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Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0230-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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González D. Identification, molecular characterization, and evolution of group I introns at the expansion segment D11 of 28S rDNA in Rhizoctonia species. Fungal Biol 2013; 117:623-37. [PMID: 24012302 DOI: 10.1016/j.funbio.2013.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 06/03/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
The nuclear ribosomal DNA of Rhizoctonia species is polymorphic in terms of the nucleotide composition and length. Insertions of 349-410 nucleotides in length with characteristics of group I introns were detected at a single insertion point at the expansion segment D11 of 28S rDNA in 12 out of 64 isolates. Eleven corresponded to Rhizoctonia solani (teleomorph: Thanatephorous) and one (AG-Q) to Rhizoctonia spp. (teleomorph: Ceratobasidium). Sequence data showed that all but AG-Q contained conserved DNA catalytic core regions (P, Q, R, and S) essential for selfsplicing. The predicted secondary structure revealed that base-paired helices corresponded to subgroup IC1. Isolates from same anastomosis group and even subgroups within R. solani were variable with regard to possession of introns. Phylogenetic analyses indicated that introns were vertically transmitted. Unfortunately, sequence data from the conserved region from all 64 isolates were not useful for delimiting species. Analyses with IC1 introns at same insertion point, of both Ascomycota and Basidiomycota indicated the possibility of horizontal transfer at this site. The present study uncovered new questions on evolutionary pattern of change of these introns within Rhizoctonia species.
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Affiliation(s)
- Dolores González
- Instituto de Ecología, A.C., Red de Biodiversidad y Sistemática, Carretera Antigua a Coatepec No. 351, El Haya, Xalapa 91070, Veracruz, Mexico.
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Yokoyama E, Arakawa M, Yamagishi K, Hara A. Phylogenetic and structural analyses of the mating-type loci inClavicipitaceae. FEMS Microbiol Lett 2006; 264:182-91. [PMID: 17064371 DOI: 10.1111/j.1574-6968.2006.00447.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Entomopathogens and other econutritional fungi belonging to Clavicipitaceae were phylogenetically analyzed on the basis of the 18S rRNA gene and mating-type genes (MAT1-1-1 and MAT1-2-1). The phylogenies of the mating-type genes yielded better resolutions than that of 18S rRNA gene. Entomopathogens (Cordyceps bassiana, Cordyceps brongniartii, Cordyceps militaris, Cordyceps sinclairii, Cordyceps takaomontana, Isaria cateniannulata, Isaria farinosa, Isaria fumosorosea, Isaria javanica, Lecanicillium muscarium and Torrubiella flava) were considered as a phylogenetically defined group, and were closely related to mycopathogens (Lecanicillium psalliotae and Verticillium fungicola). They located at more descendant positions in the mating-type trees than other fungi, and lacked the mating-type gene MAT1-1-3. The deletion of MAT1-1-3 was supposed to have occurred once in Clavicipitaceae, and a good indication for the evolution of Clavicipitaceae. Other entomopathogens (Cordyceps cylindrica, Cordyceps subsessilis, Metarhizium anisopliae and Nomuraea rileyi) and pathogens of plants, nematodes and slime molds, were relatively related to each other, and possessed MAT1-1-3, but were supposed to be heterogeneous. Root-associated fungi did not form any clade with other species.
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Affiliation(s)
- Eiji Yokoyama
- The Agricultural High-Tech Research Center, Meijo University, Nagoya, Japan.
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Watanabe N, Hattori M, Yokoyama E, Isomura S, Ujita M, Hara A. Entomogenous fungi that produce 2,6-pyridine dicarboxylic acid (dipicolinic acid). J Biosci Bioeng 2006; 102:365-8. [PMID: 17116586 DOI: 10.1263/jbb.102.365] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 08/07/2006] [Indexed: 11/17/2022]
Abstract
An inhibitor of the prophenoloxidase activation using extract from a silkworm pupa was isolated from a culture filtrate of Cordyceps militaris and identified as dipicolinic acid (DPA). The production of DPA in Clavicipitaceae fungi was examined. Entomogenous fungi that produce DPA were integrated into one group by a phylogenetic analysis based on 18S rDNA. It is suggested that the group acquired an ability to produce DPA during its evolution from plant pathogenic fungi to entomogenous fungi.
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Affiliation(s)
- Nobuko Watanabe
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya 468-8502, Japan
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Márquez M, Iturriaga EA, Quesada-Moraga E, Santiago-Álvarez C, Monte E, Hermosa R. Detection of potentially valuable polymorphisms in four group I intron insertion sites at the 3'-end of the LSU rDNA genes in biocontrol isolates of Metarhizium anisopliae. BMC Microbiol 2006; 6:77. [PMID: 16978412 PMCID: PMC1578565 DOI: 10.1186/1471-2180-6-77] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 09/15/2006] [Indexed: 11/10/2022] Open
Abstract
Background The entomopathogenic anamorphic fungus Metarhizum anisopliae is currently used as a biocontrol agent (BCA) of insects. In the present work, we analyzed the sequence data obtained from group I introns in the large subunit (LSU) of rDNA genes with a view to determining the genetic diversity present in an autochthonous collection of twenty-six M. anisopliae isolates selected as BCAs. Results DNA fragments corresponding to the 3'-end of the nuclear LSU rDNA genes of 26 M. anisopliae isolates were amplified by PCR. The amplicon sizes ranged from 0.8 to 3.4-kb. Four intron insertion sites, according to Escherichia coli J01695 numbering, were detected- Ec1921, Ec2066, Ec2449 and Ec2563- after sequencing and analysis of the PCR products. The presence/absence of introns allowed the 26 isolates to be distributed into seven genotypes. Nine of the isolates tested showed no introns, 4 had only one, 3 two, and 10 displayed three introns. The most frequent insertion sites were Ec1921 and Ec2449. Of the 26 isolates, 11 showed insertions at Ec2563 and a 1754-bp sequence was observed in ten of them. The most-parsimonious (MP) tree obtained from parsimony analysis of the introns revealed a main set containing four-groups that corresponded to the four insertion sites. Conclusion Four insertion sites of group I introns in the LSU rDNA genes allowed the establishment of seven genotypes among the twenty-six biocontrol isolates of M. anisopliae. Intron insertions at the Ec2563 site were observed for first time in this species.
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Affiliation(s)
- Marcela Márquez
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
- Area de Genética. Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 324, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Enrique A Iturriaga
- Area de Genética. Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 324, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Enrique Quesada-Moraga
- Departamento de Ciencias y Recursos Agrícolas y Forestales, Universidad de Córdoba, Edificio C4 Celestino Mutis, Campus Rabanales, 14071 Córdoba, Spain
| | - Cándido Santiago-Álvarez
- Departamento de Ciencias y Recursos Agrícolas y Forestales, Universidad de Córdoba, Edificio C4 Celestino Mutis, Campus Rabanales, 14071 Córdoba, Spain
| | - Enrique Monte
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Rosa Hermosa
- Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental lab 208, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
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Yokoyama E, Yamagishi K, Hara A. Heterothallism in Cordyceps takaomontana. FEMS Microbiol Lett 2005; 250:145-50. [PMID: 16055279 DOI: 10.1016/j.femsle.2005.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Revised: 06/28/2005] [Accepted: 07/05/2005] [Indexed: 11/25/2022] Open
Abstract
Perithecium formation of an entomopathogenic fungus Cordyceps takaomontana was promoted by treating the mycelia with cell wall-degrading enzymes and PEG 4000. Perithecia were formed in the mixed culture of both mating-type strains MAT1 and MAT2, and not in the culture of MAT1 or MAT2 alone. The MAT1 strains did not possess a mating-type gene MAT1-1-3, but could produce perithecia. These results strongly suggested that C. takaomontana is heterothallic, and does not need MAT1-1-3 for the perithecium formation. MAT1-1-3 was also not found in another entomopathogenic fungus Cordyceps militaris. On the other hand, phytopathogenic fungi Balansia sp., Claviceps purpurea and Epichloë typhina possessed MAT1-1-3. The structures of mating-type locus MAT1-1 of these phytopathogenic fungi in the family Clavicipitaceae were similar to that of a phytopathogenic fungus Gibberella fujikuroi in the family Nectriaceae, which is closely related to Clavicipitaceae. These results suggested that phytopathogen might be more ancestral group than entomopathogen in Clavicipitaceae, and that MAT1-1-3 might be lost in the course of the host shift from plants to insects.
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Affiliation(s)
- Eiji Yokoyama
- The Agricultural High-Tech Research Center, Meijo University, Tempaku-ku, Nagoya 468-8502, Japan.
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Machouart M, Lacroix C, Bui H, Feuilhade de Chauvin M, Derouin F, Lorenzo F. Polymorphisms and intronic structures in the 18S subunit ribosomal RNA gene of the fungiScytalidium dimidiatumandScytalidium hyalinum. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09789.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Yokoyama E, Yamagishi K, Hara A. Development of a PCR-based mating-type assay for Clavicipitaceae. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09697.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Gibb EA, Hausner G. A group I intron-like sequence in the nuclear small ribosomal subunit gene of the ophiostomatoid fungus Gondwanamyces proteae. ACTA ACUST UNITED AC 2003; 107:1442-50. [PMID: 15000245 DOI: 10.1017/s0953756203008773] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
During a phylogenetic study of ophiostomatoid fungi, a group I intron-like sequence was noted in the SSU rDNA gene of Gondwanamyces proteae. Secondary structure and sequence characteristics assigned the intron to the I E class. We then examined 27 related Group I-like sequences deposited in GenBank, and as a result 15 additional and previously uncategorized I E rDNA introns were identified. This study, with other recent publications, suggests that the I E class might represent a major family of group I introns that are located within the nuclear SSU and, to some extent LSU, genes in fungi.
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Affiliation(s)
- Ewan A Gibb
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Haugen P, Reeb V, Lutzoni F, Bhattacharya D. The evolution of homing endonuclease genes and group I introns in nuclear rDNA. Mol Biol Evol 2003; 21:129-40. [PMID: 14595099 DOI: 10.1093/molbev/msh005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.
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Affiliation(s)
- Peik Haugen
- Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, USA
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Yokoyama E, Yamagishi K, Hara A. Structures of the mating-type loci of Cordyceps takaomontana. Appl Environ Microbiol 2003; 69:5019-22. [PMID: 12902305 PMCID: PMC169095 DOI: 10.1128/aem.69.8.5019-5022.2003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2003] [Accepted: 05/16/2003] [Indexed: 11/20/2022] Open
Abstract
Nucleotide sequences of the mating-type loci MAT1-1 and MAT1-2 of Cordyceps takaomontana were determined, which is the first such report for the clavicipitaceous fungi. MAT1-1 contains two mating-type genes, MAT1-1-1 and MAT1-1-2, but MAT1-1-3 could not be found. On the other hand, MAT1-2 has MAT1-2-1. A pseudogene of MAT1-1-1 is located next to MAT1-2.
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Affiliation(s)
- Eiji Yokoyama
- The Agricultural High-Tech Research Center, Meijo University, Tempaku-ku, Nagoya 468-8502, Japan
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