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Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
Jack D. Rogers
Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSTAXONOMYDISCUSSIONLITERATURE CITED |
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Phylogenetic relationships were inferred among several xylariaceous genera with Nodulisporium or nodulisporium-like anamorphs based on the analyses of ß-tubulin and 
-actin sequences. One hundred nine cultures and three specimens of 83 representatives of these four genera were included in the study. Biscogniauxia taxa formed a well supported clade that was basal to the other taxa, while taxa of Hypoxylon and Daldinia comprised a large monophyletic group that contained two subclades. The first subclade encompassed Hypoxylon sect. Annulata and is accepted here as the new genus Annulohypoxylon. The second subclade contained taxa of Hypoxylon sect. Hypoxylon and Daldinia. Hypoxylon is restricted to include only those taxa in sect. Hypoxylon. Thirty-three epithets are made in Annulohypoxylon. Hypoxylon cohaerens var. microsporum is raised to the species level and accepted as A. minutellum. Hypoxylon polyporoideum is recognized as distinct from H. crocopeplum. Hypoxylon placentiforme is accepted as Daldinia placentiformis.
Key words: Annulohypoxylon, Biscogniauxia, Daldinia, Nodulisporium, nodulisporium-like, systematics, Xylariaceae
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSTAXONOMYDISCUSSIONLITERATURE CITED |
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). Those anamorphs that are atypical for Nodulisporium in their general morphology but have a similar conidiogenesis are referred to herein as nodulisporium-like.
Hypoxylon was broadly defined by Miller (1961) to comprise taxa now redistributed in Biscogniauxia, Camillea Fr., Creosphaeria Theiss., Entoleuca Syd., Hypoxylon, Jumillera J.D. Rogers et al, Kretzschmaria Fr., Kretzschmariella Viégas, Nemania S.F. Gray, Stilbohypoxylon Henn., and Whalleya J.D. Rogers et al Hypoxylon as currently defined was gradually delimited by Pouzar (1979; 1985a, b; 1986) and revised by Ju and Rogers (1996). The genus features prostrate, superficial stromata that lack a dehiscing outer juvenile layer as found in Biscogniauxia and Camillea, flattened ascal apical rings, and Nodulisporium or nodulisporium-like anamorphs. Bright- or dull-colored waxy tissue is distributed immediately beneath the stromatal surface and between perithecia and contains pigments that are extractable with a potassium hydroxide solution. The stromatal tissue below the perithecial zone is homogeneous in contrast to that in Daldinia, which is composed of concentric zone layers of two alternating tissue types. Two sections—sect. Hypoxylon and sect. Annulata—were recognized by Ju and Rogers (1996) in Hypoxylon. Section Annulata differs from sect. Hypoxylon in three major characters: ostioles that are encircled with a truncate area, carbonized stromatal tissue that discretely encloses each individual perithecium, and a thickening on the ascospore perispore that is absent in most species of sect. Hypoxylon. The ascospore perispore in sect. Hypoxylon has conspicuous or inconspicuous coil-like ornamentation.
Daldinia apparently is related closely to Hypoxylon, especially with sect. Hypoxylon, in having flattened ascal apical rings, coil-like ornamentation on the ascospore perispores in a number of species, and Nodulisporium or nodulisporium-like anamorphs. In fact Daldinia has been treated as a synonym of Hypoxylon by some other mycologists (e.g. Nitschke [1867] and Læssøe [1994]), since its establishment in 1863.
Biscogniauxia, along with Camillea, was placed in Hypoxylon sect. Applanata by Miller (1961), a puzzling disposition in that almost all earlier authorities accepted Biscogniauxia (as Nummularia) on the basis of its stromatal morphology. Its bipartite stromata led Pouzar (1979), Ju et al (1998) and Læssøe et al (1989) to re-assign taxa in sect. Applanata to either Biscogniauxia or Camillea. Biscogniauxia includes taxa with dark, smooth-walled ascospores ( Ju et al 1998), whereas Camillea has light-colored, ornamented ascospores (Læssøe et al 1989). It should be noted that the ascospores of certain Biscogniauxia species bear a small, hyaline cellular appendage on one end, a feature not found in Hypoxylon or Daldinia and believed to be also possessed by ancestral Biscogniauxia species ( Ju and Rogers 1996). The stromata of Biscogniauxia species develop in the bark of their host plants and the outer stromatal layer dehisces together with the covering host tissue to expose the inner layer beneath where developing perithecia are embedded. In contrast the stromata of Hypoxylon and Daldinia species develop superficially on the host substrata and are devoid of the outer dehiscing stromatal layer.
Various lines of evidence indicate that xylariaceous fungi may have originated from ancestors with two-celled ascospores (Rogers 1979). Ju and Rogers (1996) thus hypothesized that Hypoxylon species may have arisen from biscogniauxia-like ancestors due to the fact that numerous species of Biscogniauxia still retain a hyaline, reduced cell as the ascospore appendage. It seems likely that Biscogniauxia also retains other ancestral traits. Most noticeable is the outer dehiscing stromatal layer in Biscogniauxia, which was thought to have evolved into the stromatal tissue that overlies the ostiolar disks in Hypoxylon sect. Annulata and is sloughed away as the perithecia mature. The stromatal tissue overlying ostioles is so much reduced in Hypoxylon sect. Hypoxylon that it hardly can be recognized. Ju and Rogers (1996) also hypothesized that Daldinia appears to have branched from the H. placentiforme line of Hypoxylon sect. Hypoxylon.
Molecular studies of Sánchez-Ballesteros et al (2000) using sequences of nuclear ribosomal internal transcribed spacers (ITS) of Hypoxylon and some hypoxyloid species, including species of Biscogniauxia, Camillea, Creosphaeria, Kretzschmaria, Nemania and Whalleya, suggested that Hypoxylon in the modern sense (e.g. Pouzar 1979, 1985a, b, 1986; Ju and Rogers 1996) is monophyletic, but that taxa in sect. Hypoxylon and sect. Annulata appeared mingled. Biscogniauxia also formed a distinct clade. Their results also supported subdivision of the Xylariaceae into at least two major groups based on the anamorphs: those with Nodulisporium or nodulisporium-like anamorphs were clustered with Hypoxylon and those with Geniculosporium or geniculosporium-like anamorphs were clustered into another group ( Ju and Rogers 1996). Unfortunately, no representatives from Daldinia were included in the study of Sánchez-Ballesteros et al (2000). A recent study (Triebel et al 2005) with ITS sequences reinforced the concept that genera with Geniculosporium or geniculosporium-like anamorphs are distinct from those with Nodulisporium or nodulisporium-like anamorphs. Daldinia and Entonaema clustered closely in two groups of a subclade. One subclade had a group with H. fragiforme (Pers. : Fr.) J. Kickx fil., H. multiforme (Fr. : Fr.) Fr., and H. cohaerens (Pers. : Fr.) Fr. (the former species a member of sect. Hypoxylon and the latter two species members of sect. Annulata). Hypoxylon truncatum (Schwein. : Fr.) J.H. Miller, a member of sect. Annulata, was far removed in another subclade (Triebel et al 2005).
In the present study we selected 83 taxa from Biscogniauxia, Daldinia, and Hypoxylon—three major genera with Nodulisporium or nodulisporium-like anamorphs—and used sequences from two nuclear genes, ß-tubulin and -actin, to infer the phylogenetic relationships and subgeneric groupings among these taxa.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSTAXONOMYDISCUSSIONLITERATURE CITED |
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). Materials from which DNA was extracted were mainly from cultures accumulated from previous studies of Y.-M.J. and J.D.R. ( Ju and Rogers 1996, 1999, 2001; Ju et al 1997, 1998, 1999, 2004) and cultures isolated from specimens recently collected from Taiwan by Y.-M.J. and H.-M.H. and from France by Jacques Fournier. In total 109 cultures and 3 specimens representing 83 taxa were included in our studies; these are 18 cultures and 3 specimens of 16 taxa from Hypoxylon sect. Annulata sensu Ju and Rogers (1996), 17 cultures of 14 taxa from Biscogniauxia, 16 cultures of 12 taxa from Daldinia, and 58 cultures of 41 taxa from Hypoxylon sect. Hypoxylon sensu Ju and Rogers (1996).
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). Colonies were transferred to test tubes containing SME medium and maintained under laboratory conditions. Cultures also were deposited in the BCRC (the Bioresource Collection and Research Center) in Taiwan (see TABLE I
for accession numbers), except for those that were lost after our study. For DNA extraction, each culture was grown in 100 mL of malt extract broth (20 g Difco malt extract per liter of water) on a rotary shaker at 120 rpm for 7–14 d. Mycelium was harvested by filtration through Whatman No. 1 filter paper, freeze dried, and stored at –20 C. DNA was extracted with a modified CTAB method similar to that described in O’Donnell et al (1998). Lyophilized mycelium (ca. 25 mg) was submerged in 750 µL of extraction buffer (50 mM Tris-HCl at pH 6, 150 mM NaCl, 100 mM EDTA) and ground to homogenous slurry with mortar and pestle. The slurry was transferred into a 2 mL Eppendorf tube, suspended in 40 µL 25% SDS and incubated 1 h at 37 C. After 115 µL of 5 M NaCl and a solution containing 10% CTAB in 100 µL of 0.7 M NaCl were added, the content was gently mixed and incubated 20 min at 65 C. After an equal volume of isoamyl alcohol : chloroform (1:24) was mixed with the content and shaken drastically, cell debris was precipitated by centrifugation at 12 000 g for 12 min and the supernatant was transferred to a fresh tube. This process was repeated until a clean inter-phase was reached. The supernatant was precipitated with an equal volume of –20 C isopropanol and stored at –20 C at least 30 min. The precipitate was collected by centrifugation at 12 000 g for 12 min, washed twice with 70% ice-cold ethanol, vacuum dried and dissolved in sterilized distilled water.
Amplifying, cloning, and sequencing ß-tubulin and -actin genes.— –
Sequences of ß-tubulin and -actin genes were obtained with either direct sequencing or cloning. DNA amplifications via polymerase chain reactions (PCRs) were performed in 96-well GeneAmp® PCR System 9700 (Applied Biosystems, Foster City, California). The PCR primer pairs T1/T22 (O’Donnell and Cigelnik 1997) and ACT-512F/ACT-783R (Carbone and Kohn 1999) were used respectively to amplify portions of the ß-tubulin and -actin genes. The PCR conditions were: an initial denaturation step at 95 C for 2 min, 35 cycles of 95 C for 1 min, 45–54 C for 1.5 min, 72 C for 2 min, and a final extension at 72 C for 10 min. Reaction components for PCRs were: ca. 0.1–0.2 ng µL–1 of total DNA, 0.2 µM of each primer, 200 µM dNTP, 1.5 mM MgCL2, 0.025 U µL–1 of Taq polymerase (Invitrogen, Carlsbad, California), and 1x standard PCR buffer supplied with the Taq polymerase. PCR products were cleaned with PCR-MTM clean-up system (Viogene-Biotek Corp., Hsichih, Taipei Co., Taiwan) following the manufacturer’s protocol. DNA cloning was carried out as described in Sambrook and Russell (2001). Ligated plasmids were used to transform high efficiency competent cells of Escherichia coli strain DH5 as described in Inoue et al (1990). After incubation overnight at 37 C on LB/carbenicillin/IPTG/X-Gal plates, single transformed white bacterial colonies were picked and transferred into tubes with 6 mL LB/carbenicillin broth and incubated overnight at 37 C in shaking culture. The plasmids were extracted with a plasmid DNA extraction kit (Viogene-Biotek Corp.). ABI Big-dye primer sequencing kit (Applied Biosystems) was used for DNA sequencing, and sequencing reactions were electrophoresed on an ABI Prism 377 model DNA sequencer. Purified PCR products were directly sequenced using the same primer pairs as in the PCR reactions, whereas extracted plasmids were sequenced from both directions using T7 and R universal primers. One of the five internal sequencing primers were used for the ß-tubulin gene: (i) 5'-GGTGCTGCTTTCTGG-3', (ii) 5'-GGTGCTGCCTTCTGG-3', (iii) 5'-GGTGCCGCCTTCTGG-3', (iv) 5'-GGTGCCGCTTTCTGG-3' and (v) 5'-GGTGCCGCCTTTTGG-3'. Sequences were deposited in GenBank; the accession numbers are provided (TABLE I).
Phylogenetic analyses.— –
ß-tubulin and -actin gene sequences were aligned initially with the multiple alignment program Clustal X version 1.81 (Thompson et al 1997, IntelliGenetics Inc., Mountain View, California) with the "gap penalty" set to 10 and "gap extension penalty" to 0.2 and improved manually. Three datasets, including aligned sequences of ß-tubulin gene (TUB), aligned sequences of -actin gene (ACT), and their combined sequences (TUB-ACT), were used for subsequent phylogenetic studies. Phylogenetic analyses of the aligned sequences were performed with MrBayes 3.0b4 (Huelsenbeck and Ronquist 2003) for the Bayesian (MB) analyses and PAUP* version 4.0b10 (Swofford 2003) for the maximum parsimony (MP) analyses. For MB analyses, the settings were "gamma shape," "one substitution type" and "NY98." The number of generations was set to 1 000 000, and one tree was saved per 100 generations. The first 20% of the trees were excluded from construction of the consensus tree. The cladogram and posterior credibility values for the clades found are based on the outcome of the last 0.8 million generations. In the MP analyses, the heuristic searches were performed with AddSeq set to AsIs, MaxTrees to 1000, Steepest to yes, and Swap to "TBR". Bootstrapping for each MP analysis was performed with 1000 replicates, each with one heuristic search with the same parameter settings. All characters were assessed as independent, unordered and equally weighted. Gaps were treated as missing characters. Xylaria bambusicola Y.-M. Ju & J.D. Rogers and X. berteri (Mont.) Cooke were used as outgroup taxa for both MB and MP analyses of the TUB, ACT and TUB-ACT datasets.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSTAXONOMYDISCUSSIONLITERATURE CITED |
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-actin gene sequence sizes are listed (TABLE I). ß-tubulin gene sequences range was 1511–1754 bp among the taxa included in our analyses, with the shortest one from H. macrosporum P. Karst. and the longest from B. anceps (Sacc.) J.D. Rogers et al. The TUB dataset consisted of 110 aligned ß-tubulin gene sequences of 82 taxa and included 2390 characters in length, 1171 of which were phylogenetically informative. The -actin gene sequence range was 260–317 bp among the taxa included in our analyses, with the shortest one from H. multiforme and the longest from H. carneum Petch. The ACT dataset consisted of 111 aligned -actin gene sequences of 84 taxa and included 436 bp in length, 223 of which were phylogenetically informative. The TUB-ACT dataset consisted of the alignment of 107 combined sequences of ß-tubulin and -actin genes of 80 taxa and included 2826 bp in length, 1I84 of which were phylogenetically informative. All the three datasets included the two sequences of the outgroup taxa.
Trees generated from MB and MP analyses of the same dataset were highly similar in topology. Thus only the trees (FIGS. 1–3) generated from MB analyses are presented herein; tree topologies of the MP trees can be found in TreeBase with the study accession number Sxxxx. The tree (FIG. 1) produced from MB analysis of the TUB dataset identified three well supported clades, which received posterior probability values 100, 100 and 90% for the Biscogniauxia clade (B), for the Hypoxylon sect. Annulata clade (A), and for the Hypoxylon sect. Hypoxylon/Daldinia clade (H), respectively. Five most parsimonious trees (MPT) (L = 10 865 steps, CI = 0.2606, RI = 0.6406, RC = 0.1669) were generated from MP analysis of the same dataset. The strict consensus of these trees also identified the three clades, which received bootstrap values 100, 79 and 61% for B, A and H clades, respectively. These clades were similarly well supported in the tree (FIG. 2) produced from MB analysis (posterior probability values = 100, 94 and 91% for B, A and H clades, respectively) of the ACT dataset. While the B clade was well supported in the strict consensus tree (based on 72 MPT, with L = 1949 steps, CI = 0.2945, RI = 0.6946, RC = 0.2046) produced from MP analysis of the ACT dataset, the other two clades were less robustly supported (bootstrap values = 100, 53 and 64% for B, A and H clades, respectively). Aligned sequences of ß-tubulin and -actin genes were combined and resulted in the TUB-ACT dataset. The three clades also were well supported in the tree (FIG. 3) produced from MB analysis (posterior probability values = 100% for B, A and H clades) and in the strict consensus tree (based on 2 MPT, with L = 12 676 steps, CI = 0.2678, RI = 0.6459, RC = 0.1729) produced from MP analysis (bootstrap values = 100, 93 and 86% for B, A and H clades, respectively) of the TUB-ACT dataset.
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Sixteen taxa belonging to Hypoxylon sect. Annulata were included in our analyses. ß-tubulin gene sequences were obtained for 13 taxa but not for H. annulatum, H. thouarsianum var. macrosporum, or H. truncatum, whereas -actin gene sequences were obtained for 15 taxa but not for H. ilanense Y.-M. Ju & J.D. Rogers. Taxa of sect. Annulata formed a well supported clade in our analysis and constituted the branch coming out from the internode next to the Biscogniauxia clade. Section Annulata is thus segregated from Hypoxylon into a new genus (see Taxonomy below). Two distinct subclades were recognized within this clade on the basis of MB and MP analyses of the TUB and TUB-ACT datasets. Subclade A1, which contained H. cohaerens, H. ilanense, H. minutellum Syd. & P. Syd., and H. multiforme and its var. alaskense Y.-M. Ju & J.D. Rogers, is characterized by lacking ostiolar disks or having much reduced ostiolar disks, whereas subclade A2, which contained the rest of the studied taxa in sect. Annulata, features conspicuous ostiolar disks (
0.2 mm diam). Although the trees generated from the ACT dataset failed to discriminate between these two subclades, H. cohaerens, H. minutellum, and H. multiforme and its var. alaskense still clustered as a coherent group.
With sect. Annulata segregated from Hypoxylon into a new genus, Hypoxylon is limited to sect. Hypoxylon sensu Ju and Rogers (1996). The 41 taxa of Hypoxylon along with the 12 taxa of Daldinia formed another distinct clade. Hypoxylon clearly was separated into three subclades, H1, H2 and H3, based on the analyses of the TUB and TUB-ACT datasets. Taxa of Daldinia were included in subclade H3 and represented a clade within Hypoxylon, making the latter paraphyletic. The trees from the ACT dataset did not resolve these subclades well. Nonetheless it is noteworthy that three distinct groupings in the trees produced from the TUB and TUB-ACT datasets also were recognized in the trees produced from the ACT dataset: subclade H1, subclade H2 and the cluster composed of Daldinia taxa. The Hypoxylon taxa in subclade H3 in the trees produced from the TUB and TUB-ACT datasets did not cluster but were scattered among these three distinct groups.
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TAXONOMY |
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actin gene sequences, we propose placing the taxa assigned to Hypoxylon sect. Annulata in a new genus, for which the name Annulohypoxylon is given. Annulohypoxylon Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, gen. nov.
Hypoxylon sect. Annulata J.H. Miller, A monograph of the world species of Hypoxylon, p 86. 1961; emend. Y.-M. Ju & J.D. Rogers, A revision of the genus Hypoxylon, p 22. 1996; see Ju and Rogers (1996) for other synonyms.
Etymology.. Refers to the stromata resembling those of Hypoxylon but with ostioles frequently surrounded with a disk area.
A Hypoxylo differt in strato carbonaceo omni perithecio cengenti, in ostiolo papillato disco annulato distinguibili vel obscure plerumque cengenti et in perispora ascosporae dehiscenti cum spissescenti ca. 
longitudine ascosporae.
Differs from the genus Hypoxylon in having a carbonaceous stromatal layer discretely enclosing each perithecium, ostioles always higher than the surrounding stromatal surface and usually encircled with a distinct or highly reduced annulate disk, and ascospore perispores, when dehiscing, with a thickened area visible at the position of ca. ascospore length.
Stromata effused-pulvinate, pulvinate, glomerate, discoid, hemispherical, or spherical, solitary or confluent, attached to substrate with a broad base; surface light- or dull-colored, usually blackened with age, pruinose or polished, plane or with inconspicuous to conspicuous perithecial mounds; waxy or carbonaceous tissue immediately beneath surface and between perithecia, with KOH-extractable pigments in most cases; the tissue below the perithecial layer inconspicuous, conspicuous, or relatively large, dark brown to black, persistent. Perithecia spherical, obovoid, or less frequently tubular, monostichous, with carbonaceous stromatal layer surrounding individual perithecia. Ostioles higher than the level of stromatal surface, with the ostiolar openings papillate to conicpapillate, with conspicuous to hardly noticeable disks formed by dehiscence of surrounding tissue. Asci eight-spored, cylindrical, stipitate, persistent, with apical ring discoid, amyloid or infrequently inamyloid, distinct. Ascospores light- to dark-colored, unicellular in both mature and immature ascospores, ellipsoid or short fusoid, inequilateral, slightly inequilateral or nearly equilateral, with acute, narrowly rounded, or broadly rounded ends, with a germ slit spore-length to much less than spore-length on the convex side or less frequently on the flattened side; perispore dehiscent or indehiscent in 10% KOH, when dehiscing, with a thickened area visible at the position of ca. 1/3 ascospore length on the same side as the germ slit; epispore smooth.
Type species.. Annulohypoxylon truncatum (Schwein. : Fr.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh
Annulohypoxylon annulatum (Schwein. : Fr.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Sphaeria annulata Schwein., J. Acad. Nat. Sci. Philadelphia 5:11. 1825; Schwein. : Fr., Elench. Fung. II, p 64. 1828.
Hypoxylon annulatum (Schwein. : Fr.) Mont. apud C. Gay, Fl. Chilena VII, p 445. 1850.
Annulohypoxylon archeri (Berk.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon archeri Berk. apud J.D. Hook., Bot Antarc Voy. II, pt. II, p 280. 1860.
Annulohypoxylon atroroseum ( J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon atroroseum J.D. Rogers, Can J Bot 59:1363. 1981.
Annulohypoxylon bovei (Speg.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon bovei Speg., Bol Acad Nac Ci. 11: 201. 1887.
Annulohypoxylon bovei var. microspora ( J.H. Miller) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon bovei var. microspora J.H. Miller, Monogr. of the World Species of Hypoxylon, p 95. 1961.
Annulohypoxylon cohaerens (Pers. : Fr.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Sphaeria cohaerens Pers., Tent Disp Meth Fung, p 2. 1797; Pers. : Fr., Syst. Mycol. II, p 333. 1823.
Hypoxylon cohaerens (Pers. : Fr.) Fr., Summa Veg. Scand. II, p 384. 1849.
Annulohypoxylon discophorum (Penz. & Sacc.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon discophorum Penz. & Sacc., Malpighia 11:492. 1897.
Annulohypoxylon elevatidiscus (Y.-M. Ju, J.D. Rogers & H.-M. Hsieh) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon elevatidiscus Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, Mycologia 96:154. 2004.
Annulohypoxylon gombakense (M.A. Whalley, Y.-M. Ju, J.D. Rogers & A.J.S. Whalley) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon gombakense M.A. Whalley, Y.-M. Ju, J.D. Rogers & A. J. S. Whalley, Mycotaxon 74:137. 2000.
Annulohypoxylon hians (Berk. & Cooke) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon hians Berk. & Cooke apud Cooke, Grevillea 11:129. 1883.
Annulohypoxylon ilanense (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon ilanense Y.-M. Ju & J.D. Rogers, Mycotaxon 73:371. 1999.
Annulohypoxylon leptascum (Speg.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon leptascum Speg., Bol. Acad. Nac. Ci. 11:507. 1889.
Annulohypoxylon leptascum var. macrosporum (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon leptascum var. macrosporum Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 214. 1996.
Annulohypoxylon michelianum (Ces. & De Not.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon michelianum Ces. & De Not., Comment Soc Crittog Ital 1:199. 1863.
Annulohypoxylon microcarpum (Penz. & Sacc.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon microcarpum Penz. & Sacc., Malpighia 11:492. 1897.
Annulohypoxylon minutellum (Syd. & P. Syd.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon minutellum Syd. & P. Syd., Ann Mycol 8:37. 1910.
= Hypoxylon cohaerens var. microsporum J.D. Rogers & Cand., Mycologia 72:826. 1980.
See Ju and Rogers (1996) for other synonyms. This fungus is raised to species level because it differs from A. cohaerens in having vinaceous to rusty KOH-extractable pigments, smaller ascospores, a less than spore-length germ slit and a much wider geographical and host range. Our analyses based on ß-tubulin and -actin gene sequences also support the separation of this fungus as distinct from A. cohaerens. Of note, ITS data of Triebel et al (2005) placed Hypoxylon cohaerens var. microsporum as a sister taxon of H. cohaerens.
Annulohypoxylon moriforme (Henn.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon moriforme Henn., Bot Jahrb Syst 23: 287. 1896.
Annulohypoxylon moriforme var. microdiscus (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon moriforme var. microdiscus Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 217. 1996.
Annulohypoxylon multiforme (Fr. : Fr.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Sphaeria multiformis Fr., Observ Mycol I, p 169. 1815; Fr. : Fr., Syst. Mycol. II, p 334. 1823.
Hypoxylon multiforme (Fr. : Fr.) Fr., Summa Veg. Scand. II, p 384. 1849.
Annulohypoxylon multiforme var. alaskense (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon multiforme var. alaskense Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 219. 1996.
Annulohypoxylon nitens (Ces.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Rosellinia nitens Ces., Atti Accad Sci Fis 5:13. 1872.
Hypoxylon nitens (Ces.) Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 220. 1996.
Annulohypoxylon nothofagi (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon nothofagi Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 221. 1996.
Annulohypoxylon pouceanum (Berk. & Cooke) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon pouceanum Berk. & Cooke apud Cooke, Grevillea 11:130. 1883.
Annulohypoxylon pseudostipitatum (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon pseudostipitatum Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 223. 1996.
Annulohypoxylon purpureonitens (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon purpureonitens Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 224. 1996.
Annulohypoxylon pyriforme (Y.-M. Ju & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon pyriforme Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 224. 1996.
Annulohypoxylon squamulosum (Y.-M. Ju, J.D. Rogers & H.-M. Hsieh) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon squamulosum Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, Mycologia 96:155. 2004.
Annulohypoxylon stygium (Lév.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Sphaeria stygia Lév., Ann Sci Nat Bot, sér. III, 5:258. 1846.
Hypoxylon stygium (Lév.) Sacc., Syll. Fung. I, p 379. 1882.
Annulohypoxylon stygium var. annulatum (Rehm) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Nummularia annulata Rehm, Ann Mycol 11: 399. 1913.
Hypoxylon stygium var. annulatum (Rehm) Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 226. 1996.
Annulohypoxylon thouarsianum (Lév.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
?Basionym. Sphaeria thouarsiana Lév., Ann Sci Nat Bot, sér. III, 5:258. 1846.
Hypoxylon thouarsianum (Lév.) C. G. Lloyd, Mycol Writings 5:26. 1919.
Annulohypoxylon thouarsianum var. macrosporum (San Martín, Y.-M. Ju, & J.D. Rogers) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Hypoxylon thouarsianum var. macrosporum San Martín, Y.-M. Ju, & J.D. Rogers apud Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 228. 1996.
Annulohypoxylon truncatum (Schwein. : Fr.) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Sphaeria truncata Schwein., Schriften Naturf. Ges. Leipzig 1:44. 1822; Schwein. : Fr., Syst Mycol II, p 442. 1823; non Bolton, 1789; nec (Pers. : Fr.) Fr., 1823.
Hypoxylon truncatum (Schwein. : Fr.) J.H. Miller, Trans Brit Mycol Soc 17:130. 1932.
Annulohypoxylon urceolatum (Rehm) Y.-M. Ju, J.D. Rogers & H.-M. Hsieh, comb. nov.
Basionym. Nummularia urceolata Rehm, Philipp J Sci 8: 187. 1913.
Hypoxylon urceolatum (Rehm) Y.-M. Ju & J.D. Rogers, A Revision of the Genus Hypoxylon, p 232. 1996.
The genus Hypoxylon.— – This genus is redefined herein to exclude the taxa of the former sect. Annulata and contains only taxa of sect. Hypoxylon. Stromata usually have a colored surface when mature and are blackened only in a few species, such as H. monticulosum Mont., H. submonticulosum Y.-M. Ju & J.D. Rogers and H. rubigineoareolatum Rehm. The carbonaceous stromatal layer surrounding individual perithecia, as found in Annulohypoxylon, is absent. Ostioles usually are lower than the stromatal surface, less frequently at the same level or slightly higher than the level of stromatal surface and never encircled with an annulate disk. Ascospore perispores, when dehiscing, have conspicuous to inconspicuous transverse coil-like ornamentation.
Hypoxylon polyporoideum.— –
This name was treated by Miller (1961) and Ju and Rogers (1996) as a synonym of H. crocopeplum Berk. & M.A. Curtis, from which it differs in having thicker stromata with tubular to long tubular perithecia and conspicuous black basal tissue beneath the perithecial layer. The recognition of these taxa as distinct species is also strongly supported by the analyses of DNA sequences.
Hypoxylon polyporoideum Berk. ex Cooke, Grevillea 12:53. 1883.
= ? Hypoxylon crocatum Mont. apud C. Gay, Fl. Chilena VII, p 343. 1850.
= ? Hypoxylon ochraceofulvum Berk. & Cooke apud Cooke, Grevillea 11:133. 1883.
= Hypoxylon haematostroma Mont. subsp. haematozonum Sacc., Syll. Fung. IX, p 549. 1891.
= Hypoxylon ferrugineorufum Henn., Hedwigia 39:138. 1900.
See Ju and Rogers (1996) for collecting data of the type specimens of H. polyporoideum and its synonyms and possible synonyms. Hypoxylon crocatum and H. ochraceofulvum are possible earlier names of H. polyporoideum. However the type of H. crocatum was not located at PC, whereas that of H. ochraceofulvum at K is largely immature, having some ascospores found at a very limited part of the material.
Daldinia placentiformis.— –
Daldinia placentiformis (Berk. & M.A. Curtis) Theiss. was treated as Hypoxylon placentiforme Berk. & M.A. Curtis because it lacks conspicuous concentric zones in the stromata ( Ju and Rogers 1996). Its placement in Daldinia is strongly supported by the DNA sequence analyses. It could be considered a "ringless" Daldinia species reminiscent of the ancestral condition.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSTAXONOMYDISCUSSIONLITERATURE CITED |
|---|
-actin genes appear to be suitable for resolving relationships among Annulohypoxylon, Biscogniauxia, Daldinia and Hypoxylon. Analyses based on the TUB and TUB-ACT datasets are consistent with the evolutionary hypotheses on Hypoxylon and its related genera proposed in Ju and Rogers (1996) (see Introduction). These analyses further indicate that Annulohypoxylon can be divided into two subclades based on the presence or absence of ostiolar disks. Also, three subclades were revealed in Hypoxylon, one of which was composed largely of taxa with bright-colored stromatal granules. Owing to the fact that the -actin gene is much shorter than the ß-tubulin gene, the trees generated from the ACT dataset failed to resolve the subclades within Annulohypoxylon and Hypoxylon. We thus base our discussion on the trees produced from the TUB and TUB-ACT datasets unless otherwise noted. Nonetheless results from analyses based on the ACT dataset are also in conformity with the evolutionary hypotheses in Ju and Rogers (1996). Furthermore they reinforce certain well circumscribed groupings in the trees produced from the TUB and TUB-ACT datasets: subclade A1 in Annulohypoxylon, subclades H1 and H2 in Hypoxylon and the Daldinia cluster.
ITS sequences have been used in a previous study on molecular phylogenies of Hypoxylon and some genera or species that were segregated from Hypoxylon (Sánchez-Ballesteros et al 2000). While the ITS region is still highly useful in suggesting the identity of a given xylariaceous fungus, it does not appear suitable for addressing the problems that we intended to resolve. Not only do the considerable variations exist among ITS sequences from various xylariaceous fungi, but a long insertion in the ITS1 region, which has been found in A. stygium (as Hypoxylon stygium) and A. atroroseum (as Hypoxylon atroroseum) by Sánchez-Ballesteros et al (2000) and subsequently in other taxa of Annulohypoxylon by H.-M.H. (unpubl data), also imposes additional difficulties in aligning ITS sequences. In general Sánchez-Ballesteros et al (2000) showed that Biscogniauxia was an independent lineage basal to Hypoxylon, which is in agreement with our present study, but failed to differentiate between Hypoxylon and Annulohypoxylon. A recent study based on ITS sequences likewise did not entirely separate Hypoxylon and Annulohypoxylon (Triebel et al 2005).
The genus Biscogniauxia.— –
Biscogniauxia formed the basal clade among the genera included in our study. Among the species included in our analyses, Biscogniauxia anceps, B. philippinensis var. microspora Y.-M. Ju & J.D. Rogers and B. uniapiculata (Penz. & Sacc.) Whalley & Læssøe have an ascospore appendage; they did not form a separate clade but were scattered among those taxa lacking an ascospore appendage. Thus the recognition by Whalley et al (1990) of sect. Appendiculata in Biscogniauxia, which included only those taxa with appendaged ascospores, is not supported by our analyses. It is interesting to note that B. philippinensis var. microspora and B. latirima are more closely related to each other than to other Biscogniauxia taxa. Their ascospores are similar in being inequilateral and in having a broad germ slit running on the dorsal side ( Ju and Rogers 2001). The ascospores of B. latirima have one end broadly rounded and the other narrowly rounded or beaked. The beak might correspond with the ascospore appendage of B. philippinensis var. microspora.
The genus Annulohypoxylon.— –
Annulohypoxylon is equivalent to Hypoxylon sect. Annulata sensu Ju and Rogers (1996) and approximately includes taxa in Hypoxylon sect. Annulata sensu J.H. Miller, with the exclusion of H. subannulatum sensu J.H. Miller ( = Nemania bipapillata [Berk. & M.A. Curtis] Pouzar), as well as several taxa that fit in Miller’s Hypoxylon sect. Papillata (i.e. H. cohaerens and its var. microsporum, and H. multiforme and its var. alaskense). Two distinct subclades were formed within the genus, and they corresponded well with the conspicuousness of ostiolar disks. Those taxa that have conspicuous ostiolar disks (i.e., 0.2 mm diam) belonged to subclade A2 which included typical members of Miller’s Hypoxylon sect. Annulata, whereas those lacking ostiolar disks or with barely noticeable ostiolar disks belonged to subclade A1, which consisted of those species that formerly were placed in Miller’s Hypoxylon sect. Papillata. Stromatal KOH-extractable pigments in the known taxa of Annulohypoxylon are olivaceous, purplish or orange to rusty. Among the taxa in our studies, A. ilanense, A. minutellum, and A. multiforme yield orange to rusty pigments and were restricted to subclade A1; A. urceolatum is the only taxon yielding purplish pigments, and the others yield olivaceous pigments. Taxa of Annulohypoxylon were not grouped into clusters by the pigments extracted by KOH.
Ostiolar disks in Annulohypoxylon are formed in two processes ( Ju and Rogers 1996): the overlying stromatal layer of the disks is thrown off at once in the bovei-type but is gradually flaked away in the truncatum-type. The ostiolar disks of A. bovei var. microspora, A. squamulosum, and A. nitens are of the bovei-type, whereas those of the other Annulohypoxylon species included in our analyses are of the truncatum-type. Thus, disk formation processes do not suggest natural groupings in Annulohypoxylon.
The genus Hypoxylon.— –
All Hypoxylon species in our analyses clustered within a clade, within which three major subclades were distinguished. Included in subclade H1 were H. rubiginosum (Pers. : Fr.) Fr., H. fuscum (Pers. : Fr.) Fr., H. perforatum (Schwein. : Fr.) Fr. and others, which have dull-colored stromatal granules in most species. Hypoxylon munkii Whalley et al is the only exception, having white stromatal granules yielding no pigments in KOH. Subclade H2, including the type species of the genus H. fragiforme, consisted of those species containing bright-colored granules except for H. lenormandii Berk. & M.A. Curtis, which has dull orange brown granules. All taxa clustered in subclade H3 are like those in subclade H1 in containing dull-colored granules. Subclades H1 and H2 were monophyletic, whereas subclade H3 was paraphyletic, with the Daldinia taxa branching out from the internode shared with H. polyporum (Starb.) Y.-M. Ju & J.D. Rogers. The pigments that are extracted from the granules by KOH can be classified into three general categories among the Hypoxylon taxa: (i) olivaceous, greenish to yellow, (ii) livid to purplish and (iii) orange to reddish. Taxa in subclade H2 yield only pigments of the third category. Those in subclade H3 yield pigments of the first and second categories. Most of the taxa in subclade H1 yield pigments of the first category except for H. rubiginosum, H. petriniae M. Stadler & Fournier and H. cercidicolum (Berk. & M.A. Curtis ex Peck) Y.-M. Ju & J.D. Rogers, which yield pigments of the third category, for H. carneum, which yields pigments of the second category, and for H. munkii, which yields no pigments. While the taxa in subclade H2 are readily recognized by their granule color, those in subclades H1 and H3 cannot be unequivocally separated by granule color and other morphological traits. Within subclade H2, several taxa constantly producing tubular perithecia formed a cluster. These taxa included H. cinnabarinum (Henn.) Y.-M. Ju & J.D. Rogers, H. jecorinum Berk. & Ravenel, H. polyporoideum, and H. rickii Y.-M. Ju & J.D. Rogers. H. haematostroma Mont., which has characteristic long-tubular perithecia, curiously did not cluster with these taxa. The distinguishing feature of H. haematostroma is that its perithecia can be separated easily. The two collections of H. cinnabarinum did not come out next to each other, suggesting that it is a complex species. The several taxa included in Triebel et al (2005) with bright orange to blood-red stromatal granules did not group in the tree generated from ITS sequences.
Hypoxylon begae Y.-M. Ju & J.D. Rogers and H. polyporum are among the analyzed Hypoxylon species with relatively large stromata. Daldinia placentiformis also has been considered a relatively large Hypoxylon species due to the lack of conspicuous zonate ring structure in the stromata. Although they all belonged to subclade H3, they did not form a coherent group. Hypoxylon begae was grouped with H. vinosopurpureum Y.-M. Ju et al, H. anthochroum Berk. & Broome, and H. fuscopurpureum (Schwein. : Fr.) M.A. Curtis; H. polyporum branched out next to the Daldinia species; and D. placentiformis was inserted among the Daldinia species.
Hypoxylon fuscopurpureum was well placed in Hypoxylon in our trees generated from the TUB, ACT and TUB-ACT datasets but far removed from Hypoxylon and its related genera in the ITS-based tree generated by Triebel et al (2005). The ITS sequence AY945224
[GenBank]
that we obtained from our H. fuscopurpureum culture has a fairly low similarity to those two, AY616691
[GenBank]
and AY616692
[GenBank]
, used in Triebel et al (2005). It is possible that their sequences were obtained from another fungus invading stromata of H. fuscopurpureum.
The genus Daldinia.— –
The Daldinia species discussed herein formed a monophyletic group within subclade H3 of Hypoxylon. Hypoxylon polyporum, which was basal to the Daldinia cluster, could be considered another "ringless" Daldinia species in addition to D. placentiformis. Daldinia appears to be a relatively recent assemblage, which explains the morphological uniformity across various species. Triebel et al (2005) also showed that Daldinia species formed a cluster, except for the presence of two Entonaema A. Möller species. However the tree that they generated from ITS sequences did not provide enough resolution to clarify the relationships between Hypoxylon and Daldinia.
The presence of Daldinia within Hypoxylon makes the latter genus paraphyletic, if Daldinia is retained as a genus. As mentioned earlier, proposals to merge Daldinia with Hypoxylon have been made. Nonetheless the concentric ring structure in Daldinia seems to be an adaptation of the genus to dry environments because it provides capacity for stromatal water storage ( Ju et al 1997). We believe that the habit and concentric ring structure of Daldinia should be taken into strong account in taxonomic matters and therefore continue to keep Daldinia and Hypoxylon as separate genera until additional studies of the undoubtedly related genera Entonaema and others can be assessed. As Brummit (2002) stated, paraphyletic groups are inevitable in Linnaean hierarchical classification, and "they are after all just a product of the evolutionary process, what is left behind as evolution moves on to a new level of organization."
Comments on anamorphs, reduction of ascal apical rings, ascospore equality and ascospore perispore dehiscence.— –
With a growing number of species of Hypoxylon and related genera being cultured and their anamorphs being observed, it is now possible to take the anamorphic data into consideration along with their teleomorphic data. Four branching patterns have been found in xylariaceous species with Nodulisporium or nodulisporium-like conidiogenesis ( Ju and Rogers 1996). From our analyses it is obvious that species that are closely related can have entirely different conidiophore branching patterns. Examples can be found for H. rubiginosum and H. petriniae where their teleomorphs are highly similar but their conidiophore branching patterns respectively are nodulisporium-like and virgariella-like. Hypoxylon cercidicolum, despite the fact that its teleomorph differs from H. rubiginosum and H. petriniae primarily in lacking ascal apical rings and in having stromata surrounded with ruptured host tissue, tightly clustered with these two species. It has a different anamorph assignable to the form-genus Hadrotrichum (Petrini and Candoussau 1983). Hypoxylon lividicolor Y.-M. Ju & J.D. Rogers and H. lividipigmentum San Martín et al are also a species pair with nearly identical teleomorphs but quite different anamorphs, being sporothrix-like in the former and nodulisporium-like in the latter. On the other hand, modes of conidiogenesis in Daldinia seem phylogenetically meaningful. Daldinia decipiens Wollweber & M. Stadler, D. petriniae Y.-M. Ju et al, D. singularis, and an undescribed Daldinia species from Russian Far East can produce conidia from percurrently proliferating conidiogenous cells ( Ju et al 1999), forming a coherent group that is distinct from those species that produce conidia solely from sympodially proliferating conidiogenous cells.
Ju and Rogers (1996) considered conidiogenesis in the Xylariaceae to be fairly conservative and useful in subdividing the family into subfamilial taxa. While anamorphs of genera closely related to Hypoxylon are Nodulisporium or nodulisporium-like, those of genera closely related to Xylaria are Geniculosporium or geniculosporium-like. We have demonstrated that the phylogenetic analyses based on sequences of two protein-encoding genes—ß-tubulin and -actin—are consistant with those based on morphological features. In future projects, genera such as Camillea, Entonaema, Obolarina Pouzar, Phylacia Lév., Rhopalostroma D. Hawksworth and Thamnomyces Ehrenb., which also have Nodulisporium or nodulisporium-like anamorphs, can be subjected to similar analyses to reassess their phylogenetic relationships with Annulohypoxylon, Biscogniauxia, Daldinia and Hypoxylon. Furthermore it also will be interesting to see how Jumillera, Theissenia Maubl. and Whalleya, which are like Biscogniauxia in having bipartite stromata but differ in their anamorphs, fit among xylariaceous genera. Jumillera has libertella-like and Geniculosporium synanamorphs (Rogers et al 1997), whereas the anamorphs of Theissenia and Whalleya are characterized by needle-shaped conidia and denticulate conidial secession scars (Rogers et al 1997, Ju et al 2003).
Ascal apical rings are highly reduced or lacking in D. singularis, H. notatum, H. cercidicolum, and H. shearii var. minor San Martín et al. Although H. notatum and H. shearii var. minor branched near each other, the distances between these two species, H. cercidicolum, and D. singularis, were by no means close. It appears that the process in reducing ascal apical rings has happened more than once in independent lineages. Similarly, changes in ascospore equality and perispore dehiscence apparently have occurred independently a number of times.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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1 Corresponding author. E-mail: yumingju{at}gate.sinica.edu.tw
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