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Singh V, Lakshman DK, Roberts DP, Ismaiel A, Abhishek A, Kumar S, Hooda KS. Fungal Species Causing Maize Leaf Blight in Different Agro-Ecologies in India. Pathogens 2021; 10:1621. [PMID: 34959576 PMCID: PMC8705428 DOI: 10.3390/pathogens10121621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Foliar diseases of maize cause severe economic losses in India and around the world. The increasing severity of maize leaf blight (MLB) over the past ten years necessitates rigorous identification and characterization of MLB-causing pathogens from different maize production zones to ensure the success of resistance breeding programs and the selection of appropriate disease management strategies. Although Bipolaris maydis is the primary pathogen causing MLB in India, other related genera such as Curvularia, Drechslera, and Exserohilum, and a taxonomically distant genus, Alternaria, are known to infect maize in other countries. To investigate the diversity of pathogens associated with MLB in India, 350 symptomatic leaf samples were collected between 2016 and 2018, from 20 MLB hotspots in nine states representing six ecological zones where maize is grown in India. Twenty representative fungal isolates causing MLB symptoms were characterized based on cultural, pathogenic, and molecular variability. Internal Transcribed Spacer (ITS) and glyceraldehyde-3-phosphate dehydrogenase (GADPH) gene sequence-based phylogenies showed that the majority of isolates (13/20) were Bipolaris maydis. There were also two Curvularia papendorfii isolates, and one isolate each of Bipolaris zeicola, Curvularia siddiquii, Curvularia sporobolicola, an unknown Curvularia sp. isolate phylogenetically close to C. graminicola, and an Alternaria sp. isolate. The B. zeicola, the aforesaid four Curvularia species, and the Alternaria sp. are the first reports of these fungi causing MLB in India. Pathogenicity tests on maize plants showed that isolates identified as Curvularia spp. and Alternaria sp. generally caused more severe MLB symptoms than those identified as Bipolaris spp. The diversity of fungi causing MLB, types of lesions, and variation in disease severity by different isolates described in this study provide baseline information for further investigations on MLB disease distribution, diagnosis, and management in India.
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Affiliation(s)
- Vimla Singh
- Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University Regional Research Station, Karnal 132001, India
| | - Dilip K. Lakshman
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (D.P.R.); (A.I.)
| | - Daniel P. Roberts
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (D.P.R.); (A.I.)
| | - Adnan Ismaiel
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705, USA; (D.P.R.); (A.I.)
| | - Alok Abhishek
- ICAR-Indian Institute of Maize Research (Delhi Unit), Pusa Campus, New Delhi 110012, India;
| | - Shrvan Kumar
- Department of Mycology and Plant Pathology, Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur 231001, India;
| | - Karambir S. Hooda
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi 110012, India;
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Bhunjun CS, Dong Y, Jayawardena RS, Jeewon R, Phukhamsakda C, Bundhun D, Hyde KD, Sheng J. A polyphasic approach to delineate species in Bipolaris. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00446-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Novel Cell-Killing Mechanisms of Hydroxyurea and the Implication toward Combination Therapy for the Treatment of Fungal Infections. Antimicrob Agents Chemother 2017; 61:AAC.00734-17. [PMID: 28893786 DOI: 10.1128/aac.00734-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/28/2017] [Indexed: 01/17/2023] Open
Abstract
We have previously reported that an erg11 mutation affecting ergosterol synthesis and a hem13 mutation in the heme synthesis pathway significantly sensitize the fission yeast Schizosaccharomyces pombe to hydroxyurea (HU) (1, 2). Here we show that treatment with inhibitors of Erg11 and heme biosynthesis phenocopies the two mutations in sensitizing wild-type cells to HU. Importantly, HU synergistically interacts with the heme biosynthesis inhibitor sampangine and several Erg11 inhibitors, the antifungal azoles, in causing cell lethality. Since the synergistic drug interactions are also observed in the phylogenetically divergent Saccharomyces cerevisiae and the opportunistic fungal pathogen Candida albicans, the synergism is likely conserved in eukaryotes. Interestingly, our genetic data for S. pombe has also led to the discovery of a robust synergism between sampangine and the azoles in C. albicans Thus, combinations of HU, sampangine, and the azoles can be further studied as a new method for the treatment of fungal infections.
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Huhndorf SM, Miller AN, Fernández FA. Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832982] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sabine M. Huhndorf
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
| | - Andrew N. Miller
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496 University of Illinois at Chicago, Department of Biological Sciences, Chicago, Illinois 60607-7060
| | - Fernando A. Fernández
- Botany Department, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
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Taylor T, Hass H, Kerp H, Krings M, Hanlin R. Perithecial ascomycetes from the 400 million year old Rhynie chert: an example of ancestral polymorphism. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832862] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- T.N. Taylor
- Department of Ecology and Evolutionary Biology, and Natural History Museum and Biodiversity Research Center, University of Kansas, Lawrence, Kansas 66045
| | | | - H. Kerp
- Forschungsstelle für Paläobotanik, Westfalische Wilhelms-Universität Münster, Germany
| | - M. Krings
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 München, Germany
| | - R.T. Hanlin
- Department of Plant Pathology, University of Georgia, Athens, Georgia 30602
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Abstract
The genus Bipolaris includes important plant pathogens with worldwide distribution. Species recognition in the genus has been uncertain due to the lack of molecular data from ex-type cultures as well as overlapping morphological characteristics. In this study, we revise the genus Bipolaris based on DNA sequence data derived from living cultures of fresh isolates, available ex-type cultures from worldwide collections and observation of type and additional specimens. Combined analyses of ITS, GPDH and TEF gene sequences were used to reconstruct the molecular phylogeny of the genus Bipolaris for species with living cultures. The GPDH gene is determined to be the best single marker for species of Bipolaris. Generic boundaries between Bipolaris and Curvularia are revised and presented in an updated combined ITS and GPDH phylogenetic tree. We accept 47 species in the genus Bipolaris and clarify the taxonomy, host associations, geographic distributions and species' synonymies. Modern descriptions and illustrations are provided for 38 species in the genus with notes provided for the other taxa when recent descriptions are available. Bipolaris cynodontis, B. oryzae, B. victoriae, B. yamadae and B. zeicola are epi- or neotypified and a lectotype is designated for B. stenospila. Excluded and doubtful species are listed with notes on taxonomy and phylogeny. Seven new combinations are introduced in the genus Curvularia to accomodate the species of Bipolaris transferred based on the phylogenetic analysis. A taxonomic key is provided for the morphological identification of species within the genus.
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Affiliation(s)
- D.S. Manamgoda
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
- World Agro-forestry Centre, East and Central Asia, Kunming 650201, China
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville 20705, MA, USA
| | - A.Y. Rossman
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville 20705, MA, USA
| | - L.A. Castlebury
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville 20705, MA, USA
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - H. Madrid
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Center for Genomics and Bioinformatics and Medicine Faculty, Mayor University, Camino La Piramide 5750, Huechuraba, Santiago, Chile
| | - E. Chukeatirote
- Institute of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - K.D. Hyde
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China
- World Agro-forestry Centre, East and Central Asia, Kunming 650201, China
- Institute of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
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Thorsten Lumbsch H, Wirtz N, Lindemuth R, Schmitt I. Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data. Mycol Prog 2013. [DOI: 10.1007/s11557-006-0005-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Krimitzas A, Pyrri I, Kouvelis VN, Kapsanaki-Gotsi E, Typas MA. A phylogenetic analysis of Greek isolates of Aspergillus species based on morphology and nuclear and mitochondrial gene sequences. BIOMED RESEARCH INTERNATIONAL 2013; 2013:260395. [PMID: 23762830 PMCID: PMC3665174 DOI: 10.1155/2013/260395] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/09/2013] [Indexed: 12/13/2022]
Abstract
Aspergillus species originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes ( β -tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections of Aenei, Aspergillus, Bispori, Candidi, Circumdati, Clavati, Cremei, Flavi, Flavipedes, Fumigati, Nidulantes, Nigri, Restricti, Terrei, Usti, and Zonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA, rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rns and cox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genus Aspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus.
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Affiliation(s)
- Antonios Krimitzas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
| | - Ioanna Pyrri
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15784 Athens, Greece
| | - Vassili N. Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
| | - Evangelia Kapsanaki-Gotsi
- Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15784 Athens, Greece
| | - Milton A. Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistemiopolis, 15701 Athens, Greece
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Shapiro RS, Robbins N, Cowen LE. Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiol Mol Biol Rev 2011; 75:213-67. [PMID: 21646428 PMCID: PMC3122626 DOI: 10.1128/mmbr.00045-10] [Citation(s) in RCA: 384] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs. Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For C. albicans, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in C. neoformans and A. fumigatus, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across C. albicans, C. neoformans, and A. fumigatus provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease.
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Affiliation(s)
| | | | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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Townsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Syst Biol 2010; 59:446-57. [DOI: 10.1093/sysbio/syq025] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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11
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Lichen Systematics: The Role of Morphological and Molecular Data to Reconstruct Phylogenetic Relationships. PROGRESS IN BOTANY 2010. [DOI: 10.1007/978-3-642-02167-1_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Parallel evolution of hysterothecial ascomata in ascolocularous fungi (Ascomycota, Fungi). SYST BIODIVERS 2009. [DOI: 10.1017/s147720000999020x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Molecular phylogeny and Holarctic diversification of the subtribe Calathina (Coleoptera: Carabidae: Sphodrini). Mol Phylogenet Evol 2009; 55:358-71. [PMID: 19900569 DOI: 10.1016/j.ympev.2009.10.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 11/23/2022]
Abstract
A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).
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Wu Y, Yang J, Yang F, Liu T, Leng W, Chu Y, Jin Q. Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes. BMC Genomics 2009; 10:238. [PMID: 19457268 PMCID: PMC2693141 DOI: 10.1186/1471-2164-10-238] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 05/21/2009] [Indexed: 11/17/2022] Open
Abstract
Background Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, Epidermophyton, and Microsporum, and the evolutionary relationships between these genera are epidemiologically important. Mitochondria are considered to be of monophyletic origin and mitochondrial sequences offer many advantages for phylogenetic studies. However, only one complete dermatophyte mitochondrial genome (E. floccosum) has previously been determined. Results The complete mitochondrial DNA sequences of five dermatophyte species, T. rubrum (26,985 bp), T. mentagrophytes (24,297 bp), T. ajelloi (28,530 bp), M. canis (23,943 bp) and M. nanum (24,105 bp) were determined. These were compared to the E. floccosum sequence. Mitochondrial genomes of all 6 species were found to harbor the same set of genes arranged identical order indicating that these dermatophytes are closely related. Genome size differences were largely due to variable lengths of non-coding intergenic regions and the presence/absence of introns. Phylogenetic analyses based on complete mitochondrial genomes reveals that the divergence of the dermatophyte clade was later than of other groups of pathogenic fungi. Conclusion This is the first systematic comparative genomic study on dermatophytes, a highly conserved and recently-diverged lineage of ascomycota fungi. The data reported here provide a basis for further exploration of interrelationships between dermatophytes and will contribute to the study of mitochondrial evolution in higher fungi.
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Affiliation(s)
- Yuan Wu
- Department of Microbiology and Immunology, Medical School of Xi'an Jiaotong University, Shaanxi, 710061, PR China.
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Spinks PQ, Thomson RC, Lovely GA, Shaffer HB. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evol Biol 2009; 9:56. [PMID: 19284630 PMCID: PMC2660309 DOI: 10.1186/1471-2148-9-56] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 03/12/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support. RESULTS Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except Pseudemys concinna, P. peninsularis, and Terrapene carolina were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except Trachemys, and all species except Graptemys pseudogeographica, P. concinna, T. carolina, and T. coahuila were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported. Our simulations showed that relatively high bootstrap support values (i.e. >or= 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses. CONCLUSION Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.
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Affiliation(s)
- Phillip Q Spinks
- Department of Evolution and Ecology, Davis, USA
- Center for Population Biology, University of California, Davis, USA
| | - Robert C Thomson
- Department of Evolution and Ecology, Davis, USA
- Center for Population Biology, University of California, Davis, USA
| | - Geoff A Lovely
- Department of Evolution and Ecology, Davis, USA
- Present address Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA
| | - H Bradley Shaffer
- Department of Evolution and Ecology, Davis, USA
- Center for Population Biology, University of California, Davis, USA
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Zhao RL, Desjardin DE, Soytong K, Hyde KD. Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses. J Zhejiang Univ Sci B 2008; 9:779-86. [PMID: 18837104 PMCID: PMC2565740 DOI: 10.1631/jzus.b0860012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 08/23/2008] [Indexed: 11/11/2022]
Abstract
We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.
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Affiliation(s)
- Rui-lin Zhao
- Faculty of Biology Conservation, Southwest Forestry University, Kunming 650224, China
| | - Dennis E. Desjardin
- Department of Biology, San Francisco State University, San Francisco, California 94132, USA
| | - Kasem Soytong
- Faculty of Agricultural Technology, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Ladkrabang, Bangkok 10520, Thailand
| | - Kevin D. Hyde
- International Fungal Resource and Development Centre, the Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, China
- Fungal Research Group, School of Science, Mae Fah Luang University, Tasud, Chiang Rai 57100, Thailand
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High diversity and morphological convergence among melanised fungi from rock formations in the Central Mountain System of Spain. Persoonia - Molecular Phylogeny and Evolution of Fungi 2008; 21:93-110. [PMID: 20396580 PMCID: PMC2846131 DOI: 10.3767/003158508x371379] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Accepted: 09/09/2008] [Indexed: 11/25/2022]
Abstract
Melanised fungi were isolated from rock surfaces in the Central Mountain System of Spain. Two hundred sixty six isolates were recovered from four geologically and topographically distinct sites. Microsatellite-primed PCR techniques were used to group isolates into genotypes assumed to represent species. One hundred and sixty three genotypes were characterised from the four sites. Only five genotypes were common to two or more sites. Morphological and molecular data were used to characterise and identify representative strains, but morphology rarely provided a definitive identification due to the scarce differentiation of the fungal structures or the apparent novelty of the isolates. Vegetative states of fungi prevailed in culture and in many cases could not be reliably distinguished without sequence data. Morphological characters that were widespread among the isolates included scarce micronematous conidial states, endoconidia, mycelia with dark olive-green or black hyphae, and mycelia with torulose, isodiametric or moniliform hyphae whose cells develop one or more transverse and/or oblique septa. In many of the strains, mature hyphae disarticulated, suggesting asexual reproduction by a thallic micronematous conidiogenesis or by simple fragmentation. Sequencing of the internal transcribed spacers (ITS1, ITS2) and 5.8S rDNA gene were employed to investigate the phylogenetic affinities of the isolates. According to ITS sequence alignments, the majority of the isolates could be grouped among four main orders of Pezizomycotina: Pleosporales, Dothideales, Capnodiales, and Chaetothyriales. Ubiquitous known soil and epiphytic fungi species were generally absent from the rock surfaces. In part, the mycota of the rock surfaces shared similar elements with melanised fungi from plant surfaces and fungi described from rock formations in Europe and Antarctica. The possibility that some of the fungi were lichen mycobionts or lichen parasites could not be ruled out.
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Rokas A, Chatzimanolis S. From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain. Methods Mol Biol 2008; 422:1-12. [PMID: 18629657 DOI: 10.1007/978-1-59745-581-7_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
An important goal of phylogenetics is to be able to consistently and accurately reconstruct the historical patterns of cladogenesis among major organismic groups. Gene-scale phylogenetics is insufficient to attain this goal owing to the presence of poor resolution and incongruence in single--and few--gene phylogenies. The increasing availability of genome-scale amounts of data promises to overcome the insufficiency of gene-scale phylogenetics and uncover the genealogical tapestry uniting all living organisms with unprecedented accuracy. Here, we argue that a vast increase in data size alone--although necessary--may not be sufficient to achieve the desired accuracy for three reasons: (i) the existence of short stems in the tree of life, (ii) the saturation of phylogenetic signal in molecular sequences, and (iii) the effect of systematic error on phylogenetic inference. Devising strategies to ameliorate the effect of such challenges on sequence evolution will be critical to the success of current efforts to reconstruct the tree of life.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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Pantou MP, Kouvelis VN, Typas MA. The complete mitochondrial genome of Fusarium oxysporum: Insights into fungal mitochondrial evolution. Gene 2008; 419:7-15. [DOI: 10.1016/j.gene.2008.04.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 11/26/2022]
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20
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FIORENTINO VIVIANA, SALOMONE NICOLA, MANGANELLI GIUSEPPE, GIUSTI FOLCO. Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01023.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Ober KA, Maddison DR. Phylogenetic relationships of tribes within Harpalinae (Coleoptera: Carabidae) as inferred from 28S ribosomal DNA and the wingless gene. JOURNAL OF INSECT SCIENCE (ONLINE) 2008; 8:63. [PMID: 20302528 PMCID: PMC3127421 DOI: 10.1673/031.008.6301] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 12/19/2007] [Indexed: 05/29/2023]
Abstract
Harpalinae is a large, monophyletic subfamily of carabid ground beetles containing more than 19,000 species in approximately 40 tribes. The higher level phylogenetic relationships within harpalines were investigated based on nucleotide data from two nuclear genes, wingless and 28S rDNA. Phylogenetic analyses of combined data indicate that many harpaline tribes are monophyletic, however the reconstructed trees showed little support for deeper nodes. In addition, our results suggest that the Lebiomorph Assemblage (tribes Lebiini, Cyclosomini, Graphipterini, Perigonini, Odacanthini, Lachnophorini, Pentagonicini, Catapiesini and Calophaenini), which is united by a morphological synapomorphy, is not monophyletic, and the tribe Lebiini is paraphyletic with respect to members of Cyclosomini. Two unexpected clades of tribes were supported: the Zuphiitae, comprised of Anthiini, Zuphiini, Helluonini, Dryptini, Galeritini, and Physocrotaphini; and a clade comprised of Orthogoniini, Pseudomorphini, and Graphipterini. The data presented in this study represent a dense sample of taxa to examine the molecular phylogeny of Harpalinae and provide a useful framework to examine the origin and evolution of morphological and ecological diversity in this group.
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Affiliation(s)
- Karen A. Ober
- Interdisciplinary Program in Insect Science, University of Arizona, Tucson, Arizona 85721, U.S.A
- Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610, U.S.A
- Present address: Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610
| | - David R. Maddison
- Department of Entomology, University of Arizona, Tucson, Arizona 85721, U.S.A
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22
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Abstract
The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.
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Affiliation(s)
- Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
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23
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Yang Y, Yang E, An Z, Liu X. Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences. Proc Natl Acad Sci U S A 2007; 104:8379-84. [PMID: 17494736 PMCID: PMC1895958 DOI: 10.1073/pnas.0702770104] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2006] [Indexed: 11/18/2022] Open
Abstract
Among fungi, the basic life strategies are saprophytism, parasitism, and predation. Fungi in Orbiliaceae (Ascomycota) prey on animals by means of specialized trapping structures. Five types of trapping devices are recognized, but their evolutionary origins and divergence are not well understood. Based on comprehensive phylogenetic analysis of nucleotide sequences of three protein-coding genes (RNA polymerase II subunit gene, rpb2; elongation factor 1-alpha gene, ef1-alpha; and ss tubulin gene, bt) and ribosomal DNA in the internal transcribed spacer region, we have demonstrated that the initial trapping structure evolved along two lineages yielding two distinct trapping mechanisms: one developed into constricting rings and the other developed into adhesive traps. Among adhesive trapping devices, the adhesive network separated from the others early and evolved at a steady and gentle speed. The adhesive knob evolved through stalk elongation, with a final development of nonconstricting rings. Our data suggest that the derived adhesive traps are at a highly differentiated stage. The development of trapping devices is felicitous proof of adaptive evolution.
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Affiliation(s)
- Ying Yang
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China; and
| | - Ence Yang
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China; and
| | - Zhiqiang An
- Merck Research Laboratories, WP26A-4000, 770 Sumneytown Pike, West Point, PA 19486-0004
| | - Xingzhong Liu
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences 3A Datun Rd, Chaoyang District, Beijing 100101, China
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24
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Makimura K. [Pathogenic fungi, mycoses and current Japanese problems in human sources for mycological research in the medical field]. Nihon Saikingaku Zasshi 2007; 62:295-312. [PMID: 17575796 DOI: 10.3412/jsb.62.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Koichi Makimura
- Department of Molecular Biology and Gene Diagnosis, Institute of Medical Mycology and Genome Research Center, Graduate School of Medical Science and Faculty of Medicine, Teikyo University
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25
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Liu Y, Bell-Pedersen D. Circadian rhythms in Neurospora crassa and other filamentous fungi. EUKARYOTIC CELL 2007; 5:1184-93. [PMID: 16896204 PMCID: PMC1539135 DOI: 10.1128/ec.00133-06] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9040, USA.
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26
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Dutilh BE, van Noort V, van der Heijden RTJM, Boekhout T, Snel B, Huynen MA. Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 2007; 23:815-24. [PMID: 17237036 DOI: 10.1093/bioinformatics/btm015] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology. RESULTS Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content. CONCLUSIONS Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- B E Dutilh
- Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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27
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Tang AMC, Jeewon R, Hyde KD. Phylogenetic utility of protein (RPB2, β-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi). Antonie van Leeuwenhoek 2006; 91:327-49. [PMID: 17072532 DOI: 10.1007/s10482-006-9120-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 09/15/2006] [Indexed: 10/24/2022]
Abstract
The Sordariomycetes is an important group of fungi whose taxonomic relationships and classification is obscure. There is presently no multi-gene molecular phylogeny that addresses evolutionary relationships among different classes and orders. In this study, phylogenetic analyses with a broad taxon sampling of the Sordariomycetes were conducted to evaluate the utility of four gene regions (LSU rDNA, SSU rDNA, beta-tubulin and RPB2) for inferring evolutionary relationships at different taxonomic ranks. Single and multi-gene genealogies inferred from Bayesian and Maximum Parsimony analyses were compared in individual and combined datasets. At the subclass level, SSU rDNA phylogenies demonstrate their utility as a marker to infer phylogenetic relationships at higher levels. All analyses with SSU rDNA alone, combined LSU rDNA and SSU rDNA, and the combined 28 S rDNA, SSU rDNA and RPB2 datasets resulted in three subclasses: Hypocreomycetidae, Sordariomycetidae and Xylariomycetidae, which correspond well to established morphological classification schemes. At the ordinal level, the best resolved phylogeny was obtained from the combined LSU rDNA and SSU rDNA datasets. Individually, the RPB2 gene dataset resulted in significantly higher number of parsimony informative characters. Our results supported the recent separation of Boliniaceae, Chaetosphaeriaceae and Coniochaetaceae from Sordariales and placement of Coronophorales in Hypocreomycetidae. Microascales was found to be paraphyletic and Ceratocystis is phylogenetically associated to Faurelina, while Microascus and Petriella formed another clade and basal to other members of Halosphaeriales. In addition, the order Lulworthiales does not appear to fit in any of the three subclasses. Congruence between morphological and molecular classification schemes is discussed.
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Affiliation(s)
- Alvin M C Tang
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Hong Kong, SAR, Republic of China.
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28
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Pantou MP, Kouvelis VN, Typas MA. The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification. Curr Genet 2006; 50:125-36. [PMID: 16733756 DOI: 10.1007/s00294-006-0079-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The complete sequence (27,184 bp) of the mitochondrial (mt) genome of the phytopathogenic fungus Verticillium dahliae has been determined. It contains 14 protein-coding genes related to oxidative phosphorylation, two rRNA genes and a set of 25 tRNA genes. A single intron, that harbors an intronic ORF coding for a putative ribosomal protein (rps), is located within the large rRNA gene (rnl). Gene order comparisons of V. dahliae mtDNA and complete mt genomes of Pezizomycotina revealed four units of synteny for Sordariomycetes, namely rnl-trn ((11-12))-nad2-nad3, nad4L-nad5-cob-cox1, nad1-nad4-atp8-atp6 and rns-trn ((1-5))-cox3-trn ((1-5))-nad6-trn ((2-5)). These four units, in different combinations, merged to single continuous unit in the orders of Hypocreales and Sordariales. V. dahliae (Phyllachorales) and all members of the genus showed a unique feature which is the translocation of the nad1-nad4-atp8-atp6-rns-cox3-nad6 region in between genes nad3 and atp9 of the Hypocreales mtDNA gene order. Analysis of mt intergenic sequences of Verticillium species permitted the design of a species-specific primer allowing the discrimination of V. longisporum against V. dahliae and V. albo-atrum. By considering the protein-coding gene sequences as one unit, a phylogenetic comparison with representatives of Ascomycota complete mtDNA was performed.
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Affiliation(s)
- Malena P Pantou
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Greece
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29
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Wortley AH, Rudall PJ, Harris DJ, Scotland RW. How much data are needed to resolve a difficult phylogeny?: case study in Lamiales. Syst Biol 2006; 54:697-709. [PMID: 16195214 DOI: 10.1080/10635150500221028] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Reconstructing phylogeny is a crucial target of contemporary biology, now commonly approached through computerized analysis of genetic sequence data. In angiosperms, despite recent progress at the ordinal level, many relationships between families remain unclear. Here we take a case study from Lamiales, an angiosperm order in which interfamilial relationships have so far proved particularly problematic. We examine the effect of changing one factor-the quantity of sequence data analyzed-on phylogeny reconstruction in this group. We use simulation to estimate a priori the sequence data that would be needed to resolve an accurate, supported phylogeny of Lamiales. We investigate the effect of increasing the length of sequence data analyzed, the rate of substitution in the sequences used, and of combining gene partitions. This method could be a valuable technique for planning systematic investigations in other problematic groups. Our results suggest that increasing sequence length is a better way to improve support, resolution, and accuracy than employing sequences with a faster substitution rate. Indeed, the latter may in some cases have detrimental effects on phylogeny reconstruction. Further molecular sequencing-of at least 10,000 bp-should result in a fully resolved and supported phylogeny of Lamiales, but at present the problematic aspects of this tree model remain.
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Affiliation(s)
- Alexandra H Wortley
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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30
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Kruys A, Eriksson OE, Wedin M. Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position. ACTA ACUST UNITED AC 2006; 110:527-36. [PMID: 16769507 DOI: 10.1016/j.mycres.2006.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/06/2006] [Accepted: 03/01/2006] [Indexed: 11/22/2022]
Abstract
The purpose of this study was to investigate the natural relationships within the large bitunicate order Pleosporales, with special focus on the coprophilous families Delitschiaceae, Phaeotrichaceae and Sporormiaceae. Parsimony and Bayesian analyses were performed using nSSU, nLSU and mtSSU rDNA sequence data. We also investigated the placement of a number of taxa with uncertain position. Our results showed that Pleosporales, including Delitschiaceae, Sporormiaceae, Zopfiaceae and Testudinaceae, form a monophyletic group with strong support. Although Delitschiaceae has been considered a synonym of Sporormiaceae, the two families do not form one monophyletic group. Similarly, Zopfiaceae and Testudinaceae should be retained as separate families as they did not group together or with Phaeotrichaceae or Sporormiaceae. Zopfiaceae and Delitchiaceae did group together, but without significant support. Eremodothis angulata (currently in Testudinaceae) is closely related to Westerdykella in Sporormiaceae. Phaeotrichaceae and Venturiaceae formed a group with strong BS support on a branch outside Pleosporales, but an alternative topology including Phaeotrichaceae and Venturiaceae within Pleosporales could not be rejected. All taxa in the present study that were placed with uncertain position in Dothideomycetes/Chaetothyriomycetes in the current classification by Eriksson, grouped within the monophyletic Dothideomycetes.
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Affiliation(s)
- Asa Kruys
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden.
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31
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Redhead SA, Cushion MT, Frenkel JK, Stringer JR. Pneumocystis and Trypanosoma cruzi: Nomenclature and Typifications. J Eukaryot Microbiol 2006; 53:2-11. [PMID: 16441572 DOI: 10.1111/j.1550-7408.2005.00072.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Published phylogenetic reclassifications of Pneumocystis as a fungus resulted in a nomenclatural shift from the Zoological Code to the International Code of Botanical Nomenclature. The same may be true for all microsporidians and sundry other organisms. This resulted in the invalidation of names and subsequently precipitated changes to the botanical code to accommodate Pneumocystis and microsporidian names. The repercussions following application of the 2005 Vienna Code to Pneumocystis nomenclature are detailed. Validity of the name for the human pathogen, Pneumocystis jirovecii, is re-established from its 1976 publication under the Zoological Code, contrary to interpretation of validity under earlier botanical codes. Pneumocystis jirovecii is lectotypified and epitypified. The rat parasite, Pneumocystis carinii, is neotypified, separating it from Pneumocystis wakefieldiae. The original 1909 description of Trypanosoma cruzi, type species for Schizotrypanum, and causal agent of Chagas' disease, included parts of the life cycle of Pneumocystis. Trypanosoma cruzi is neotypified by the true Trypanosoma elements, thereby completing the nomenclatural separation from Pneumocystis and ensuring that Schizotrypanum is not applicable to Pneumocystis as an earlier name. The neotypes for P. carinii and T. cruzi represent the strains currently being investigated by their two respective genome projects. They were selected in light of their medical importance, physiological characterizations, and absence of lectotypifiable materials. The classification and nomenclature of Pneumocystis is reviewed and guidelines given for the publication of new species.
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Affiliation(s)
- Scott A Redhead
- National Program on Environmental Health-Biodiversity, Agriculture and Agri-Food Canada, Central Experimental Farm, KW Neatby Building, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
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32
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Letcher PM, Powell MJ, Chambers JG, Longcore JE, Churchill PF, Harris PM. Ultrastructural and molecular delineation of the Chytridiaceae (Chytridiales). ACTA ACUST UNITED AC 2005. [DOI: 10.1139/b05-115] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Chytridiomycota is in need of taxonomic revision, especially the largest order, the Chytridiales. We analyzed 25 isolates in, or allied to, the Chytridium clade of this order. Isolates were selected based on one or more of the following criteria: (i) having a large subunit molecular sequence similar to that of the type of the genus Chytriomyces, (ii) having specific zoospore morphology, and (iii) currently classified as a species in the genus Chytriomyces . We examined ultrastructural characters and partial sequences of large subunit and small subunit rDNA and generated a phylogenetic hypothesis using maximum parsimony and Bayesian analyses. The sequence analyses strongly supported the Chytridiaceae, Phlyctochytrium, and Chytriomyces angularis clades, and each clade had a specific zoospore type. Developmental morphology of the thallus did not mirror the DNA-based phylogeny. Based on the results of phylogenetic analyses of sequences and ultrastructural characters, we emend the Chytridiaceae by including exogenous and polycentric development and define the family on the basis of a single zoospore type. Species identified as being in the genus Chytriomyces occur in several separate, well-supported clades along with species currently classified in seven other genera ( Asterophlyctis , Entophlyctis , Obelidium , Physocladia , Podochytrium , Rhizoclosmatium , and Siphonaria ), indicating that Chytriomyces as currently defined is polyphyletic.
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Affiliation(s)
- Peter M. Letcher
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
| | - Martha J. Powell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
| | - James G. Chambers
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
| | - Joyce E. Longcore
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
| | - Perry F. Churchill
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
| | - Phillip M. Harris
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Biological Sciences, University of Maine, Orono, ME 04469, USA
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33
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MANGANELLI GIUSEPPE, SALOMONE NICOLA, GIUSTI FOLCO. A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora). Biol J Linn Soc Lond 2005. [DOI: 10.1111/j.1095-8312.2005.00514.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Padovan ACB, Sanson GFO, Brunstein A, Briones MRS. Fungi evolution revisited: application of the penalized likelihood method to a Bayesian fungal phylogeny provides a new perspective on phylogenetic relationships and divergence dates of Ascomycota groups. J Mol Evol 2005; 60:726-35. [PMID: 15909224 DOI: 10.1007/s00239-004-0164-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 12/15/2004] [Indexed: 10/25/2022]
Abstract
The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous Ascomycetes and probably maintain ancestor characters since their representatives are intermingled among other filamentous fungi. Also, we show that the evolutionary rate heterogeneity within Ascomycota precludes the assumption of a global molecular clock. Accordingly, we used the penalized likelihood method, and for calibration we included a 400 million-year-old Pyrenomycete fossil considering two distinct scenarios found in the literature, one with an estimated date of 1576 Myr for the plant-animal-fungus split and the other with an estimated date of 965 Myr for the animal-fungus split. Our data show that the current classification of the fossil as a Pyrenomycete is not compatible with the second scenario. Estimates under the first scenario are older than dates proposed in previous studies based on small subunit rDNA sequences but support estimates based on multiprotein analysis, suggesting that the radiation of the major Ascomycota groups occurred into the Proterozoic era.
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Affiliation(s)
- Ana Carolina B Padovan
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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35
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Stensrud O, Hywel-Jones NL, Schumacher T. Towards a phylogenetic classification of Cordyceps: ITS nrDNA sequence data confirm divergent lineages and paraphyly. ACTA ACUST UNITED AC 2005; 109:41-56. [PMID: 15736862 DOI: 10.1017/s095375620400139x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The ascomycetous genus Cordyceps accommodates endoparasitic species that attack arthropods or other fungi. Analyses of ITS nrDNA sequence data of 72 taxa from the teleomorph genera Cordyceps, Claviceps, Epichloë, and the anamorph genera Akanthomyces, Beauveria, Metarhizium, Hirsutella, Hymenostilbe, Paecilomyces, Polycephalomyces, and Tolypocladium assigned the taxa to four main evolutionary lineages not reflected in the current classification of Cordyceps. Ten subclades were recognized from separate analyses of data subsets. Judged from the ITS phylogenies, Cordyceps spp. with branched stromata were highly supported as a divergent lineage. Host specificity was found to be of limited phylogenetic significance, and several host shifts are suggested to have occurred during the evolution of Cordyceps. Similar ascospore morphology was not reflected in the phyletic groups, and closely related taxa showed large interspecific variation with respect to the number of segments in which the ascospores are divided. However, combinations of selected characters were found to delimitate some lineages, e.g. all Cordyceps spp. that attack hosts in the insect orders Coleoptera and Lepidoptera, and with non-immersed perithecia and clavate to acicular, brightly yellowish to reddish stromata, constituted a separate clade. Furthermore, all Cordyceps spp. with perithecia obliquely immersed in the stroma were recognized as a distinct monophyletic group. This clade is additionally characterized by the formation of anamorphs ascribable to the genus Hymenostilbe. The mycogenous Cordyceps spp. grouped in a separate subclade, interspersed by two cicadaen parasites and all Tolypocladium spp. except T. parasiticum. Tolypocladium and Beauveria were found to be polyphyletic. The included Claviceps and Epichloë taxa appeared to be derived within Cordyceps, thus making Cordyceps paraphyletic as suggested in other studies.
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Affiliation(s)
- Oyvind Stensrud
- Division of Botany and Plant Physiology, Department of Biology, University of Oslo, P.O. Box 1045, Blindern, 0316 Oslo, Norway.
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Lumbsch HT, Schmitt I, Lindemuth R, Miller A, Mangold A, Fernandez F, Huhndorf S. Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol Phylogenet Evol 2005; 34:512-24. [PMID: 15683926 DOI: 10.1016/j.ympev.2004.11.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 10/14/2004] [Accepted: 11/02/2004] [Indexed: 10/26/2022]
Abstract
The inoperculate euascomycetes are filamentous fungi that form saprobic, parasitic, and symbiotic associations with a wide variety of animals, plants, cyanobacteria, and other fungi. The higher-level relationships of this economically important group have been unsettled for over 100 years. A data set of 55 species was assembled including sequence data from nuclear and mitochondrial small and large subunit rDNAs for each taxon; 83 new sequences were obtained for this study. Parsimony and Bayesian analyses were performed using the four-region data set and all 14 possible subpartitions of the data. The mitochondrial LSU rDNA was used for the first time in a higher-level phylogenetic study of ascomycetes and its use in concatenated analyses is supported. The classes that were recognized in Leotiomyceta (=inoperculate euascomycetes) in a classification by Eriksson and Winka [Myconet 1 (1997) 1] are strongly supported as monophyletic. The following classes formed strongly supported sister-groups: Arthoniomycetes and Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes, and Leotiomycetes and Sordariomycetes. Nevertheless, the backbone of the euascomycete phylogeny remains poorly resolved. Bayesian posterior probabilities were always higher than maximum parsimony bootstrap values, but converged with an increase in gene partitions analyzed in concatenated analyses. Comparison of five recent higher-level phylogenetic studies in ascomycetes demonstrates a high degree of uncertainty in the relationships between classes.
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Affiliation(s)
- H Thorsten Lumbsch
- Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
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Seif E, Leigh J, Liu Y, Roewer I, Forget L, Lang BF. Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms. Nucleic Acids Res 2005; 33:734-44. [PMID: 15689432 PMCID: PMC548346 DOI: 10.1093/nar/gki199] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5′ and 3′ termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3′ RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3′ termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380–395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.
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MESH Headings
- Bacteria/enzymology
- Bacteria/genetics
- Base Sequence
- Conserved Sequence
- DNA Transposable Elements
- DNA, Mitochondrial/chemistry
- Endonucleases/genetics
- Fungi/classification
- Fungi/genetics
- Gene Transfer, Horizontal
- Genes, Fungal
- Genetic Code
- Genome, Fungal
- Introns
- Magnoliopsida/genetics
- Mitochondria/enzymology
- Mitochondria/genetics
- Mitochondrial Proteins/classification
- Mitochondrial Proteins/genetics
- Molecular Sequence Data
- Phylogeny
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Mitochondrial
- RNA, Ribosomal/chemistry
- Ribonuclease P/genetics
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Affiliation(s)
- Elias Seif
- Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4
| | - Jessica Leigh
- Department of Biochemistry and Molecular Biology, Dalhousie UniversityHalifax (Nova Scotia), Canada B3H 4H7
| | - Yu Liu
- Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4
| | - Ingeborg Roewer
- Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4
| | - Lise Forget
- Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4
| | - B. Franz Lang
- Program in Evolutionary Biology, Canadian Institute for Advanced Research; Centre Robert Cedergren, Département de Biochimie, Université de Montréal2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4
- To whom correspondence should be addressed. Tel: +1 514 343 5842; Fax: +1 514 343 2210;
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Kouvelis VN, Ghikas DV, Typas MA. The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications. Fungal Genet Biol 2004; 41:930-40. [PMID: 15341915 DOI: 10.1016/j.fgb.2004.07.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2003] [Accepted: 07/10/2004] [Indexed: 11/24/2022]
Abstract
The mitochondrial genome (mtDNA) of the entomopathogenic fungus Lecanicillium muscarium (synonym Verticillium lecanii) with a total size of 24,499-bp has been analyzed. So far, it is the smallest known mitochondrial genome among Pezizomycotina, with an extremely compact gene organization and only one group-I intron in its large ribosomal RNA (rnl) gene. It contains the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, one intronic ORF coding for a possible ribosomal protein (rps), and a set of 25 tRNA genes which recognize codons for all amino acids, except alanine and cysteine. All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed some characteristic common features like uninterrupted gene pairs, overlapping genes, and extremely variable intergenic regions, that can all be exploited for the study of fungal mitochondrial genomes. Moreover, a minimum common mtDNA gene order could be detected, in two units, for all known Sordariomycetes namely nad1-nad4-atp8-atp6 and rns-cox3-rnl, which can be extended in Hypocreales, to nad4L-nad5-cob-cox1-nad1-nad4-atp8-atp6 and rns-cox3-rnl nad2-nad3, respectively. Phylogenetic analysis of all fungal mtDNA essential protein-coding genes as one unit, clearly demonstrated the superiority of small genome (mtDNA) over single gene comparisons.
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Affiliation(s)
- Vassili N Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Panepistemiopolis, Athens 157 01, Greece
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Schrettl M, Winkelmann G, Haas H. Ferrichrome in Schizosaccharomyces pombe ? an iron transport and iron storage compound. Biometals 2004; 17:647-54. [PMID: 15689108 DOI: 10.1007/s10534-004-1230-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Schizosaccharomyces pombe has been assumed not to produce siderophores. Nevertheless, the genomic sequence of this fission yeast revealed the presence of siderophore biosynthetic genes for hydroxamates. Applying a bioassay based on an Aspergillus nidulans strain deficient in siderophore biosynthesis, and using reversed-phase HPLC and mass spectrometry analysis, we demonstrate that S. pombe excretes and accumulates intracellularly the hydroxamate-type siderophore ferrichrome. Under iron-limiting conditions, the cellular ferrichrome pool was present in the desferri-form, while under iron-richconditions, in the ferri-form. In contrast to S. pombe, hydroxamate-type siderophores could not be detected intwo other yeast species, Saccharomyces cerevisiae and Candida albicans.
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Affiliation(s)
- Markus Schrettl
- Department of Molecular Biology, Medical University Innsbruck, A-6020 Innsbruck, Austria
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40
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Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J. Molecular phylogeny of Zygomycota based on EF-1alpha and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol Phylogenet Evol 2004; 30:438-49. [PMID: 14715234 DOI: 10.1016/s1055-7903(03)00185-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Earlier molecular phylogenetic analyses based on nuclear small subunit ribosomal DNA (nSSU rDNA) suggest that the Zygomycota are polyphyletic within the Chytridiomycota. However, these analyses failed to resolve almost all interordinal relationships among basal fungi (Chytridiomycota and Zygomycota), due to lack of sufficient characters within the nSSU rDNA. To further elucidate the higher-level phylogeny of Zygomycota, we have sequenced partial RPB1 (DNA dependent RNA polymerase II largest subunit) and EF-1alpha (translation elongation factor 1 alpha) genes from 10 and 3 zygomycete fungi, respectively. Independent molecular phylogenetic analyses were performed based on each sequence by distance and maximum likelihood methods. Although deep phylogenetic relationships among basal fungi still remain poorly resolved using either gene, the RPB1-based phylogeny identified a novel monophyletic clade consisting of the Dimargaritales, Harpellales, and Kickxellales. This result suggests that regularly formed septa (cross walls that divide hyphae into segments) with a lenticular cavity are plesiomorphic for this clade, and indicates the importance of septal pore ultrastructure in zygomycete phylogeny. In addition, a peculiar mucoralean genus Mortierella, which was considered to be distantly related to the other Mucorales based on previous nSSU rDNA analyses, was resolved as the basal most divergence within the Mucorales, consistent with traditional phenotypic-based taxonomy. Although the taxa included in our analysis are restricted, the monophyly of each order suggested by nSSU rDNA phylogeny is supported by the present RPB1-based analysis. These results support the potential use of RPB1 as an alternative marker for fungal phylogenetic studies. Conversely, the overall fungal phylogeny based on EF-1alpha sequence is poorly resolved. A comparison of numbers of observed substitutions versus inferred substitutions within EF-1alpha indicates that this gene is much more saturated than RPB1. This result suggests that the EF-1alpha gene is unsuitable for resolving higher-level phylogenetic relationships within the Fungi.
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Affiliation(s)
- Yuuhiko Tanabe
- Environmental Biology Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.
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41
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Reeb V, Lutzoni F, Roux C. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phylogenet Evol 2004; 32:1036-60. [PMID: 15288074 DOI: 10.1016/j.ympev.2004.04.012] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 04/09/2004] [Indexed: 10/26/2022]
Abstract
Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).
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Affiliation(s)
- Valérie Reeb
- Department of Biology, Duke University, Durham, NC 27708-0338, USA.
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42
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Bruns TD, Shefferson RP. Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions. ACTA ACUST UNITED AC 2004. [DOI: 10.1139/b04-021] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three biggest advances in fungal molecular phylogenetics in the last few years have been (1) the huge expansion in data sets, (2) the development of nonribosomal loci for phylogenetic analysis, and (3) the use of increasingly sophisticated types of analyses. In addition, advances in parallel computing hold great promise for dramatic increases in speed of analysis. These changes have had, or will have, a direct impact on mycorrhizal ecology through the use of sequence-based identification and an indirect impact through the conclusions drawn from such studies. One problem in the field has been the accidental addition of erroneous sequences to the public databases through a variety of means, including polymerase change reaction contamination. We discuss several examples, suggest ways to identify errors, and argue the case for third-party annotations of sequences. Multiple studies have produced compelling evidence that the ectomycorrhizal habit has developed convergently in multiple lineages of fungi and plants. We reexamine the case for loss of the ectomycorrhizal habit in fungi and show that the results are model dependent.Key words: internal transcribed spacer (ITS) region, peroxidase genes, likelihood models, erroneous data, ectomycorrhizal habit.
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43
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Lumbsch HT, Schmitt I, Palice Z, Wiklund E, Ekman S, Wedin M. Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences. Mol Phylogenet Evol 2004; 31:822-32. [PMID: 15120381 DOI: 10.1016/j.ympev.2003.11.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Revised: 10/27/2003] [Indexed: 11/28/2022]
Abstract
Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.
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44
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Ekendahl S, O'Neill AH, Thomsson E, Pedersen K. Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian Shield. MICROBIAL ECOLOGY 2003; 46:416-428. [PMID: 14502418 DOI: 10.1007/s00248-003-2008-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2003] [Accepted: 04/28/2003] [Indexed: 05/24/2023]
Abstract
The diversity of prokaryotes in the groundwater deep below the surface of the Baltic Sea at the Aspö Hard Rock Laboratory (HRL) in southeast Sweden is well documented. In addition, there is some evidence that eukaryotes, too, are present in the deep groundwater at this site, although their origins are uncertain. To extend the knowledge of eukaryotic life in this environment, five yeast, three yeastlike, and 17 mold strains were isolated from Aspö HRL groundwater between 201 and 444 m below sea level. Phenotypic testing and phylogenetic analysis of 18S rDNA sequences of the five yeast isolates revealed their relationships to Rhodotorula minuta and Cryptococcus spp. Scanning and transmission electron microscopy demonstrated that the strains possessed morphological characteristics typical for yeast, although they were relatively small, with an average length of 3 micro m. Enumeration through direct counting and most probable number methods showed low numbers of fungi, between 0.01 and 1 cells mL(-1), at some sites. Five of the strains were characterized physiologically to determine whether they were adapted to life in the deep biosphere. These studies revealed that the strains grew within a pH range of 4-10, between temperatures of 4 degrees C and 25-30 degrees C, and in NaCl concentrations from 0 to 70 g L(-1). These growth parameters suggest a degree of adaptation to the groundwater at Aspö HRL. Despite the fact that these eukaryotic microorganisms may be transient members of the deep biosphere microbial community, many of the observations of this study suggest that they are capable of growing in this extreme environment.
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Affiliation(s)
- S Ekendahl
- Department of Cell and Molecular Biology (CMB), Microbiology, Göteborg University, Box 462, SE 405 30, Göteborg, Sweden
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45
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Bullerwell CE, Forget L, Lang BF. Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Res 2003; 31:1614-23. [PMID: 12626702 PMCID: PMC152866 DOI: 10.1093/nar/gkg264] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have determined the complete mitochondrial DNA (mtDNA) sequences of three chytridiomycete fungi, Monoblepharella15, Harpochytrium94 and Harpochytrium105. Our phylogenetic analysis based on concatenated mitochondrial protein sequences confirms the placement of Mono blepharella15 together with Harpochytrium spp. and Hyaloraphidium curvatum within the taxonomic order Monoblepharidales, with overwhelming support. These four mtDNA sequences encode the standard fungal mitochondrial gene complement and, like certain other chytridiomycete fungi, encode a reduced complement of 7-9 tRNAs, some of which require 5'-tRNA editing to be functional. Highly conserved sequence elements were identified upstream of almost all protein-coding genes in the mtDNAs of Monoblepharella15 and both Harpochytrium species. Finally, a guanosine residue is conserved upstream of the predicted ATG or GTG start codons of almost every protein-coding gene in these genomes. The appearance of this G residue correlates with the presence of a non-canonical cytosine residue at position 37 in the anticodon loop of the mitochondrial initiator tRNAs. Based on the unorthodox features in these four genomes, we propose that a 4 bp interaction between the CAUC anticodon of these tRNAs and GAUG/GGUG codons is involved in translation initiation in monoblepharidalean mitochondria. Intriguingly, a similar interaction may also be involved in mitochondrial translation initiation in the sea anemone Metridium senile.
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Affiliation(s)
- C E Bullerwell
- Program in Evolutionary Biology, Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Québec H3T 1J4, Canada
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46
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Bullerwell CE, Leigh J, Forget L, Lang BF. A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res 2003; 31:759-68. [PMID: 12527786 PMCID: PMC140500 DOI: 10.1093/nar/gkg134] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The fission yeasts are members of the fungal order Schizosaccharomycetales, a candidate deep-diverging group within Ascomycota. Although a great deal of molecular information is available from Schizosaccharomyces pombe, a model eukaryote, very little is available from other members of this group. In order to better characterize mitochondrial genome evolution in this fungal lineage, the mitochondrial DNA (mtDNA) of two additional fission yeasts, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus var. japonicus, was sequenced. Whereas the mtDNA of S.pombe is only 19 431 bp, the mtDNA of S.octosporus is 44 227 bp, and that of S.japonicus var. japonicus is over 80 kb. The size variation of these mtDNAs is due largely to non-coding regions. The gene content in the latter two mtDNAs is almost identical to that of the completely sequenced S.pombe mtDNA, which encodes 25 tRNA species, the large and small mitochondrial ribosomal RNAs (rnl and rns), the RNA component of mitochondrial RNaseP (rnpB), mitochondrial small subunit ribosomal protein 3 (rps3), cytochrome oxidase subunits 1, 2 and 3 (cox1, cox2 and cox3) and ATP-synthase subunits 6, 8 and 9 (atp6, atp8 and atp9). However, trnI2(cau) (C modified to lysidine) is absent in the S.octosporus mtDNA, as are corresponding ATA codons in its protein-coding genes, and rps3 and rnpB are not found in the mtDNA of S.japonicus var. japonicus. The mtDNA of S.octosporus contains five double hairpin elements, the first report of these elements in an ascomycete. This study provides further evidence in favor of the mobility of these elements, and supports their role in mitochondrial genome rearrangement. The results of our phylogenetic analysis support the monophyly of the Schizosaccharomycetales, but question their grouping within the Archiascomycota.
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Affiliation(s)
- C E Bullerwell
- Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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47
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Evolution of the Fungi and their Mitochondrial Genomes. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1874-5334(03)80010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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48
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Jahnulales (Dothideomycetes, Ascomycota): a new order of lignicolous freshwater ascomycetes. ACTA ACUST UNITED AC 2002. [DOI: 10.1017/s095375620200638x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Moncalvo JM, Vilgalys R, Redhead SA, Johnson JE, James TY, Catherine Aime M, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Greg Thorn R, Jacobsson S, Clémençon H, Miller OK. One hundred and seventeen clades of euagarics. Mol Phylogenet Evol 2002; 23:357-400. [PMID: 12099793 DOI: 10.1016/s1055-7903(02)00027-1] [Citation(s) in RCA: 357] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5(') end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.
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50
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An KD, Nishida H, Miura Y, Yokota A. Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses. BMC Evol Biol 2002; 2:6. [PMID: 11931673 PMCID: PMC103663 DOI: 10.1186/1471-2148-2-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2001] [Accepted: 04/03/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fungi, aminoadipate reductase converts 2-aminoadipate to 2-aminoadipate 6-semialdehyde. However, other organisms have no homologue to the aminoadipate reductase gene and this pathway appears to be restricted to fungi. In this study, we designed degenerate primers for polymerase chain reaction (PCR) amplification of a large fragment of the aminoadipate reductase gene for divergent fungi. RESULTS Using these primers, we amplified DNA fragments from the archiascomycetous yeast Saitoella complicata and the black-koji mold Aspergillus awamori. Based on an alignment of the deduced amino acid sequences, we constructed phylogenetic trees. These trees are consistent with current ascomycete systematics and demonstrate the potential utility of the aminoadipete reductase gene for phylogenetic analyses of fungi. CONCLUSIONS We believe that the comparison of aminoadipate reductase among species will be useful for molecular ecological and evolutionary studies of fungi, because this enzyme-encoding gene is a fungal-specific gene and generally appears to be single copy.
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Affiliation(s)
- Kwang-Deuk An
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiromi Nishida
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yoshiharu Miura
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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