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Mycologia. 102(5), 20lO, pp. 1042-1057. DOl: lO.3852/09-213 1::-- 2010 by The Mycological Society of America, Lawrence, KS 66044-8897 Improved resolution of major clades within Tuberand taxonomy of species within the Tubergibbosum complex Gregory Bonito1 INTRODUCTION Department of Biology, Duke University, Durham, In 1899 H.W. Harkness published his seminal paper North Carolina 27708-0338 on California hypogeous fungi, the first serious work James M. Trappe on these fungi in North America. Tuber gibbosum Department of Forest Ecosystems and Society, Oregon Harkn. was included among the 48 new species he State University, Corvallis, Oregon 97331-5752 described. Gilkey (1925) described a related species, Pat Rawlinson T. giganteum Gilkey, but later reduced that species to North American TrujJling Society, P. O. Box 296, synonymy with T. gibbosum (Gilkey 1939). Tuber Corvallis, Oregon 97339 gibbosumappeared to be the most abundant species of the genus in the Pacific Northwest, ranging from the Rytas Vilgalys San Francisco Bay area of California north to Department of Biology, Duke University, Durham, North Carolina 27708-0338 Vancouver Island, British Columbia. It was thought to fruit from early autumn through winter and into the early summer and to be primarily, if not Abstract: Tuber gibbosum Harkn., described from exclusively, associated with Douglas-fir (Pseudotsuga northern California, originally was thought to be a menziesii) at relatively low elevations west of the single, variable species that fruited from autumn Cascade Mountains. Tuber gibbosumhas been hypoth through winter to spring. It has become popular as a esized to be part of the Puberulum clade, based on culinary truffle in northwestern USA, where it is morphology, because of its light-colored fruit body commercially harvested. Morphological studies sug and alveolate-reticulate spore ornamentation (Wang gested it might be a complex that includes at least two et al. 2007). species. We conducted morphological and phyloge Tuber gibbosum is called the Oregon white truffle netic studies of the complex to determine how many because of being white when immature and its species it might contain and how they differed aromatic resemblance to Tuber magnatum Pico, the morphologically, geographically and seasonally. We Italian white truffle. However several color and also provide the first LSU phylogeny for the genus aromatic differences have been detected among Tuber. Phylogenetic analyses resolve nine major seasonal collections of T. gibbosum and amateur clades in the genus with high bootstrap support and collectors have differentiated two varieties, autumn distinguish the Gibbosum clade from the Aestivum, and spring. Since the 1980s both have been commer Excavatum, Macrosporum, Magnatum, Melanos cially harvested from forests in the Pacific Northwest porum, Puberulum, Rufum and Spinoreticulatum (Lefevre et al. 2001). clades. Further analyses of ITS and LSU regions The aim of this study was to use both molecular revealed four distinct species in the Gibbosum phylogenetics and morphology to assess species complex. Although morphologically similar the four diversity within the Tuber gibbosum complex and to species differ in spore size and shape and in peridial place them within the larger context of the genus anatomy. These species share the synapomorphy of Tuber. We selected a broad geographic and seasonal having suprapellis hyphae with distinctive, irregular array of collections for rDNA sequencing and wall swellings at maturity; we have not seen this morphological analyses. As a result we present a hyphal type in any other Tuber spp. worldwide. The comprehensive LSU phylogeny for the genus Tuber three new species are named and described as T. that included representative taxa from North Amer bellisporum Bonito & Trappe, T. castellanoi Bonito & ica, Europe and Asia, established a new epitype for T. Trappe and T. oregonense Trappe, Bonito & Raw gibbosum and described three other species in the linson. Gibbosum complex. Key words: Ascomycota, hypogeous fungi, ITS, LSU, mycorrhizae, Oregon white truffle, Pezizales, MATERIALS AND METHODS phylogeny, Tuberaceae Material studied.-We investigated more than lOO collec Submitted 27 Aug 2009; accepted for publication 2 Feb 20lO. tions from the Tuber gibbosum complex, representing a I Corresponding author. E-mail: [email protected] broad geographic and seasonal range, from the mycological 1042 BO�ITO ET AL.: GENUS TuBER PHYLOGENY 1043 collections of the Oregon State University Herbarium were calculated by PAUP 4.0bl0 with 1000 random addition (OSC). Fresh specimens of other species found during sequences and 5000 bootstrap replicates (Swofford 2002). the study in North America, Italy and China also were Maximum likelihood (ML) searches were conducted with studied and accessioned into OSC. Types and paratypes GARLI (Zwickl 2006) and Bayesian inference (BI) with were examined and molecular data from these collections MrBayes (Ronquist and Huelsenbeck 2003). Alignments have been included whenever possible. Specimens from the have been accessioned in TreeBASE (s2482), and the 133 National Fungus Collections (BPI) and the Herbarium of sequences are available on GenBank under accession Universita di Bologna (BOLO), Italy, also were studied. numbers FJ 809749-FJ809882 (TABLE I). Collection numbers and geographic origin of collections used in molecular analyses are provided (TABLE I). Light microscopy.-Herbarium specimens were hand-sec tioned with a razorblade and rehydrated in water or Molecular methods.-DNA was extracted by the chloroform embedded in paraffin, thin-sectioned (± 8 11m thick), extraction technique (Gardes and Bruns 1993). For DNA stained with safranin-fast green and made into permanent extraction glebal tissue was ground, dried in cetyl trimeth slides, then characterized anatomically by light microscopy. ylammonium bromide (CTAB) in sterile sand and large Six morphological characters were assessed from multiple cubic zirconium beads in a mini bead-beater 1-2 min collections of T. gibbosum and the three new species (Biospec Products, Bartlesville, Oklahoma). The internal described here: (i) peridial structure and thickness as transcribed spacer region (ITSl, 5.8S and ITS2) and part of measured in cross section; (ii) glebal trama and sterile vein the nuclear ribosomal large subunit (LSU) locus were structure; (iii) ascus shape, size, wall thickness; (iv) length amplified with universal fungal primer sets ITS5- ITS4, 5.8S and width of spores (n = 40) in one-, two-, three-, four- and LR3 and LROR- LRS (Vilgalys and Hester 1990, White et al. five-spored asci (excluding ornamentation) for at least three 1990). The PCR protocol began with an initial denaturation collections of each species; (v) spore ornamentation at 94 C (3 min), followed by 35 cycles at 94 C (l min), 50 C (height, number of alveolae along spore length, size of annealing (30 s), and a 72 C extension (1 min), with a final alveolae); (vi) presence of surface hyphae with irregular wall extension at 72 C (7 min). Each 25 ilL PCR reaction thickenings. To determine the significance of spore size consisted of 4 ilL dNTP (1.25 11M, 2.5 ilL PCR buffer, 1 ilL variation among species analysis of variance (ANOVA) and BSA, 1.25 ilL primer 1 (10 11M), 1.25 ilL primer 2 (10 11M), Tukey's honestly significant difference tests were calculated 0.15 ilL TaqDNA polymerase (0.5 U), 4.8 ilL water and 10 ilL with R statistical software (http://www.r-project.org). DNA extract ( � 10 ng/I1L). Two microliters of each PCR Where two dimensions of structures are reported in the product were loaded into a 1.0% agarose gel buffered with descriptions, length is followed by width. Q refers to the TAE and stained with 2 ilL SYBR Safe (Invitrogen, Carlsbad, length/width ratio. California) per 80 mL TAE. Gel electrophoresis products were viewed on a GelDoc XR imager (Bio-Rad Laboratories Scanning electron microscopy.-Cross sections of dried Inc., Hercules, California). PCR products were cleaned in herbarium specimens were attached to aluminum mounts QIAGEN quick-clean columns and used for PCR sequenc with double-sticky tape. These were gold-palladium sputter ing reaction. Sanger sequencing was performed with Big coated at a nominal coating thickness of 15 nm with a Dye chemistry 3.1 (Applied Biosystems, Foster City, Califor Hummer 6.2 system (Anatech Ltd., Springfield, Virginia). nia) with the forward primer ITS5, 5.8S or LROR and the Peridial, glebal and spore structures were characterized at 10 kv reverse primer ITS4, LR3 or LRS. DNA sequences were with a Philips XL30 environmental scanning electron micro determined on an ABI3700 capillary sequencer (Applied scope under high vacuum (FEI Co., Hillsboro, Oregon). Biosystems, Foster City, California). Phylogenetic analyses.-DNA sequences were manually RESULTS trimmed and edited with Sequencher 4.0 (Gene Codes Molecular analyses.-Phylogenetic inferences of LSD Corp., Ann Arbor, Michigan) and sequence-similarity values rDNA with a GTR G I model of nucleotide were calculated. Both ITS and LSU sequences were queried + + against the NCB! public database GenBank by use of the substitution having four substitution classes, 64 BLASTN algorithm to verify that sequences were of Tuber ingroup taxa and 537 unambiguously aligned charac (Altschul et al. 1990). DNA sequences were aligned in ters (174 parsimony informative characters) support MacClade 4.0 and adjusted by eye (Maddison and Maddison Tuber as monophyletic and place the T. gibbosum 2002).