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Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
P. Lumyong
Department of Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand 50200
T. Seelanan
Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
D.C. Park
E.H.C. McKenzie
Landcare Research, Private Bag 92170, Auckland, New Zealand
K.D. Hyde
Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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ABSTRACT |
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The phylogenetic relationships of Pyricularia species and species from related genera were established from sequences of the internal transcribed spacer ribosomal RNA gene. Phylogenetic analysis disclosed a consistent correlation with spore morphology. Most Pyricularia species studied, and two species of Dactylaria that have obpyriform conidia, fell within the Magnaporthaceae cluster with high bootstrap support. Pyricularia variabilis was more related to Dactylaria, Tumularia or Ochroconis species than to the Magnaporthaceae. Dactylaria and species of Nakataea, Ochroconis, Pyriculariopsis and Tumularia were distinct from the Magnaporthaceae, and the genus Dactylaria is polyphyletic. The combination of morphological and molecular characters, such as spore morphology and ITS ribosomal DNA sequences data, suggested that conidial shape could be a primary character to distinguish Pyricularia from related genera.
Key words: Dactylaria, ITS rDNA, phylogeny, systematics, 5.8S rDNA
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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with the type species, P. grisea (Cooke) Sacc., which originally was described from crabgrass (Digitaria sanguinalis L.). The name "Pyricularia" refers to the pyriform shape of the conidia. Cavara (1892) subsequently described P. oryzae Cav. from rice (Oryza sativa L.), a taxon with similar morphology to P. grisea. Despite the lack of obvious morphological differences, these two taxa have been maintained as separate species. Rossman et al (1990) argued that P. oryzae should be synonymized with P. grisea and grouped these two anamorphs under the teleomorph Magnaporthe grisea (Hebert) Barr. Recent molecular genetic analyses, however, have indicated that Pyricularia species isolated from different hosts are genetically distinct (Borromeo et al 1993, Shull and Hamer 1994, Kato et al 2000). Based on RFLP and DNA sequence analysis, Borromeo et al (1993) and Kato et al (2000) suggested that the Pyricularia isolates from Digitaria sp. and rice represent distinct species. Using a molecular approach based on three genes (actin, beta-tubulin and calmodulin), Couch and Kohn (2002) described the teleomorph Magnaporthe oryzae B. Couch (associated with Oryza sativa and other cultivated grasses) as a species distinct from M. grisea (associated with the grass genus Digitaria Haller).
Pyricularia has been well circumscribed (Ellis 1971, 1976), although the distinction between it and some Dactylaria species is not always clear (Goh and Hyde 1997). The conidiogenous cells of Dactylaria and Pyricularia are polyblastic, integrated on the conidiophores, and are sympodial, cylindrical, geniculate and denticulate. The conidia are solitary, dry, acropleurogenous, simple, variously shaped, and hyaline to pale brown (Ellis 1971, 1976). In Pyricularia, however, denticles usually are cut off by a septum to form a separating cell (rhexolytic secession) and the conidia are mostly obpyriform. In Dactylaria there is no separating cell in the denticles (schizolytic secession) and the conidia are of various shapes, usually fusiform, naviculate or more or less cylindrical (Ellis 1976). The presence of a separating cell and cylindrical denticles in Pyricularia were characteristics used by Ellis (1976) to delineate Pyricularia from Dactylaria. Furthermore Pyricularia species are important pathogens, while Dactylaria species are usually saprobes (Cai et al 2002, Ho et al 2002, Bussaban et al 2003, Paulus et al 2003, Luo et al 2004).
Analysis of ribosomal DNA frequently has been used in mycological investigations (Bruns et al 1991). In this study the phylogenetic relationships among 41 isolates of Pyricularia and related genera were determined by analyzing complete sequences of the ITS regions (including 5.8S rRNA gene). The aims were to determine whether the morphological characters used to distinguish between Dactylaria and Pyricularia are supported by molecular data and also to establish relationships with Nakataea, Pyriculariopsis and Tumularia, whose species originally were described in or transferred to Pyricularia. The potential of rDNA sequences in the analysis of anamorph-teleomorph relationships at the generic level or using sequence analysis of rDNA combined with PCR-fingerprinting to prove the connection between an anamorph species and an ascomycete has been demonstrated (Guadet et al 1989, Rehner and Samuels 1994, 1995, Kuhls et al 1997). A further aim of this study, therefore, was to establish whether molecular techniques can determine anamorph-teleomorph relationships of species of Dactylaria or Pyricularia.
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MATERIALS AND METHODS |
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). They were obtained from culture collections (International Collection of Microorganisms from Plants, Landcare Research, Auckland, New Zealand, ICMP; Mycotheque de l’ Université Catholique de Louvain, Louvain-la-Neuve, Belgium, MUCL; National Institute of Technology and Evaluation Biological Resource Center, Osaka, Japan, NBRC) or from case studies (Bussaban et al 2001a, b, c, 2003). These isolates were recovered from healthy plants, dead or decaying plant tissues, or those exhibiting symptoms of leaf blast, leaf spot, or leaf streak. For morphological study, mounts were prepared in lactophenol, examined with both differential interference phase contrast and bright field phase contrast microscopy.
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). All isolates were grown in Nobles broth (1.2% malt extract) at 22 C for 10 d. Mycelia including conidia were harvested, freeze dried, frozen in liquid nitrogen and ground into a fine powder with a mortar and pestle. About 15 mg of powdered mycelia including conidia were suspended in 1 mL of ice-cold lysis buffer (150 mM NaCl, 50 mM EDTA, 10 mM Tris-HCl, pH 7.4, 30 µg/mL proteinase K), transferred into 1.5 mL Eppendorf tube and kept at 4 C to prevent endonuclease activity during rehydration of the sample. SDS was added to a final concentration of 2%, vortexed and incubated 30 min at 65 C. After centrifugation for 15 min at 14 000 rpm, the supernatant was transferred to a new sterile 1.5 mL Eppendorf tube. The volume of supernatant was measured and the NaCl concentration was adjusted to 1.4 M and one-tenth volume of 10% CTAB buffer (10% CTAB, 500 mM Tris-HCl, 100 mM EDTA, pH 8.0) was added. The solution was thoroughly mixed and incubated 10 min at 65 C. After cooling 2 min at 15 C, an equal volume of chloroform isoamyl alcohol (24 : 1 v/v) was added, thoroughly mixed and the tube was centrifuged 15 min at 14 000 rpm. The extraction was repeated until the interface was clear. The supernatant was removed to a new Eppendorf tube, containing 2 volumes of cold 100% ethanol. After DNA precipitation, the pellet was centrifuged 15 min at 14 000 rpm, 4 C. Then the pellet was washed with 70% ethanol and dried at room temperature. It was resuspended in 100 µL of 0.002% RNase (5 µg/mL) in TE buffer and incubated 1 h at 37 C (Liou and Tzean 1997). The suspension was stored at –20 C pending use for PCR amplification.
PCR amplification and sequencing.— –
The internal transcribed spacer (ITS) regions 1 and 2, including 5.8S rDNA, were amplified in a 25 µL reaction on a GeneAmp 9700 thermal cycler (Applied Biosystems) under these reaction conditions: 1 µL of template DNA at a 1 : 20 dilution of the DNA extraction, 0.2 mM each dNTP, 0.2 µL of FastTaq (Applied Biosystems), 0.2 µM each of primers ITS1 and ITS4, 2.5 µL of the supplied 10 x PCR buffer with MgCl2, and sterile water to bring volume to 25 µL. Thermal cycling was initiated by denaturation at 95 C for 4 min. This was followed by 35 cycles of denaturation at 94 C for 1 min, annealing at 45 C for 1 min, and extension at 72 C for 1 min, with a final extension at 72 C for 7 min. PCR products were analyzed by electrophoresis on 1% agarose gels in TAE buffer (20 mM Tris-Acetate, 1 mM EDTA, pH 8.0) (Sambrook et al 1989) and viewed by staining with ethidium bromide. Residual nucleotides and primers were removed with High Pure PCR Product Kit (Roche Molecular Biochemicals) according to the manufacturer’s instructions. Amplified products were sequenced with BigDye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) on an ABI PRISM 310 or ABI PRISM 377 automated DNA sequencer. Sequences were determined on both strands with sequencing primers, ITS1 forward and ITS4 reverse (White et al 1990).
DNA sequence alignment and phylogenetic analysis.— –
Sequences were assembled with Sequencher 3.1.1 for Macintosh (Applied Biosystems). Sequences were submitted to http://bioweb.pasteur.fr/seqanal/clustalw, for multiple alignment with Clistal W 1.82 (Thompson et al 1994) and manually adjusted with GeneDoc 2.6.002 (Nicholas and Nicholas 1997). Calculation of base pair (bp) differences was carried out by pairwise comparison of strains from the alignment. Twenty-six new sequences were deposited in GenBank with accession numbers AY265315
[GenBank]
-AY265340
[GenBank]
. Fifteen previously published sequences were obtained from GenBank for inclusion in analyses (TABLE II). Phylogenetic trees were inferred with PAUP*4.0b10 (Swofford 2002). Heuristic searches were performed with the criterion of maximum parsimony (MP) with tree-bisection-reconnection-branch swapping algorithm. Starting trees were obtained via stepwise addition with 100 random sequence input orders. The parsimony tree scores, including tree length and consistency, retention, rescaled consistency and homoplasy indices (TL, CI, RI, RC and HI), also were calculated. The neighbor joining (NJ) method based on a Kimura two-parameter distance measurement also was used to infer a phylogenetic tree. All molecular characters were unordered and given equal weight during analysis. Relative branch support was estimated with 1000 bootstrap replications (Felsenstein 1985) for NJ and MP analyses. Anamorphic Orbiliaceae, Arthrobotrys amerospora S. Schenck, W.B. Kendr. & Pramer, A. musiformis Drechsler and Dactylella cylindrospora (R.C. Cooke) A. Rubner were used to root for phylogenetic tree. DNA sequence alignment and trees were deposited in TreeBase, accession number SN1368.
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RESULTS |
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). Boundaries of the ITS1 and ITS2 regions were determined by comparison with published sequences of the ITS region. ITS regions varied in length from 402 to 623 bp. The length of the 5.8S gene was consistent: 157(±1) bp for strains investigated. No sequence variation is detectable within species and low among species within both the genera Pyricularia and Gaeumannomyces.
Molecular phylogeny.— –
Of 680 total characters in the aligned sequence data, maximum parsimony analysis was conducted for 442 potentially phylogenetically informative characters. Forty sites ambiguously aligned were excluded from the analysis to avoid fragmentary ambiguities. A total of 90 equally most parsimonious trees (TL = 1967, CI = 0.519, RI = 0.698, RC = 0.370 and HI = 0.481) were obtained and compared for the best topology with the Kishino-Hasegawa test (FIG. 1). Those parsimony informative characters in the alignment also were analyzed by means of the NJ method with the Kimura two-parameter distance measurement, assuming equal base frequencies of entire sequences across taxa, and unequal transition to transversion ratio. Supports for grouping in NJ trees were evaluated with 1000 bootstrap replications, which produced a similar tree topology, giving high bootstrap values for the relevant clades.
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), while the remaining taxa were basal to this group. With the exception of P. variabilis Bussaban, all Pyricularia species studied fell within the Magnaporthaceae. In the MP tree Nakataea fusispora (Matsush.) Matsush. formed a sister taxon of the Magnaporthaceae with 82% bootstrap support (FIG. 1). The Magnaporthaceae comprises two sister taxa corresponding to the teleomorph genera Magnaporthe and Gaeumannomyces. The Magnaporthe clade included the type of the genus, M. grisea and the anamorphic species, P. angulata Hashioka, P. costina Sarbajna, Pyricularia higginsii Luttr., P. juncicola MacGarvie and Pyricularia sp. (ICMP14468, ICMP14469). The Gaeumannomyces clade comprised four Gaeumannomyces species, Phialophora graminicola (Deacon) J. Walker, Pyricularia zingiberis Nishik. and P. longispora Bussaban with 90% bootstrap support. Also in this clade, Gaeumannomyces amomi Bussaban and Pyricularia zingiberis isolates from Zingiberaceae plants were related closely with 100% bootstrap support. The Gaeumannomyces isolates from grass also were related closely to the Zingiberaceae isolates. Gaeumannomyces cylindrosporus D. Hornby, Slope, Gutter. & Sivan. and Phialophora graminicola clustered with 100% bootstrap support, and Pyricularia longispora occurred separately. The remaining taxa were related distantly to the Magnaporthaceae. In the MP analysis Pyriculariopsis parasitica (Sacc. & Berl.) M.B. Ellis formed a closely related cluster (100% bootstrap support) with Dactylaria appendiculata Cazau, Aramb. & Cabello and Dactylaria sp. ICMP14618. Tumularia aquatica (In-gold) Marvanová & Descals and D. ampulliformis (Tubaki) G.C. Bhatt & W.B. Kendr. are clustered but with low bootstrap support (64% ). Ochroconis humicola (G.L. Barron & L.V. Busch) de Hoog & von Arx and D. purpurella (Sacc.) Sacc. are clustered with 100% bootstrap support and formed a sister cluster of this former cluster with 75% bootstrap support. Pyricularia variabilis seems to be a taxon different from the other Pyricularia species studied. This species clustered with Dactylaria sp. isolate P24 (89% bootstrap support). They showed 24.4% of sequence variation and formed a sister group of members including the type species of Dactylaria, D. purpurella. However this branch lacked bootstrap support. Similar clusters resulted in the NJ tree but with differing bootstrap support.
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DISCUSSION |
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)). Pyricularia grisea is the cause of gray leaf spot of St Augustine grass (Malca and Owen 1957). Other Pyricularia species cause diseases on members of Cannaceae, Commelinaceae, Marantaceae, Musaceae and Zingiberaceae (Meredith 1963; Asuyama 1965; Hashioka 1971, 1973; Kotani and Kurata 1992; Pappas and Paplomatas 1998). Pyricularia penniseti Prasada & Goyal and P. setariae Nishik., morphologically similar pathogens, have been reported on cereals and grasses (Nishikado 1917, Sprague 1950, Malca and Owen 1957, Bailey and van Eijnatten 1961, Asuyama 1965, Wells et al 1969, Prasada and Goyal 1970). Pyricularia zingiberis, P. costina, P. curcumae Rathaiah and P. distorta Hashioka are pathogenic on Zingiberaceae (Nishikado 1917, Hashioka 1971, Rathaiah 1980, Sarbajna 1990). Bussaban et al (2001a, b, 2003) reported several Pyricularia species, including P. costina, living as endophytes in healthy wild ginger.
The criterion used by Ellis (1976) for separating Pyricularia from Dactylaria is that the conidia of Pyricularia secede in a rhexolytic manner, with the denticle acting as a separating cell, and with a protruding hilum on the conidia, whereas those of Dactylaria secede in a schizolytic manner. However subsequent revisions of Dactylaria (de Hoog 1985, Goh and Hyde 1997) are not consistent with this method of conidiogenesis in Dactylaria. Two species originally described in Pyricularia (P. higginsii Luttr. and P. juncicola MacGarvie) that secede in a schizolytic manner, were transferred to Dactylaria (Ellis 1976). The name Dactylaria juncicola was occupied already by a different fungus, D. juncicola (MacGarvie) G.C. Bhatt & W.B. Kendr., thus Ellis (1976) proposed the new name D. junci. Nakataea fusispora also was transferred to Pyricularia fusispora because of its rhexolytic conidial secession (Zucconi et al 1984). However the phylograms inferred from ITS sequence data presented here did not disclose any consistent correlation with the type of conidial secession. Nonetheless it did reveal an interesting correlation between this clade and conidial morphology. With the exception of P. variabilis, all Pyricularia species studied including two species of Pyricularia (P. higginsii and P. juncicola, previously renamed Dactylaria) that have obpyriform conidia were grouped within the family Magnaporthaceae with high bootstrap support. This suggested the clade might represent a monophyletic lineage of species with obpyriform conidia. Following this conidial morphology criterion, the originally named Pyricularia higginsii and P. juncicola therefore should be maintained in Pyricularia. Likewise Nakataea fusispora also should be maintained in Nakataea because this species has distinctive, verrucose, fusiform conidia and it formed a sister cluster of members in Magnaporthaceae.
Pyricularia variabilis was the only species of Pyricularia studied that did not group in the Magnaporthaceae. This taxon has swollen, terminal and intercalary nodes on the conidiophores, and variously shaped conidia. Analyses of ITS sequence data showed that P. variabilis was unrelated phylogenetically to the other Pyricularia species studied but more closely related to Dactylaria, Tumularia or Ochroconis species. Further work is needed to establish the appropriate placement of this taxon and determine its relationships.
Our results indicated that the rest of Dactylaria and species of Pyriculariopsis, Tumularia and Ochroconis were distinct from the Magnaporthaceae and that the genus Dactylaria is polyphyletic. Dactylaria is a form genus and includes species with many conidia born at the apical region of conidiophores on cylindrical or tapering denticles. Conidia, however, are shaped variously and therefore taxa may be unrelated. Furthermore this type of conidiogenesis might have evolved more than once. Our results support this conjecture.
Dactylaria purpurella is the type species of Dactylaria and has short conidiophores with cylindrical or tapering denticles bearing navicular conidia. In the ITS sequence analysis it was clustered with Ochroconis humicola with 100% BS. Ochroconis humicola was described originally as a species of Scolecobasidium and subsequently included in Ochroconis (de Hoog and von Arx 1973). Ochroconis and Scolecobasidium are members of the Dactylaria complex characterized by rhexolytic conidium secession and pale brown conidia. Most species of Ochroconis have ellipsoidal, clavate or fusiform conidia, while Scolecobasidium species have trilobate conidia (de Hoog and von Arx 1973, de Hoog 1985). The other species of Dactylaria appear to be unrelated to D. purpurella and further work is needed to understand this genus complex.
Tumularia aquatica and Pyriculariopsis parasitica originally were described in Pyricularia and later accommodated in newly introduced genera (Ingold 1943, Hughes 1958, Ellis 1971, Marvanová and Descals 1987). Tumularia aquatica differs from Pyricularia in lacking denticles and having lemon-shaped conidia. Pyriculariopsis parasitica differs in having straight or curved, obclavate and rostrate conidia. The exclusion of these taxa from Pyricularia, therefore, is justified and supported by morphological and molecular data.
Anamorph-teleomorph connections.— –
Anamorphic fungi that have not been linked to any teleomorphs make up a large proportion of known fungi. The inability to identify such links lies in inherent difficulties in experimentally proving anamorph-teleomorph connections and the fact that many fungi will not sporulate in culture. The present classification system for anamorphic genera therefore uses three categories of information to identify taxa (Kirk et al 2001): conidiomatal types, Saccardo’s spore groups and conidiogenous events. Relationships suggested by such information, however, do not necessarily reflect evolutionary relationships (Hawksworth et al 1995), and the need for identifying relationships of anamorphs with their teleomorphs with molecular techniques has been advocated by Rossman et al (2001). Dactylaria and Pyricularia have similar types of conidiogenesis and spore types and are hyphomycetes (Ellis 1976). Species of Pyricularia have been characterized by morphological, physiological or molecular information (Ellis 1971, 1976; Matsuyama et al 1977; Kato et al 2000; Couch and Kohn 2002) and have been linked to Magnaporthe teleomorphs (Hebert 1971, Kato et al 1976). Species of Dactylaria differ from Pyricularia in the absence of a separating cell in the denticles, and the conidia also are of various shapes, usually fusiform, naviculate, or more or less cylindrical (Ellis 1976). Teleomorphs of Dactylaria species have not been reported commonly. Carmichael et al (1980) mentioned the occurrence of an anamorph for Acrospermum compressum Tode. This anamorph bears some similarity to Subulispora minima P.M. Kirk and to Dactylaria graminicola Årsvoll. Sivichai et al (2002) reported a teleomorph-anamorph connection between an unidentified teleomorph and Dactylaria.
Carbone and Kohn (1993) demonstrated the confirmations of anamorph-teleomorph connection by comparative sequence analysis of amplified products of Sclerotinia and Sclerotium, which showed 98% sequence homology in the ITS region of rDNA. Kuhls et al (1997) established the connection between Trichoderma anamorphs and Hypocrea teleomorphs where five Trichoderma-Hypocrea connections were supported by 100% identity in ITS1 and ITS2 sequences. Egger and Sigler (1993) investigated the ex type strains of the anamorph Scytalidium vaccinii Dalpé, Litten & Sigler and the ascomycete Hymenoscyphus ericae (D.J. Read) Korf & Kernan. They found 1.2–3.5% divergence in the ITS1 and ITS2 regions and concluded from these data and morphological observations that S. vaccinii and H. ericae are anamorph and teleomorph of a single taxon. In our study phylogenies showed Pyricularia zingiberis and Geaumannomyces amomi isolated from Zingiberaceae plants were grouped strongly and closely related to other Gaeumannomyces species from grasses. Our isolates from Zingiberaceae contained up to six nucleotide differences in the entire ITS sequences, while nucleotide sequences of P. zingiberis isolate NBRC9624 and G. amomi isolate ICMP14648 were identical. Geographical separation or host specialization (TABLE I) could be an explanation for the nucleotide sequence differences present in P. zingiberis from Japan, isolates MUCL9449 (Zingiber officinale Rosc.) and NBRC9624 (Zingiber mioga Rosc.), in comparison with G. amomi isolates ICMP14650 (Alpinia malaccensis (Burm.) Rosc.) and ICMP14648 (Amomum siamense Craib.) from Thailand. However information from a larger number of isolates is required to confirm this. According to ITS sequences, and a distinct morphological character of sickle-shaped conidia, Harpophora W. Gams, a genus comprising phialidic anamorphs of the Magnaporthaceae was introduced with H. radicicola (Cain) W. Gams (= Phialophora radicicola Cain) as type (Ward and Bateman 1999, Gams 2000). A connection between H. graminicola (Deacon) W. Gams (= P. graminicola (Deacon) J. Walker) and Gaeumannomyces cylindrosporus also was supported by ITS sequences similarity (Walker 1980, Bryan et al 1995). Likewise Couch and Kohn (2002) extracted DNA directly from freeze dried perithecia of Magnaporthe and mycelia of anamorphic Pyricularia isolates and the result, based on three genes (actin, beta-tubulin and calmodulin), supported the anamorph-teleomorph connection demonstrated by Hebert (1971) and Yaegashi (1977). Our results are consistent with the possibility that heterogenous P. zingiberis might be the anamorph state of Gaeumannomyces amomi.
Molecular studies have suggested that Pyricularia spp. isolated from different hosts are genetically distinct (Borromeo et al 1993, Shull and Hamer 1994, Kato et al 2000, Couch and Kohn 2002, Goodwin et al 2003) or provided information on the genetic diversity among different population of rice blast fungi, Pyricularia grisea or P. oryzae (Lebrun et al 1991, Levy et al 1991, Zhu et al 1992, Chen et al 1995, George et al 1998). In our study the combination of morphological characters (e.g., spore morphology) and molecular characters (ITS ribosomal DNA sequences data) may confidently let us distinguish Pyricularia from Dactylaria species, especially if sexual structures are not readily produced in culture. We conclude that conidial shape can be used as a primary character to distinguish Pyricularia species from related genera such as Dactylaria.
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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1 Corresponding author. E-mail: scboi009{at}chiangmai.ac.th
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LITERATURE CITED |
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95% are strongly supported (Felsenstein 1985