moreau P-A, Peintner U, Gardes M. 2006. Phylogeny of the ectomycorrhizal mushroom genus Alnicola (Basidiomycota, Cortnariaceae) based on rDNA sequences with special emphasis on host specificity and morphological characters. Mol Phylogenet Evol 38:794–807, doi:10.1016/j.ympev.2005.10.008
  • Nara K, Nakaya H, Wu B, Zhou Z, Hogetsu T. 2003. Underground primary succession of ectomycorrhizal fungi in a volcanic desert on Mount Fuji. New Phytol 159:743–756, doi:10.1046/j.1469-8137.2003.00844.x
  • Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. 2008. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform 4:193–201.
  • Nylander JAA. 2004. MrModeltest. Version 2. Uppsala, Sweden: Evolutionary Biology Centre: Program distributed by the author.
  • Pacioni G, Comandini O. 1999. Tuber. In: Cairney JWG, Chambers SM, eds. Ectomycorrhizal fungi. Key genera in profile. New York: Springer. p 163–186.
  • Potenza L, Amicucci A, Rossi I, Palma F, de Bellis R, Cardoni P, Stocchi V. 1994. Identification of Tuber magnatum Pico DNA markers by RAPD analysis. Biotechnol 8:93–98.
  • Riousset G, Riousset L, Chevalier G, Bardet MC. 2001. Truffle d’Europe et de Chine. Paris: INRA.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574, doi:10.1093/bioinformatics/btg180
  • Ryberg M, Nilsson RH, Kristiansson E, Töpel M, Jacobsson S, Larsson E. 2008. Mining metadata from unidentified ITS sequences in GenBank: a case study in Inocybe (Basidiomycota). BMC Evol Biol 8:50–64, doi:10.1186/1471-2148-8-50
  • Sato H, Yumoto T, Murakami N. 2007. Cryptic species and host specificity in the ectomycorrhizal genus Strobilomyces (Strobilomycetaceae). Am J Bot 94:1630–1641, doi:10.3732/ajb.94.10.1630
  • Sung G-H, Sung J-M, Hywel-Jones NL, Spatafora JW. 2007. A multigene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Mol Phylogenet Evol 44:1204–1223, doi:10.1016/j.ympev.2007.03.011
  • Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis software. Mol Biol Evol 24:1596–1599.
  • Taylor JW, Turner E, Jeffrey P, Townsend JP, Dettman JR, Jacobson D. 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Phil Trans Roy Soc B 361: 1947–1963, doi:10.1098/rstb.2006.1923
  • Tedersoo L, Jairus T, Horton BM, Abarenkov K, Suvi T, Saar I, Kjøller R. 2008. Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon-specific primers. New Phytol 180:479–490, doi:10.1111/j.1469-8137.2008.02561.x
  • Trappe JM. 1976. Notes on Japanese hypogeous ascomycetes. Trans Mycol Soc Japan 17:209–217.
  • Vilgalys R. 2003. Taxonomic misidentification inPUBLIC DNA databases. New Phytol 160:4–5, doi:10.1046/j.1469-8137.2003.00894.x
  • ———, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238–4246.
  • Wang Y, He XY. 2002. Tuber huidongense sp. nov. from China. Mycotaxon 83:191–194.
  • ———, Hu H-T. 2008. Paradoxa gigantospora comb. nov. from China. Mycotaxon 106:199–202.
  • Wang YJ, Tan ZM, Murat C, Jeandroz S, Le Tacon F. 2007. Molecular taxonomy of Chinese truffles belonging to the Tuber rufum and Tuber puberulum groups. Fungal Divers 24:301–328.
  • ———, ———, Zhang DC, Murat C, Jeandroz S, Le Tacon F. 2006a. Phylogenetic relationships between Tuber pseudoexcavatum, a Chinese truffle, and other Tuber species based on parsimony and distance analysis of four different gene sequences. FEMS Microbiol Lett 259:269–281, doi:10.1111/j.1574-6968.2006.00283.x
  • ———, ———, ———, ———, ———, ———. 2006b. Phylogenetic and populational study of the Tuber indicum complex. Mycol Res 110:1034–1045, doi:10.1016/j.mycres.2006.06.013
  • White TJ, Bruns TD, Lee SS, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. New York: Academic Press. p 315–322.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.