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Mycologia, 94(4), 2002, pp. 683-693.
© 2002 by The Mycological Society of America

A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea


Brett C. Couch 1
Linda M. Kohn

     Department of Botany, University of Toronto, Mississauga Ontario, Canada L5L 1C6

    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 

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


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Magnaporthe grisea (Hebert) Barr is the causal agent of rice blast and gray leaf spot of grasses. Blast is the most important fungal disease of rice worldwide due to its widespread occurrence and destructiveness under conducive conditions. M. grisea has been reported to occur on more than 50 grass species (Ou 1987Citation). Borromeo and coworkers (1993)Citation 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 Shull and Hamer (1994)Citation reviewed unpublished data for mtDNA RFLPs which indicated that pathogens of Digitaria and Pennisetum are distinct from other host specific forms of Pyricularia grisea.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 1994Citation). 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 1987Citation). 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 1991Citation, 1993Citation, Correa Victoria et al 1994Citation). DNA fingerprinting and RFLP studies have identified genetically distinct, host-specific populations of M. grisea (Borromeo et al 1993Citation, Hamer et al 1989Citation, Kato et al 2000Citation). RFLP and DNA sequencing studies have resolved highly divergent lineages within M. grisea from Digitaria sp. and O. sativa (Borromeo et al 1993Citation, Bunting et al 1996Citation, Kato et al 2000Citation). Borromeo et al (1993)Citation and Kato et al (2000)Citation suggested that the divergent lineages from Digitaria and rice represent distinct species. No new species have been described.

Hebert (1971)Citation 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 1982Citation), Eleusine indica (L.) Gaertn. x E. indica (Yaegashi and Udagawa 1978Citation), E. coracana (L.) Gaertn x E. coracana (Yaegashi and Udagawa 1978Citation), O. sativa x E. indica (Yaegashi and Udagawa 1978Citation), and O. sativa x E. coracana (Ueyama and Tsuda 1976Citation)]. 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)Citation 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 1977Citation).

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 1987Citation). 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 1950Citation). The morphological similarity of Pyricularia isolates from different grass hosts has led to the view that P. oryzae and P. grisea are synonymous (Sprague 1950Citation, Ou 1987Citation, Rossman et al 1990Citation). Rossman et al (1990)Citation 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 1978Citation). However, no successful crosses of isolates from Digitaria and from Oryza have been reported (Hebert 1971Citation, Kato et al 2000Citation). Based on overlap in conidial morphology and interfertility among isolates from rice and other grasses, Rossman et al (1990)Citation 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.


    MATERIALS AND METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Fungal isolates – All isolates (Table I) were maintained on potato dextrose agar (PDA) (Difco, Sparks, Maryland). Storage of isolates was on filter paper inoculated and colonized by the fungus, then desiccated and maintained at -20 C. Matings of M. grisea isolates were performed on oatmeal agar [20 g of oats in 1 L of distilled water was heated to 70 C for 1 h, then filtered through cheesecloth, then adjusted to 1 L, to which 18 g of agar (Difco, Sparks, Maryland) was added before autoclaving]. Isolates were inoculated approximately 2.5 cm apart and incubated under fluorescent lights at a distance of 52.5 cm. Matings were first performed between the isolates 8465 and 8470 in order to test their fertility, then between each of these fertile isolates and JP34, Py-D, JP37, BK-6, K76–79, RW12, G48, and G8. Isolates of M. poae Landschoot & Jackson, and M. rhizophila Scott & Deacon were grown on PDA and incubated under fluorescent lights to induce production of anamorphs or teleomorphs for microscopic observation (Scott and Deacon 1983Citation).


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TABLE I. Magnaporthe isolates used in this study

 
DNA extraction – Isolates were grown in 100 mL of liquid Fries medium (30 g sucrose, 5 g ammonium tartrate, 1.0 g NH4NO3, 0.5 g MgSO4 · 7H2O, 1.0 g KH2PO4, 0.1 g NaCl, 0.13 g CaCl2 · 2H2O, 0.02 g FeSO4 · 7H2O, 1.0 g yeast extract, per liter of H2O) on a rotary shaker at 100 rpm for 4–5 d. Mycelium was harvested by filtration through Miracloth (Calbiochem, La Jollia, California), dried in a Savant Speed Vac (Savant Instruments, Inc., Farmingdale, New York) and stored at -20 C. DNA was extracted from approximately 15 mg of dried mycelium following the procedure of Zolan and Pukkila (1986)Citation.

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 1999Citation, Glass and Donaldson 1995Citation). 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 1994Citation) 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 1998Citation). 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)Citation. To assess the support for each branch, bootstrapping (Felsenstein 1985Citation) 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 1996Citation)], performed with 100 replicates, and Templeton's summed ranks test (Templeton 1983Citation), both implemented in PAUP 4.0b3 (Swofford 1998Citation).

Maximum likelihood analysis – Heuristic searches were also performed using the optimality criterion of maximum likelihood (Felsenstein 1981Citation). 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.


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Cultural studies and crosses – Characteristic anamorphs were observed in isolates of M. grisea and M. salvini (Sclerotium oryzae Cattaneo), but not M. rhizophila or M. poae. Teleomorphs were not observed in the two isolates of M. rhizophila but did develop in the following crosses: 8465 x 8470 (Table I), 8465 x RW12 (Eleusine coracana), 8470 x NI909 (Eragrostis curvula (Schrad.) Nees), and 8470 x G48 (Setaria sp.). In these successful crosses, perithecia containing asci with ascospores were observed; ascospores were germinable. Attempts to germinate ascospores from the type specimen of Ceratosphaeria grisea (BPI 625033) were unsuccessful.

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)Citation] 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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 FIG. 1. Phylogenies of M. grisea isolates inferred from three genes: actin, beta-tubulin and calmodulin. Labels on the phylogeny are, from left to right: isolate number, origin of each strain as either the host from which it was isolated or the Fungal Genetics Stock Center (FGSC), and the species determination from the present study as M. oryzae or M. grisea. Where host species epithets are not provided, either multiple species within the genus were sampled or the host species was unreported. Bootstrap values, based on 500 replicates, are indicated above the branches appearing in the consensus tree. A. The single most parsimonious tree produced based on the actin gene. The tree length is 20 and the consistency index (CI) = 1.0. B. The single most parsimonious tree based on the beta-tubulin gene. The tree length is 34 and the CI = 1.0. C. The single most parsimonious tree based on the calmodulin gene. The tree length is 75 and the CI = 1

 


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 FIG. 2. One of five most parsimonious trees inferred for Magnaporthe grisea isolates from the combined data for the actin, beta-tubulin and calmodulin genes. Labels on the phylogeny are, from left to right: isolate number, origin of each strain as either the host from which it was isolated or the Fungal Genetics Stock Center (FGSC), and the species determination from the present study as M. oryzae or M. grisea. Where host species epithets are not provided, either multiple species within the genus were sampled or the host species was unreported. Bootstrap values, based on 500 replicates, are indicated above the branches appearing in the consensus tree. The tree length is 130, one step longer than the minimum length tree and the consistency index is 0.992. The host from which the isolates were derived from is indicated in brackets

 

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TABLE II. Polymorphic sites in the actin gene which differentiate M. grisea isolates from Digitaria spp. and Oryza sativa. Numbers at the top of columns indicate base positions in the alignment

 

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TABLE III. Polymorphic sites in the beta-tubulin gene which differentiate M. grisea isolates from Digitaria spp. and Oryza sativa. Numbers at the top of columns indicate base positions in alignment

 

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TABLE IV. Polymorphic sites in the calmodulin gene which differentiate M. grisea isolates from Digitaria spp. and Oryza sativa. Numbers at the top of columns indicate base positions in alignment

 
Phylogenetic analysis of Magnaporthe species – Two clades within M. grisea are resolved in phylogenies inferred for Magnaporthe species based on the beta-tubulin and calmodulin genes (Fig. 3). A single most parsimonious tree was inferred from the beta-tubulin gene (Fig. 3A). A single most parsimonious, minimum length tree was inferred from the data for the calmodulin gene (Fig. 3B). Both trees have the same topology as the trees generated using maximum likelihood. The evolution of both the beta-tubulin and calmodulin genes in M. grisea was consistent with a molecular clock (P > 0.25, P > 0.999 respectively). The exon sequences from the actin gene which were alignable across all Magnaporthe species do not contain characters which resolve the relationships among isolates of M. grisea from different hosts. Consequently, the actin region was not used for phylogenetic analysis among all Magnaporthe species.



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 FIG. 3. Phylogenies of Magnaporthe species inferred from beta-tubulin and calmodulin genes. Labels on the phylogeny are, from left to right: isolate number, origin of each strain as either the host from which it was isolated or the Fungal Genetics Stock Center (FGSC), and the species determination from the present study as M. oryzae or M. grisea. Where host species epithets are not provided, either multiple species within the genus were sampled or the host species was unreported. Bootstrap values, based on 500 replicates, are indicated above the branches appearing in the consensus tree. A. The single most parsimonious tree produced based on the beta-tubulin gene. The tree length is 66, 5 steps longer than the minimum length tree and the CI is 0.924. B. The single most parsimonious, minimum length, tree produced based on the calmodulin gene. The tree length is 21 and the CI is 1

 
A single most parsimonious tree was produced for the combined datasets of the beta-tubulin and calmodulin genes (Fig. 4). The tree has a length of 87, which is 5 steps longer than the minimum length tree (CI = 0.943) and is equal to the sum of tree lengths for each region separately. Since the phylogeny inferred from the combined dataset is not longer than the sum of the tree lengths for each individual dataset, it is appropriate to combine the datasets for both genes (Farris et al 1995Citation). 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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 FIG. 4. A single most parsimonious tree inferred for Magnaporthe species based on combined data for the beta-tubulin and calmodulin genes. Labels on the phylogeny are, from left to right: isolate number, origin of each strain as either the host from which it was isolated or the Fungal Genetics Stock Center (FGSC), and the species determination from the present study as M. oryzae or M. grisea. Where host species epithets are not provided, either multiple species within the genus were sampled or the host species was unreported. Bootstrap values, based on 500 replicates, are indicated above the branches appearing in the consensus tree. The tree length is 87 and the consistency index is 0.943

 
PCR-RFLP – A PCR-RFLP assay (Chehab et al 1987Citation) 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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 FIG. 5. PCR-RFLP of the beta-tubulin gene. The beta-tubulin gene was amplified from 23 isolates and digested with Hpa II: lanes 3–6 contain isolates from Digitaria, 81T4, Py-D, 91T16, and JP34, lanes 7 and 8 contain Lolium perenne isolates 330, 365, lanes 9 and 10 contain Setaria isolates G-48, 1152, lanes 11 and 12 contain Eleusine coracana isolates RW 12, 1122, lanes 13 and 14 contain Eragrostis curvula isolates NI909, K76–79, lanes 15–25 contain Oryza sativa isolates, R694–2b, ML-56, R707–1E, ML-91, Guy 11, BK-6, BK-19, A598, A347, A264, and A119. Lanes 1 and 27 contain the Mass Ruler size standard (MBI Fermentas, Flamborough, Ontario), the sizes of size standard fragments are indicated on the left. Lanes 2 and 26 were not loaded

 

    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Based on the inferred phylogenies (Figs. 1–4), M. grisea contains two distinct lineages, one associated with Digitaria, and the other associated with O. sativa and other grasses. Four lines of evidence indicate that these lineages represent two distinct species: (i) they constitute two well supported, monophyletic clades; (ii) they have only one shared polymorphism against a preponderance of fixed differences; (iii) they are associated with different groups of hosts; (iv) they are reproductively isolated and have been so for a long time. This is supported by infertility in laboratory crosses (the present study, as well as Hebert 1971Citation, Kato et al 2000Citation). 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)Citation. 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)Citation 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 1971Citation, Kato et al 2000Citation). In contrast, there have been fertile crosses between isolates from Digitaria (Hebert 1971Citation, Kato et al 2000Citation), and between isolates from Oryza (Oryza x Oryza) (Kato and Yamaguchi 1982Citation), from Eleusine (Eleusine x Eleusine) (Yaegashi and Udagawa 1978Citation), 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 1990Citation, Yaegashi and Udagawa 1978Citation). When Yaegashi and Udagawa (1978)Citation 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 1993Citation, Shull and Hamer 1994Citation, Bunting et al 1996Citation, Kato et al 2000Citation). 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)Citation; Fig. 5, Couch and Kohn (this paper).

= Magnaporthe grisea sensu Yaegashi and Udagawa, Can. J. Bot. 56:180–183 (1978)

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 1997Citation) 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).


    ACKNOWLEDGMENTS
 
We thank B. Valent, B. Wang, J. Kumar, T. Marchetti, M. Milgroom, N. Tisserat, and the National Institute of Agrobiological Resources (Tskuba, Japan) for providing isolates. We are grateful to J. Krug for preparing the Latin diagnosis and providing valuable advice on the manuscript. This work was supported by grants from the USDA CSREES (to M. Milgroom), the Natural Sciences and Engineering Research Council of Canada (to L. M. Kohn) and Ontario Graduate Scholarships to B. Couch.


    FOOTNOTES
 
1 Corresponding author, Email: bcouch{at}credit.erin.utoronto.ca Back

Accepted for publication November 29, 2001.


    LITERATURE CITED
 TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 LITERATURE CITED
 
Barr ME., 1977 Magnaporthe, Telimenella, and Hyponectria (Physosporellaceae). Mycologia 69:952-966

Borromeo ES, Nelson RJ, Bonman JM, Leung H., 1993 Genetic differentiation among isolates of Pyricularia infecting rice weed hosts. Phytopathology 83:393-399

Bunting TE, Plumley KA, Clarke BB, Hillman BI., 1996 Identification of Magnaporthe poae by PCR and examination of its relationship to other fungi by analysis of their nuclear rDNA ITS-1 regions. Phytopathology 86:398-404

Carbone I, Kohn L., 1999 A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91:553-556

———, ———. 2001 A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Mol Ecol 10:947-964[Medline]

Chehab FF, Doherty M, Cai S, Kan YW, Cooper S, Rubin EM., 1987 Detection of sickle cell anaemia and thalassaemias. Nature 329:293-294[Medline]

Correa Victoria F, Zeigler R, Levy M., 1994 Virulence characteristics of genetic families of Pyricularia grisea in Colombia. In: Zeigler R, Leong S, Teng P, eds. Rice blast disease. Wallingford: CAB International. p 211–229

Cracraft J., 1983 Species concepts and speciation analysis. Current Ornithology 1:159-187

Farris JS, Kallersjö M, Kluge AG, Bult C., 1995 Testing significance of incongruencies. Cladistics 10:315-319

Felsenstein J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376[Medline]

———. 1985 Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791

Glass NL, Donaldson GC., 1995 Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Appl Environ Microbiol 61:1323-1330[Abstract/Free Full Text]

Hamer JE, Farrall L, Orbach MJ, Valent B, Chumley FG., 1989 Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal plant pathogen. Proc Natl Acad Sci USA 86:9981-9985[Abstract/Free Full Text]

Hebert TT., 1971 The perfect stage of Pyricularia grisea. Phytopathology 61:83-87

Huelsenbeck JP, Bull JJ, Cunningham CW., 1996 Combining data in phylogenetic analysis. Trends Ecol Evol 11:152-158

Kato H, Tamamoto M, Yamaguchi-Ozaki T, Kadouchi H, Iwamoto Y, Nakayashiki H, Tosa Y, Mayama S, Mori N., 2000 Pathogenicity, mating ability and DNA restriction fragment length polymorphisms of Pyricularia populations isolated from Gramineae, Bambusideae and Zingiberaceae plants. J Gen Plant Pathol 66:30-47

———, Yamaguchi T., 1982 The perfect state of Pyricularia oryzae Cav. from rice plants in culture. Ann Phytopathol Soc Jpn 48:607-612

Levy M, Correa Victoria FJ, Zeigler RS, Xu S, Hamer JE., 1993 Genetic diversity of the rice blast fungus in a disease nursery in Colombia. Phytopathology 83:1427-1433

———, Romao J, Marchetti MA, Hamer JE., 1991 DNA fingerprinting with a dispersed repeated sequence resolves pathotype diversity in the rice blast fungus. Plant Cell 3:95-102[Abstract/Free Full Text]

Nitta N, Farman ML, Leong SA., 1997 Genome organization of Magnaporthe grisea: integration of genetic maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theor Appl Genet 95:20-32

Ou SH., 1987 Rice diseases. Surrey: The Commonwealth Mycological Institute. p 109–201

Rossman AY, Howard RJ, Valent B., 1990 Pyricularia grisea, the correct name for the rice blast disease fungus. Mycologia 82:509-512

Shull V, Hamer JE., 1994 Genomic structure and variability in Pyricularia grisea. In: Zeigler R, Leong S, Teng P, eds. Rice blast disease. Wallingford: CAB International. p 65–86

Scott DB, Deacon JW., 1983 Magnaporthe rhizophila sp. nov., a dark mycelial fungus with a Phialophora conidial state, from cereal roots in South Africa. Trans Br Mycol Soc 81:77-81

Sprague R., 1950 Diseases of cereals and grasses in North America. Ronald Press: New York. 538 p

Swofford DL., 1998 PAUP*. Phylogenetic analysis using parsimony (*and Other Methods) Beta Version 4.0b3. Sunderland, Massachusetts: Sinauer Associates

Tajima F., 1993 Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607[Abstract]

Templeton AR., 1983 Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244

Thompson JD, Higgins DG, Gibson TJ., 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680[Abstract/Free Full Text]

Ueyama A, Tsuda M., 1976 Formation of the perfect state in culture of Pyricularia sp. from some graminaceous plants (preliminary report). Trans Mycol Soc Jpn 16:420-422

Yaegashi H, Udagawa S., 1978 The taxonomical identity of the perfect sate of Pyricularia grisea and its allies. Can J Bot 56:180-183

Zolan ME, Pukkila PJ., 1986 Inheritance of DNA methylation in Coprinus cinereus. Mol Cell Biol 6:195-200[Abstract/Free Full Text]




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