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Department of Biological Sciences, College of Natural Sciences, Seoul National University, San 56-1 Shillim-9-dong, Kwanak-gu, Seoul 151-747, Korea
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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A new polypore in the genus Fomitopsis was discovered in Kangwon Province, Korea. The species was morphologically similar to Fomitopsis rosea and F. cajanderi, but the pinkish white pore surface, the size and shape of the pores and the number of sterigmata were different enough for it to be distinguished from the recorded species of Fomitopsis. Based on the results of morphological and phylogenetic analyses, this new polypore is proposed as Fomitopsis incarnatus sp. nov.
Key words: Fomitopsis cajanderi, Fomitopsis rosea, internal transcribed spacer, mitochondrial small subunit rDNA, phylogeny, second largest subunit of RNA polymerase II
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, Ryvarden and Gilbertson 1993). The genus is placed in the Daedalea group among 12 groups of the Polyporaceae (Ryvarden 1991) and is included phylogenetically in the strongly clustered Fomitopsis-Daedalea-Piptoporus group characterized by brown rot and a bipolar mating system (Hibbett and Thorn 2001). The genus is characterized by sessile to effused-reflexed basidiocarps with white to rose-colored pore surfaces; di- to trimitic hyphal systems with clamps in the generative hyphae; clavate basidia with four sterigmata; hyaline, cylindrical or allantoid to subglobose, and smooth-walled basidiospores; and brown rot activity on living or dead wood (Donk 1974, Carranza-Morse and Gilbertson 1986, Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993).
Fomitopsis rosea (Alb. & Schwein.) P. Karst. and its taxonomic position in the genus has been discussed among mycologists (Carranza-Morse and Gilbertson 1986, Kotlaba and Pouzar 1990, Ryvarden 1991, Ryvarden and Gilbertson 1993, Kotlaba and Pouzar 1998). Kotlaba and Pouzar (1990, 1998) suggested a narrow generic concept for Fomitopsis, emphasizing the wall thickness of basidiospores. Fomitopsis pinicola (Sw.) P. Karst. (the type species of Fomitopsis) has thick-walled basidiospores and a resinous substance on the upper surface of basidiocarps, while F. rosea is characterized by thin-walled spores, the rose context and the absence of a resinous crust on the pileal surface (Kotlaba and Pouzar 1998). Based on such morphological differences, a monotypic genus, Rhodofomes Kotl. & Pouzar typified by R. roseus (Alb. & Schwein.) Vlasak (= F. rosea), was segregated from Fomitopsis into a new genus (Kotlaba and Pouzar 1990). However Ryvarden (1991) and Ryvarden and Gilbertson (1993) argued that the rose-colored context is not of sufficient taxonomic importance to warrant segregation into a new genus.
Many genetic markers recently have been applied to resolve fungal phylogenetic relationships. Internal transcribed spacers of nuclear rDNA (nuclear ITS), the small subunit mitochondrial rDNA (mt-SSU) and the genes encoding the second largest subunit of RNA polymerase II (RPB2) have become especially useful to classify fungal taxa at the species and genus levels (Ko and Jung 1999, 2002, Lim and Jung 2003, Desjardin et al 2004, Hong and Jung 2004, Matheny 2005). When the sequences of nuclear ITS, mt-SSU and RPB2 were used for molecular phylogenetic analyses of the collected fungus the thinness of the wall of the basidiospores that typifies the genus Rhodofomes proved to be of no significant generic value and our new polypore occupied a unique lineage separated from F. cajanderi and F. rosea. The fungus was related closely to F. rosea (= R. roseus) in our study, but the phylogenetic results rejected the genetic concept of Rhodofomes and suggested that the fungus should be placed in Fomitopsis. In this study we propose a new member of Fomitopsis, based on an evaluation of the generic concepts of Fomitopsis and Rhodofomes through morphological observation of basidiocarps and phylogenetic analyses of molecular sequences.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). Those for the new polypore were numbered SNU (Seoul National University Herbarium) m-04010313 and m-05072501. Basidiocarps were examined in a mounting solution of 3% KOH (w/v) and 1% phloxine (w/v) under a light microscope. Kornerup and Wanscher (1978) were consulted for color descriptions of specimens.
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) were obtained from collection centers (ATCC, CBS, DSMZ and MUCL) and grown at 25 C on potato-dextrose agar (PDA). Total genomic DNA were extracted from specimens and strains with the AccuPrep® Genomic DNA Extraction Kit (Bioneer, Daejeon, Korea). PCR and sequencing primer information for three regions are listed (TABLE I) in this order: nuclear ITS, mitochondrial SSU, and RPB2. Quick PCR Premix (GENENMED, Daejeon, Korea) and AccuPower® PCR Premix (Bioneer, Daejeon, Korea) were used to amplify those regions, and a PCR reaction was conducted in a PTC100 Thermal Cycler (MJ Research, Watertown, Massachusetts). The nuclear ITS region was amplified with primer set ITS5 and ITS4 (White et al 1990). Together with the primers used for PCR, ITS1 (White et al 1990) was used for sequencing. The degenerate primers bRPB2-6F and bRPB2-7.1R (Matheny 2005) were used to amplify the region between conserved motifs 6 and 7 of RPB2 (Liu et al 1999, Matheny 2005). To obtain a sufficient concentration for sequencing, all amplicons for RPB2 were diluted 50x and amplified and sequenced with degenerate primers bRPB2-6F and bRPB2-7R (Matheny 2005). Partial mt-SSU rDNA were amplified with primers MS1 and MS2 (White et al 1990). For the genomic DNA for which the former primer set functioned with a low affinity, primers BMS05 and BMS173 (Hong et al 2002) were used for the amplification of almost complete mt-SSU; the PCR product that was diluted 50x was amplified by MS1 and MS2. PCR conditions for nuclear ITS and almost complete mt-SSU were accomplished respectively according to the methods of Ko and Jung (2002) and Hong and Jung (2004). PCR conditions for partial RPB2 were initial denaturation at 95 C for 10 min, followed by denaturation at 94 C for 1 min, primer annealing at 55 C for 1 min, extension at 72 C for 1 min + 3 s/cycle for 39 cycles and a final extension at 72 C for 10 min. PCR conditions to amplify partial mt-SSU were primer annealing at 54 C for 30 s and extension at 72 C for 30 s; the remaining conditions were identical to those used for the PCR reaction of RPB2. Amplified PCR products were detected on 0.75% agarose gel and purified with an AccuPrep® PCR Purification Kit (Bioneer, Daejeon, Korea). Purified products were sequenced with the primer combinations (TABLE I) using an ABI3700 automated DNA sequencer (Applied Biosystems, Foster City, California). T vector cloning was conducted for purified PCR products that generated uncertain or mixed base-calling in the sequencing reaction. Purified amplicons and T vectors were ligased at 4 C for 12 h with pGEM-T EasyVector System I (Promega, Madison, Wisconsin). Recombinant plasmids were transformed into Escherichia coli strain JM109 with MicroPulserTM Electroporator at 2.5 kV (BIO-RAD, Hercules, California). The E. coli colony containing the recombinant plasmid was cultivated in terrific broth (tryptone: 12 g/L, yeast extract: 24 g/L, 10% glycerol, 0.17 M KH2PO4 and 0.72 M K2HPO4) at 37 C for 20 h. The plasmids of cultured E. coli were miniprepared with the Plasmid Spin Kit (GENENMED, Daejeon, Korea). Miniprepared DNA was incubated with the restriction enzyme EcoRI at 37 C for 4 h on 0.75% agarose gel to check the size of inserts. The inserted region was sequenced with T vector primers T7 and SP6 (TABLE I) using the automated DNA sequencer.
Sequence alignments, phylogenetic analyses and genetic distance.— –
Sequences of nuclear ITS, mt-SSU and RPB2 were aligned with Clustal X v1.83 (Thompson et al 1997) with default penalties for gaps. Ambiguous and uninformative variable characters were removed with BioEdit v5.0.9 (Hall 1999). The three aligned sequence datasets were deposited in TreeBase (SN2821) and submitted to phylogenetic analyses. Parsimony analysis was conducted with a heuristic search method with PAUP 4.0b10 (Swofford 2002), with tree bisection reconnection (TBR) branch swapping and unrestricted MAXTREES. To determine confidence levels for internal nodes of the most parsimonious trees 1000 nonparametric bootstrap replications (branch swapping, TBR; MAXTREES, unrestricted) were used (Felsenstein 1985). All parsimonious trees were rooted by outgroup taxon, Buglossoporus pulvinus (Pers.) Donk. A partition homogeneity test (replicates = 1000; branch swapping, TBR; MAXTREES, unrestricted; Farris et al 1994) was performed to check the compatibility for the dataset combining the sequences of the three regions (nuclear ITS, RPB2 and mt-SSU). Genetic distances between species were calculated with MEGA3 (Kumar et al 2004) under the Kimura 2-parameter distance model.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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FIG. 1
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HOLOTYPE: KOREA. Mount Chiak, Kangwon Province, ca. 37°24'N, 128°3'E, ca. 400 m a.s.l., on the base of Fraxinus mandshurica, 25 Jul 2005, J. S. Lee and K. M. Kim SNU m-05072501 (culture ex-holotype SNU m-05072501 = SFCC m-05072501).
Basidiocarps perennial, sessile, semicircular and broadly attached, effused-reflexed to ungulate, up to 13 x 6 x 7 cm; upper surface with broad concentric bulges, frequently fissured, brownish gray (10F2) to grayish black (H1) with age; margin acute, becoming light brown (6D5) to grayish black (H1); pore surface pinkish white (12A2); pores circular, 6–8 per mm; hymenophore tubulate, stratified, up to 1–1.2 cm thick, sometimes separated by a thin layer of contextual tissue; context brownish yellow (5C8), azonate, fibrous or woody, up to 3–5 mm thick. Hyphal system trimitic; generative hyphae with clamps, 2.3–3 µm wide; skeletal hyphae thick-walled, nonseptate, yellow to brown (5B7–5E7) in KOH, straight, 2.3–4 µm wide; contextual binding hyphae thick-walled, nonseptate, much branched, yellow to brown (5B7–5E7) in KOH, 1.8–3.4 µm wide; basidia clavate, 2-sterigmate, 15–19 x 4–6.3 µm, simple septate at the base; basidiospores ellipsoid, frequently curved, thin-walled, hyaline, smooth, 4.5–6.3 x 2.2–2.9 µm.
Etymology. – "incarnatus": paler than pale pure red.
Known distribution. – Oak-pine mixed forests of the Taebaek Mountains, Kangwon Province, Korea.
Other specimen. – Mount Taebaek, Kangwon Province, 37°06'15.7″N, 128°55'56.2″E, ca. 1240 m a.s.l., on timber of Pinus sp., 13 Jan 2001, J. S. Lee (SNU m-04010313, paratype).
Remarks. – Fomitopsis incarnatus has a pinkish white pore surface and effused-reflexed to ungulate basidiocarps and is morphologically similar to the closely related species, F. rosea and F. cajanderi. However the size of the pores (6–8/mm) was apparently smaller than those of F. rosea (3–5/mm) and F. cajanderi (4–5/mm). Together with the size of pores the pinkish white pore surface made it possible to discriminate the species from the above two species. Microscopically the basidiospores of F. incarnatus were less elongated than those of F. cajanderi and commonly tended to be curved in contrast to those of F. rosea. While F. cajanderi and F. rosea have four sterigmata on a basidium, F. incarnatus had only two.
Phylogenetic analyses and genetic distances.— –
From five specimens of Fomitopsis and 22 strains including Fomitopsis, Antrodia P. Karst., Buglossoporus Kotl. & Pouzar, Daedalea Pers., Fomes (Fr.) Fr., Melanoporia Murrill and Piptoporus P. Karst. the regions of nuclear ITS, partial RPB2 and partial mt-SSU were amplified and sequenced (TABLE I). All sequences generated in this study were deposited in GenBank (TABLE I). The region of nuclear ITS had sequences 592–630 bp long. The aligned sequences 666 bp long with 232 parsimony informative characters. Analyzing the aligned dataset of nuclear ITS sequences with the parsimony method resulted in five most parsimonious trees (tree length = 949, CI = 0.530, RI = 0.575), one of which is shown (FIG. 2). In this phylogenetic tree two strains of the new polypore F. incarnatus were strongly clustered together having a bootstrap value of 99%. The three species of F. cajanderi, F. rosea and F. incarnatus formed a monophyletic group (clade A) with a 75% bootstrap value. Within this clade F. cajanderi was more closely grouped with F. rosea than with F. incarnatus. Fomitopsis pinicola, together with Piptoporus betulinus (Bull.) P. Karst., F. palustris (Berk. & M.A. Curtis) Gilb. & Ryvarden and F. meliae (Underw.) Murrill, formed a separate clade (B) with a 79% bootstrap value. Clades A and B were separated distinctly from species of Antrodia, Daedalea quercina (L.) Pers. and F. dochmia (Berk. & Broome) Ryvarden and had a paraphyletic relationship to each other. Fomitopsis cupreorosea (Berk.) J. Carranza & Gilb., F. lilacinogilva (Berk.) J.E. Wright & J.R. Deschamps, F. feei (Fr.) Kreisel, F. spraguei (Berk. & M.A. Curtis) Gilb. & Ryvarden and F. africana Mossebo & Ryvarden were grouped together independently and moderately supported by 60% bootstrap value. In an exceptional one of most parsimonious trees this clade clustered paraphyletically with the group of A. serialis (Fr.) Donk and A. variiformis (Peck) Donk, maintaining the separation of clades A from B. The group of A. juniperina (Murrill) Niemela & Ryvarden and F. dochmia and the group of A. serialis and A. variiformis maintained a sister relationship in all most parsimonious trees, but branch exchanges existed between the groups.
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). The phylogenetic tree of RPB2 showed a somewhat different topology compared to that of the nuclear ITS. In clade A (FIG. 3) F. rosea was more closely related to F. incarnatus than to F. cajanderi with a bootstrap value of 57%. Melanoporia nigra (Berk.) Murrill positioned at the basal line of the nuclear ITS tree (FIG. 2) was clustered with clade A as the closest sister taxon. The group that comprised F. cupreorosea, F. feei, F. lilacinogilva, F. africana, F. dochmia and D. quercina had a paraphyletic relationship with clade A. Among the species outside clades A and B in the nuclear ITS tree (FIG. 2) the group of Antrodia albida (Fr.) Donk, A. heteromorpha (Fr.) Donk and A. xantha were clustered by 75% bootstrap value and positioned on the basal line of the RPB2 tree (FIG. 3). The variable topologies shown at higher relationships among clade A, clade B and their sister taxa also were indicated by bootstrap values of less than 50% at inner nodes (FIGS. 2, 3). Four most parsimonious trees generated from RPB2 sequences showed the same topology for clade A, clade B and the group of F. cupreorosea, F. feei, F. lilacinogilva, F. africana, F. dochmia and D. quercina.
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) and RPB2 (FIG. 3) clades A and B members also were maintained in the mt-SSU tree (FIG. 4). Within clade A F. cajanderi and F. incarnatus formed a strongly supported group (bootstrap = 92%), which was clustered to F. rosea with 84% bootstrap support. The group including clade A and its four sister taxa was separated from the group including clade B and its seven sister taxa by 100% bootstrap support (FIG. 4). The group of F. cupreorosea, F. feei, F. lilacinogilva and F. africana was related more closely to clade B than to A. Most taxa whose phylogenetic positions were variable on the trees of nuclear ITS and RPB2 were placed as single lineages or clustered groups, which were supported by bootstrap of 50% or less. The partition homogeneity test on the combined dataset of three regions (nuclear ITS, RPB2 and mt-SSU) generated a P value of 0.001. Because this test result was much lower than the significance level of 0.05, subsequent phylogenetic analyses were not conducted for the combined dataset. Genetic distances of nuclear ITS, RPB2 and mt-SSU were estimated (FIG. 5) for the specimens and strains of F. cajanderi, F. incarnatus and F. rosea. Fomitopsis incarnatus diverged from F. cajanderi and F. rosea by sequence differences of 0.032–0.073, but the sequence variations within the species was 0–0.013.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, Ryvarden and Gilbertson 1993) and F. rosea (3–5/mm; Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993). Microscopically the basidiospores (4.5–6.3 x 2.2–2.9 µm) of F. incarnatus were slightly shorter and less elongated than those (5–7 x 1.5–2 µm; Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993) of F. cajanderi (FIG. 1B). While the spores of F. rosea (5.5–7.5 x 2–2.5 µm; Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993) are straight, those of F. incarnates frequently were curved. The widths of generative and binding hyphae are similar among the three species, but the skeletal hyphae (2.3–4 µm wide) of F. incarnatus were thinner than those of the two other species (2.5–6 µm for F. cajanderi, 4–6 µm for F. rosea; Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993). Although the basidia of the three species were nearly identical in their dimensions and shapes, only two sterigmata were observed in F. incarnatus unlike four sterigmata in the other two species (Gilbertson and Ryvarden 1986, Ryvarden and Gilbertson 1993). Fomitopsis incarnatus possesses sufficient morphologically different features to differentiate it from the two closely related taxa, F. cajanderi and F. rosea.
In the three phylogenetic trees (FIGS. 2–4), F. cajanderi, F. incarnatus and F. rosea always formed a monophyletic group (clade A, FIGS. 2–4) moderately supported respectively by bootstrap values of 75%, 69% and 84% in ITS, RPB2 and mt-SSU trees. However the strains of each species were tightly clustered at the species level by bootstrap values of 93% to mostly 100% (FIGS. 2–4). The low within-species divergence (0–1.3%) and the high between-species divergence (2.7–7.3%) showed that each species has an independent genetic boundary (FIG. 5). The bootstrap values and genetic distances indicate that the new species occupies an independent specific lineage that can be characterized and separated from those of F. cajanderi and F. rosea (FIGS. 2–5); thus it comes under the new phylogenetic species concept defined by Cracraft (1983).
Fomitopsis incarnatus formerly was related closely to F. rosea (= R. roseus) in three phylogenetic trees; therefore to determine the generic position of the new species it was necessary to evaluate whether the segregation of Rhodofomes from Fomitopsis is proper. Genus Rhodofomes is characterized by thin-walled basidiospores when compared with F. pinicola. In addition the presence of clamps on thin-walled generative hyphae, the rose-colored context and the absence of a resinous crust on the upper surface of the basidiocarps were defined as generic keys for Rhodofomes (Kotlaba and Pouzar 1990, 1998). Genus Pilatoporus Kotl. & Pouzar typified by P. palustris (= F. palustris) also was described by thin-walled basidiospores together with the presence of pseudoskeletal hyphae (Kotlaba and Pouzar 1990). In our phylogenetic trees (FIGS. 2–4) F. pinicola was strongly clustered with F. palustris, P. betulinus and F. meliae in clade B (bootstrap values: ITS = 79%, RPB2 = 100%, mt-SSU = 100%) while F. rosea was separated distinctly from F. pinicola. If the spore wall thickness is significant enough for the generic delimitation between Rhodofomes and Fomitopsis then the thin-walled character of the spores might have been derived synapomorphically from a common ancestor of the group that comprises F. rosea and its closely related taxa, while such a character has been absent in the species of the group that comprises F. pinicola and its relatives. However F. palustris with thin-walled basidiospores was distinctly separated from the lineage of F. rosea and was strongly clustered with F. pinicola with thick-walled basidiospores (Kotlaba and Pouzar 1990) as well as P. betulinus and F. meliae (FIGS. 2–4). This indicates that the character of thin-walled basidiospores has evolved autapomorphically in the phylogeny of Fomitopsis, Antrodia, Daedalea, Fomes, Melanoporia and Piptoporus (FIGS. 2–4).
The rose-colored context along with the wall thickness of the basidiospores also was suggested by Kotlaba and Pouzar (1990, 1998) to be of importance for segregation of Rhodofomes from Fomitopsis. In our phylogenetic trees (FIGS. 2–4) members of the F. rosea complex consisting of F. cajanderi, F. cupreorosea, F. dochmia, F. feei, F. lilacinogilva and F. rosea (Carranza-Morse and Gilbertson 1986) developed polyphyletic lineages, indicating that the rose-colored context is not an absolute key that can define Rhodofomes. Based on present phylogenetic analyses it is suggested that the characters of the spore wall thickness and the context color have no independent generic values to separate Rhodofomes from other Fomitopsis species, which coincides with the view of Ryvarden and Gilbertson (1993) that the character of the rose-colored context is not enough to establish a new genus from Fomitopsis. The phylogenetic character of F. incarnatus (FIGS. 2–4) indicates that the species should be placed in Fomitopsis as a new member and F. rosea (= R. roseus) needs to be retained in Fomitopsis until morphologically appropriate and phylogenetically synapomorphic new characters are surveyed.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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1 Present address: Polar Biocenter, Korea Polar Research Institute, KORDI, Songdo Techno Park, 7-50 Songdo-dong, Yeonsu-gu, Incheon 406-840, Korea. 
2 Corresponding author. E-mail: minervas{at}snu.ac.kr
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LITERATURE CITED |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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