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Department of Botany, University of Toronto, Mississauga Ontario, Canada L5L 1C6
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Magnaporthe oryzae is described as a new species distinct from M. grisea. Gene trees were inferred for Magnaporthe species using portions of three genes: actin, beta-tubulin, and calmodulin. These gene trees were found to be concordant and distinguished two distinct clades within M. grisea. One clade is associated with the grass genus Digitaria and is therefore nomenclaturally tied to M. grisea. The other clade is associated with Oryza sativa and other cultivated grasses and is described as a new species, M. oryzae. While no morphological characters as yet distinguish them, M. oryzae is distinguished from M. grisea by several base substitutions in each of three loci as well as results from laboratory matings; M.oryzae and M. grisea are not interfertile. Given that M. oryzae is the scientifically correct name for isolates associated with rice blast and grey leaf spot, continued use of M. grisea for such isolates would require formal nomenclatural conservation.
Key words: gray leaf spot, Pyricularia grisea, Pyricularia oryzae, rice blast
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). Borromeo and coworkers (1993) identified four major, highly distinct groups of Pyricularia (anamorph of Magnaporthe, see below) isolates by means of RFLPs: (i) isolates from Digitaria ciliaris (Retz.) Koeler and Eragrostis sp., (ii) a single isolate from Cenchrus echinatus L., (iii) isolates from Cyperus brevifolius (Rottb.) Endl. ex Hassk and Cyperus rotundus L., and (iv) isolates from Oryza sativa L. and other grasses. Shull and Hamer (1994) reviewed unpublished data for mtDNA RFLPs which indicated that pathogens of Digitaria and Pennisetum are distinct from other host specific forms of Pyricularia grisea. Combined data for rDNA, mtDNA, and nuclear DNA haplotypes identified two groups among isolates from species of Digitaria and two groups among isolates from species of Pennisetum. (Shull and Hamer 1994). Our studies focus on species delimitation among isolates associated with Digitaria and Oryza.
Host association appears to define fundamentally distinct groups within M. grisea: species, populations, and clonal lineages. Several host range studies have been performed in the laboratory or greenhouse, with conflicting results (reviewed by Ou 1987). Such laboratory studies may not reflect host range in nature. The realized host range is likely better understood through sampling from field populations. Clonal lineages from O. sativa in the USA and Colombia, identified by DNA fingerprinting using repetitive elements, have been found to be associated with distinct assemblages of rice cultivars (Levy et al 1991, 1993, Correa Victoria et al 1994). DNA fingerprinting and RFLP studies have identified genetically distinct, host-specific populations of M. grisea (Borromeo et al 1993, Hamer et al 1989, Kato et al 2000). RFLP and DNA sequencing studies have resolved highly divergent lineages within M. grisea from Digitaria sp. and O. sativa (Borromeo et al 1993, Bunting et al 1996, Kato et al 2000). Borromeo et al (1993) and Kato et al (2000) suggested that the divergent lineages from Digitaria and rice represent distinct species. No new species have been described.
Hebert (1971) described Ceratosphaeria grisea based on a cross between isolates of the anamorph, Pyricularia grisea (Cook) Sacc., from Digitaria sanguinalis (L.) Scop. (crabgrass). A teleomorph produced as a result of a cross between isolates from D. sanguinalis (D. sanguinalis x D. sanguinalis) was reported to be morphologically identical to the teleomorphs produced in crosses of isolates from other grasses [O. sativa x O. sativa (Kato and Yamaguchi 1982), Eleusine indica (L.) Gaertn. x E. indica (Yaegashi and Udagawa 1978), E. coracana (L.) Gaertn x E. coracana (Yaegashi and Udagawa 1978), O. sativa x E. indica (Yaegashi and Udagawa 1978), and O. sativa x E. coracana (Ueyama and Tsuda 1976)]. As a consequence of observations made of these crosses, no teleomorph distinct from that described by Hebert from isolates from Digitaria has been described for isolates from rice or other grasses.
Yaegashi and Udagawa (1978) produced a teleomorph consistent with Hebert's description and morphologically identical to authentic material of C. grisea, from a cross between Pyricularia isolates from E. indica (C10 and T28). They provided a detailed description and accompanying illustration of the teleomorph produced from these isolates. Their comparison of this teleomorph with M. salvinii (Cattaneo) Kraus and Webster, the type species of Magnaporthe, led them to transfer C. grisea to Magnaporthe. This transfer was, however, subsequent to that of Barr, who did not provide an illustrated description (Barr 1977).
Two form-species names have been applied to the anamorph of M. grisea. Pyricularia grisea was described from D. sanguinalis, and P. oryzae Cavara was described from O. sativa. Pyricularia oryzae was distinguished from P. grisea based on its sparse, usually nonseptate hyphae and larger, biseptate conidia (reviewed by Ou 1987). The usage of the names P. grisea and P. oryzae has generally reflected the host from which the fungus was isolated rather than any morphological differences, with the name P. oryzae applied to isolates from rice and P. grisea to isolates from cereals and other grasses (Sprague 1950). The morphological similarity of Pyricularia isolates from different grass hosts has led to the view that P. oryzae and P. grisea are synonymous (Sprague 1950, Ou 1987, Rossman et al 1990). Rossman et al (1990) confirmed the morphological similarity after examination of the type specimens of P. grisea and P. oryzae. Fully fertile matings between isolates from rice and isolates from other grasses were interpreted as evidence for the existence of a single biological species (Yaegashi and Udagawa 1978). However, no successful crosses of isolates from Digitaria and from Oryza have been reported (Hebert 1971, Kato et al 2000). Based on overlap in conidial morphology and interfertility among isolates from rice and other grasses, Rossman et al (1990) synonymized P. oryzae under P. grisea. The synonymizing of these names may have been premature and is evaluated in the present study.
The objective of this study was to investigate the phylogenetic relationship among M. grisea isolates from different grass hosts using a multilocus gene genealogy of DNA sequences from portions of three genes. If M. grisea isolates from Digitaria species and rice belong to diagnosably distinct monophyletic clades, a new species epithet is required for the clade including isolates from rice. Alternatively, if polyphyletic or paraphyletic groups were inferred, isolates from both Digitaria and Oryza should continue to be accommodated under M. grisea. If isolates representing these clades are not interfertile, the segregation of a new species from M. grisea, as both a phylogenetic and a biological species, is further indicated.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Polymerase chain reaction (PCR) and DNA sequencing –
DNA amplification reactions were performed in either a Perkin-Elmer 9600 or 9700 thermocycler (Perkin Elmer, Foster, City, California) following the protocol provided with PCR core reagents (Roche Molecular Systems Inc., Branchburg, New Jersey). The reaction volume was 20 µL containing 10 µL of template DNA at a 1:200 dilution of the DNA extraction. The PCR primers ACT-512F, ACT-783R, Bt1a, Bt1b, CAL-228F, and CAL-737R were used to amplify portions of the actin, beta-tubulin, and calmodulin genes, respectively. Sequences for these primers have been published previously (Carbone and Kohn 1999, Glass and Donaldson 1995). The PCR conditions used for all primers were as follows: an initial denaturation step at 95 C for 8 min, 30 cycles of 95 C for 30 s, 55 C for 20 s, 72 C for 1 min and a final extension at 72 C for 5 min. PCR products were purified using QIAquick spin columns (Qiagen Inc. Mississauga, Ontario) following the manufacturer's instructions.
Both forward and reverse strands were sequenced using the same primers used in the amplification reactions. Sequencing reactions were performed using an ABI Prism Big Dye Terminator Cycle Sequencing kit (Applied Biosystems, Foster City, California), following the manufacturer's instructions, with the exception that only 1/4 of the recommended volume of terminator mix was used. Sequencing reactions were subjected to capillary electrophoresis on an ABI 310 Genetic Analyzer. Electropherograms were interpreted with Sequence Analysis Software version 3.3 (Applied Biosystems, Foster City, California).
DNA sequence alignment –
Analyzed sequences were imported into Sequencher 3.1.1 (Gene Codes Corporation, Ann Arbor, Michigan), checked visually and placed in contigs. All sequences were deposited in GenBank, with accession numbers AF395947 to AF396033 and AY063734 to AY063739. Sequences were aligned using CLUSTAL W Version 1.74 (Thompson et al 1994) and edited manually using Sequence Alignment Editor version 1.0 alpha 1 (http://evolve.zoo.ox.ac.uk/software/Se-Al/Se-Al.html). The intron and exon positions were identified by aligning Magnaporthe sequences with the following sequences: beta-tubulin 1 from Neurospora crassa Shear and Dodge (GenBank accession number M13630), calmodulin from M. grisea (AF104986), and actin from Acremonium chrysogenum (Thirumalachar and Sukapure) Gams (AF056976). Percentage divergence was calculated by dividing the number of variable positions in the aligned sequence by the total length of the consensus sequence.
Phylogenetic analysis –
Phylogenetic analysis was first performed using only M. grisea isolates. Phylogenies were inferred from each of the three genes individually, then from the combined data for all three genes. A second analysis was performed using all Magnaporthe species. All phylogenetic analyses were performed using PAUP 4.0b3 (Swofford 1998). Trees and DNA sequence alignments were deposited in TreeBASE, accession number SN1015. Heuristic searches were performed using the optimality criterion of maximum parsimony. Starting trees were obtained via stepwise addition with a simple addition sequence using M. salvinii as a reference taxon. The branch swapping algorithm used was tree-bisection-reconnection. In the analysis of M. grisea isolates, unrooted trees were produced which were then rooted using isolates from species of Digitaria. In the analysis of all Magnaporthe species, trees were left unrooted. The molecular clock hypothesis was tested using the one degree of freedom method of Tajima (1993). To assess the support for each branch, bootstrapping (Felsenstein 1985) was performed with 500 replicates using the heuristic search option. Phylogenies were inferred from each of the three genes individually and then for the combined data for the beta-tubulin and calmodulin genes. Phylogenetic congruence was determined by the partition homogeneity test [(PHT); (Huelsenbeck et al 1996)], performed with 100 replicates, and Templeton's summed ranks test (Templeton 1983), both implemented in PAUP 4.0b3 (Swofford 1998).
Maximum likelihood analysis –
Heuristic searches were also performed using the optimality criterion of maximum likelihood (Felsenstein 1981). Nucleotide frequencies were calculated from the data, all sites were assumed to evolve at the same rate and a molecular clock was not enforced.
PCR-RFLP diagnostic for species identification – The beta-tubulin region was amplified as described above. PCR reactions were precipitated using sodium acetate and ethanol then resuspended in 50 µL of H2O. Five µL of DNA was digested with Hpa II (New England Biolabs, Boston, Massachusetts) according to the manufacturer's instructions and separated on a 1.5% agarose gel containing ethidium bromide and visualized under UV light.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Morphological examination – The teleomorph produced in the 8465 x 8470 cross, as well as the type specimen of M. grisea (see taxonomic part below) and all anamorphs were examined. Ascospores and conidia were measured and perithecial morphology was compared among specimens and against published descriptions. Consistent with the literature, no morphological differences were observed between materials associated with Digitaria and those associated with Oryza and other non-Digitaria grasses.
DNA extraction, sequencing and alignment – Due to the paucity of perithecia in the type specimen of Ceratosphaeria grisea (BPI 625033), DNA extraction for PCR amplification was not attempted. DNA extraction was successful from as few as 20 freeze-dried perithecia from the cross of isolates 8465 x 8470 (designated in the present study as the holotype of M. oryzae), but was unsuccessful from 5 or 10 perithecia. The actin, beta-tubulin and calmodulin genes could be amplified from all Magnaporthe species. The exon sequences for these genes were easily alignable across all species. Alignments of the intron sequences were unambiguous within species, but were more complicated among species. As a result, intron sequences were eliminated from the phylogenetic analyses in which all species were included. The intron sequences from M. grisea isolates were alignable with each other and were included in the phylogenetic analysis restricted to M. grisea isolates.
Phylogenetic analysis of M. grisea –
Single most parsimonious trees were inferred for M. grisea isolates based on data from each of the three genes (Fig. 1). In each phylogeny, isolates from Digitaria sp. were distinct from the isolates from O. sativa and other grasses. The isolates C10 and T28 [the voucher isolates from Eleusine indica used in Yaegashi and Udagawa's cross (1978)] clustered within the clade containing isolates from O. sativa. In the PHT, no significant incongruence (P = 0.7) was found among phylogenies inferred from the actin, beta-tubulin and calmodulin genes. Similar results were obtained with Templeton's signed rank test (P > 0.3 for all tests). As a result, data from each of these genes could be combined. Five most parsimonious trees, one step longer than the minimum length tree, were inferred from the combined data; one representative tree is presented (Fig. 2). These trees each have a consistency index (CI) of 0.992 and differ from one another only in the branching order within the clade containing isolates from O. sativa. Isolates from Digitaria sp. are separated from the other isolates by a total of 123 steps. Polymorphisms distinguishing Digitaria isolates from O. sativa isolates are presented in Tables II, III and IV.
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). The maximum likelihood tree produced for this dataset has the same topology as the maximum parsimony tree. In this phylogeny, two clades are clearly resolved within M. grisea.
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) was developed as a simple, rapid diagnostic for distinguishing members of the two clades within M. grisea. The G-A transition at position 160 and the G-C transversion at position 161 in the beta-tubulin gene result in the absence of the Hpa II restriction site in isolates from Digitaria. Consequently, isolates from Digitaria can be distinguished from isolates from rice and other grasses based on the PCR-RFLP phenotype for the beta-tubulin region (Fig. 5). Twenty-two Chinese isolates from three hosts, Digitaria sp. (6 isolates), Eleusine coracana (5 isolates), and O. sativa (11 isolates), were used to evaluate this assay. Twenty-one isolates were found to have the predicted PCR-RFLP phenotype. One isolate (94–118–1a), reportedly from Digitaria, possessed a PCR-RFLP phenotype characteristic of isolates from O. sativa. To confirm the identity of this isolate the beta-tubulin gene was sequenced and was found to be identical to isolates from O. sativa. This suggests that the isolate was either mislabeled and is not from Digitaria, or that M. oryzae may occur rarely on Digitaria.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, Kato et al 2000). These lines of evidence also indicate that the two lineages are not divergent populations within the same species. The large number of base substitutions separating these two lineages within M. grisea is consistent with a long period of isolation. When data from all three genes were combined in analysis of isolates of M. grisea, 123 steps separated the clade including isolates from Digitaria from the clade composed of isolates from O.sativa and other grasses (Figs. 1, 2). In order to evaluate the monophyly of these groups, species-level phylogenies (including all Magnaporthe species) were constructed (Figs. 3, 4). In this analysis, the two lineages were clearly resolved as monophyletic and separated by a total of 13 steps.
In the species-level phylogenies M. rhizophila, represented by two isolates, was paraphyletic. One isolate was from the United States and one was from South Africa. These isolates may represent distinct species.
The ecological and reproductive isolation of the two lineages within Magnaporthe grisea has resulted in what appear to be multiple fixed DNA sequence differences between the lineages. Only one polymorphism is shared by the two lineages within M. grisea. At position 48 in the beta-tubulin gene the rice isolate A119 and the isolates from Digitaria have a C, the remaining isolates have a T at this position. This shared polymorphism may represent a character reversal.
The differentiation of population divergence from speciation events has been addressed recently by Carbone and Kohn (2001). Nested cladistic and coalescent analyses at both the population and species levels were used to order population divergence within Sclerotinia sclerotiorum (Lib.) de Bary and speciation events within Sclerotinia. Species were distinguished from populations based on differences in coalescence times; populations coalesce before species. Within S. sclerotiorum the most divergent populations differed by 22 base pairs out of a total of 4000, or 0.55%. In the species level analysis, the two closely related species S. minor Jagger and S. trifoliorum Erikss. differed by 22 base pairs out of a total of 1250, or 1.76%. In comparison, based on data from three genes, the divergence between the two lineages resolved within M. grisea was 9.7%. In the species level analysis, the divergence between the two lineages within M. grisea was 2.21% (substitution rates were clock-like). This level of divergence is comparable to the species level divergence found in Sclerotinia. Considering both the level of divergence between the two clades within M. grisea and their monophyly, they could be considered phylogenetic species under Cracraft's (1983) definition in which a phylogenetic species is recognized as a diagnosably distinct, monophyletic, basal group of organisms.
The association of each clade with different hosts indicates ecological specialization. Digitaria species are ubiquitous weeds and often occur adjacent to rice cultivation, yet host association is maintained. This host association may be maintained by ecological factors such as the life history or microhabitat occupied by the host. Alternatively, host association may be maintained by the inability to overcome resistance genes present in other grass hosts.
Interfertility between isolates from Digitaria and isolates from Oryza and other grasses has not been reported (Hebert 1971, Kato et al 2000). In contrast, there have been fertile crosses between isolates from Digitaria (Hebert 1971, Kato et al 2000), and between isolates from Oryza (Oryza x Oryza) (Kato and Yamaguchi 1982), from Eleusine (Eleusine x Eleusine) (Yaegashi and Udagawa 1978), as well as between isolates from both grass genera (Oryza x Eleusine). This further supports the reproductive isolation of Digitaria isolates from isolates from rice and other hosts evident in the phylogenetic analyses. Biological species boundaries are congruent with phylogenetic species boundaries.
Based on our own as well as published observations, there are no known morphological characters that distinguish isolates from Oryza or other grasses from Digitaria isolates (Rossman et al 1990, Yaegashi and Udagawa 1978). When Yaegashi and Udagawa (1978) mated the isolates from Eleusine, C10 and T28, they concluded that based on morphology, the teleomorph was consistent with Hebert's description of C. grisea and that their teleomorph matched those preserved by Hebert. In this study, based on DNA sequence data, the isolates C10 and T28 could be distinguished from isolates from species of Digitaria and therefore from Hebert's concept of M. grisea which was based on isolates from Digitaria. Although these two lineages within M. grisea do not seem to be morphologically differentiated, they are differentiated by molecular characters and host association. Unfortunately, no authentic living material attributable to Hebert seems to exist and ascospores preserved in his type specimen of C. grisea are no longer viable.
Describing a new species based upon DNA sequence differences and host of origin makes identification difficult if DNA sequencing facilities are not available or the host of origin is not known. To address this difficulty, we have developed the diagnostic PCR-RFLP test and demonstrated its utility.
This study conclusively demonstrates that there are two species within the present circumscription of M. grisea. The two lineages have been detected in previous studies using other molecular methods (Borromeo et al 1993, Shull and Hamer 1994, Bunting et al 1996, Kato et al 2000). Because the name M. grisea is nomenclaturally tied to isolates from Digitaria, the scientifically correct name for isolates from Oryza and other grasses is M. oryzae. If the user community desires to continue applying the name M. grisea in a scientifically accurate way for isolates associated with rice blast and grey leaf spot, formal nomenclatural conservation through proposals to the International Committee on Fungal Nomenclature will be required. If successful, a new epithet for isolates from Digitaria would be required.
Description of species – A new species is described for the strains of Magnaporthe from O. sativa and closely related isolates from other grasses, which are phylogenetically distinct from isolates from Digitaria.
Magnaporthe oryzae B. Couch sp. nov. Fig. 1, Yaegashi and Udagawa (1978); Fig. 5, Couch and Kohn (this paper).
Teleomorphus ut in Magnaporthe grisea simili sed ab hac specie differt: in gramina Eragrostis curvula et Eleusine coracana et Lolium perenne et Setaria spp. et Oryza sativa sed haud Digitaria spp. genitus; gens beta-tubulin vocata locis 160 et 161 situ rumpenti Hpa II vocato exemplis PCR-Bt1a et PCR-Bt1b amplicata exhibens; PCR-RFLP enzymato Hpa II vocato fragmenta duo 188 fasciarum et 362 fasciarum praebens. Anamorphus est Pyricularia oryzae vocatus.
Teleomorph similar to Magnaporthe grisea but differs from that species: parasitic on grasses Eragrostris curvula, Eleusine coracana, Lolium perenne, Setaria spp., and Oryza sativa, but not Digitaria spp. Among many polymorphisms in each of three gene loci, those polymorphisms in the beta-tubulin gene at positions 160 and 161, when amplified using primers Bt1a and Bt1b, result in the addition of an Hpa II restriction site. PCR amplification followed by restriction digestion with Hpa II yields two DNA fragments, one of 188 base pairs and the other 362 base pairs. Anamorph is Pyricularia oryzae.
Type specimen: GUYANA and OTHER LOCALITIES: cross of the mapping strains 8465 by 8470 (Nitta 1997) which were the progeny of a cross of Guy11, from Oryza sativa in Guyana, and 2539, a fertile lab strain derived from several fertile strains crossed successively to increase fertility, originally isolated from Eleusine and Oryza sativa from unreported localities (HOLOTYPE—BPI 841383; duplicate, TRTC 52742; strains available from Fungal Genetics Stock Center, Department of Microbiology, University of Kansas Medical Center Kansas City, Kansas 66160-7420 USA).
Etymology. Latinized from oryza, Greek = rice, referring to the name of the anamorph, Pyricularia oryzae, which was first described from rice.
Anamorph. Pyricularia oryzae Cavara, Fungi Longobardiae Exsiccati No. 49. 1892.
= Dactylaria oryzae (Cavara) Sawada, Trans. Nat. Hist. Soc. Taiwan 6:242. 1916.
Specimens examined. UNITED STATES. NORTH CAROLINA: Barley grain and rice straw, 1971 Jan 00, T. T. Hebert, BPI 625033 (Holotype of Ceratosphaeria grisea).
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ACKNOWLEDGMENTS |
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FOOTNOTES |
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Accepted for publication November 29, 2001.
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LITERATURE CITED |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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 B. C. Couch, I. Fudal, M.-H. Lebrun, D. Tharreau, B. Valent, P. van Kim, J.-L. Notteghem, and L. M. Kohn Origins of Host-Specific Populations of the Blast Pathogen Magnaporthe oryzae in Crop Domestication With Subsequent Expansion of Pandemic Clones on Rice and Weeds of Rice Genetics, June 1, 2005; 170(2): 613 - 630. [Abstract] [Full Text] [PDF]
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C. R. Grunig and T. N. Sieber Molecular and phenotypic description of the widespread root symbiont Acephala applanata gen. et sp. nov., formerly known as dark-septate endophyte Type 1 Mycologia, May 1, 2005; 97(3): 628 - 640. [Abstract] [Full Text] [PDF]
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 N. Kadotani, H. Nakayashiki, Y. Tosa, and S. Mayama One of the Two Dicer-like Proteins in the Filamentous Fungi Magnaporthe oryzae Genome Is Responsible for Hairpin RNA-triggered RNA Silencing and Related Small Interfering RNA Accumulation J. Biol. Chem., October 22, 2004; 279(43): 44467 - 44474. [Abstract] [Full Text] [PDF]
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