The β-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex

Huang, Chien‐Hsun; Lee, Fwu-Ling; Tai, Chun-Ju

doi:10.1007/s10482-008-9296-1

Cited by 17 publications

(15 citation statements)

References 42 publications

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“…The PCR reaction mixture was comprised of 10 µL fungal DNA, 5 µL 10× PCR buffer, 1.5 µL of 50 mM MgCl 2 , 1 µL of 10 mM dNTP, 0.25 µL Taq polymerase, 40 pM of each forward and the reverse primers in a total reaction volume of 50 µL [13]. The PCR amplification was performed in a GeneAmp® 9700 Thermal Cycler with the following thermal protocol: initial strand denaturation at 94℃ for 5 min, followed by 35 cycles of 94℃ for 1 min, 59℃ for 1 min and 72℃ for 1.5 min and a final extension step at 72℃ for 7 min [17]. The PCR products were analysed by 2% agarose gel electrophoresis and visualised using ethidium bromide under UV illumination in a Kodak gel logic 100 gel documentation system.…”

Section: Methodsmentioning

confidence: 99%

Multi-loci Molecular Characterisation of Endophytic Fungi Isolated from Five Medicinal Plants of Meghalaya, India

Bhagobaty

Joshi

2011

Mycobiology

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The phylogenetic relationships of the most dominant and morphologically cryptic endophytic fungal isolates from each of five selected medicinal plants, namely Potentilla fulgens, Osbeckia stellata, Osbeckia chinensis, Camellia caduca, and Schima khasiana of the biodiversity rich state of Meghalaya, were assessed with random amplification of polymorphic DNA and PCR-restriction fragment length polymorphism profiles. Sequencing of the internal transcribed spacer 1, small subunit rRNA and partial β-tubulin gene fragments was also conducted to determine the phylogenetic relationships of these isolates with fungal sequences available in Genbank, NCBI. The identity of the fungal isolates is suggested based on the molecular phylogenetic data.

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Section: Methodsmentioning

confidence: 99%

Multi-loci Molecular Characterisation of Endophytic Fungi Isolated from Five Medicinal Plants of Meghalaya, India

Bhagobaty

Joshi

2011

Mycobiology

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“…Phylogenetic relationships among taxa of Ascomycota (Schoch et al 2009a) have been inferred using a variety of protein-coding genes such as the mitochondrial ATP synthase-subunit 6 (Castlebury et al 2004, Sung et al 2007), β-tubulin (Ayliffe et al 2001, Hansen et al 2005, Huang et al 2009, Hsieh et al 2010, Miller and Huhndorf 2004, Tang et al 2007), alpha-actin (Hsieh et al, 2010), glyceraldehyde 3-phosphate dehydrogenase (Berbee et al 1999, Smith 1989) RNA polymerase including the largest and second largest subunits (RPB1, RPB2; Liu et al 1999, Liu and Hall 2004, Zhang and Blackwell 2002, Tang et al 2007, Schmitt et al 2009a, Hsieh et al 2010, and translation elongation factor alpha TEF1 (Mugambi and Huhndorf 2009a, Rehner and Buckley 2005. Use of these protein-coding genes has become increasingly common in systematic studies within the fungal kingdom (Blackwell et al 2006, James et al 2006, Lutzoni et al 2004.…”

Section: Introductionmentioning

confidence: 99%

Testing the phylogenetic utility of MCM7 in the Ascomycota

Raja¹,

Schoch²,

Hustad³

et al. 2011

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The Ascomycota are a group of filamentous fungi that occur as saprobes, pathogens, and symbionts. They are of immense industrial, medical, ecological, and economical importance. The search for new markers appropriate for molecular phylogenetic analysis of Ascomycota remains a challenging problem. In this study, we explore the phylogenetic utility of a single copy protein-coding gene, MCM7; newly recognized as useful for inferring phylogenetic relationships among the major classes of the Ascomycota. Our specific goals were to: 1) test the phylogenetic utility of MCM7 for estimating phylogenies at various taxonomic ranks (class and below) with an emphasis on non-lichenized ascomycetes; and, 2) compare the congruence, robustness and resolving power of MCM7-based phylogenies with that of nuclear large subunit rDNA (LSU)-based phylogenies for the same taxon set. A dataset of sequence data for MCM7 as well as LSU was assembled for 80 species belonging to 63 genera of lichenized and non-lichenized ascomycetes in the classes Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes. We obtained 93 new sequences of which 65 are MCM7 and 28 are LSU. MaximumLikelihood and Bayesian analyses were performed using single as well as combined gene datasets and partitions. We also assessed substitution saturation for the MCM7 gene. Results indicate that MCM7 can be used successfully for determining phylogenetic relationships of ascomycetes and provided good resolution and support at half the cost compared to LSU. Phylogenetic informativeness profiles showed that MCM7 was more phylogenetically informative than LSU. The MCM7 gene is also a valuable phylogenetic marker for both lower as well as higher level phylogenetic analyses within the Ascomycota, especially when used in MycoKeysLaunched to accelerate biodiversity research Huzefa A. Raja et al. / MycoKeys 1: 63-94 (2011) 64 combination with the LSU gene. We found that although the third codon position of MCM7 is saturated, it was better to analyze the dataset with all codon positions included. Phylogenetic performance of MCM7 with and without the third codon position is discussed.

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“…Therefore, molecular taxonomy needs to be developed. Current techniques for the molecular taxonomy of yeast include DNA fingerprinting ( RAPD , AFLP , DGGE , SSCP , microsatellites, RFLP ), species‐specific PCR (SS‐PCR), unigene sequencing, multilocus sequence analysis (MLSA) and DNA hybridization (Azumi and Goto‐Yamamoto, ; Hennequin et al ., ; Huang et al ., , ; Kurtzman and Robnett, ; Manzano et al ., ; Wang et al ., ). However, some of these techniques are complicated, time‐intensive, costly and cannot easily be used in industrial laboratories…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, molecular taxonomy needs to be developed. Current techniques for the molecular taxonomy of yeast include DNA fingerprinting (RAPD, AFLP, DGGE, SSCP, microsatellites, RFLP), species-specific PCR (SS-PCR), unigene sequencing, multilocus sequence analysis (MLSA) and DNA hybridization (Azumi and Goto-Yamamoto, 2001;Hennequin et al, 2001;Huang et al, 2008Huang et al, , 2009Kurtzman and Robnett, 2003;Manzano et al, 2004;Wang et al, 2008). However, some of these techniques are complicated, time-intensive, costly and cannot easily be used in industrial laboratories Large subunit (LSU; 26S) ribosomal DNA has been sequenced for almost all known yeasts and can be act as an identification tool (Fell et al, 2000;Suh et al, 2006;Kurtzman and Robnett, 1998).…”

Section: Introductionmentioning

confidence: 99%

Species identification ofWickerhamomyces anomalusand related taxa usingβ‐tubulin(β‐tub) DNA barcode marker

Huang

Chang

Huang

2012

Yeast

Self Cite

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Wickerhamomyces anomalus is used in food and feed processing, although the species has been reported as an opportunistic human pathogen, predominantly in neonates. Neither phenotypic nor the most frequently applied genotypic marker (D1/D2 LSU ribosomal DNA) provide sufficient resolution for accurate identification of this yeast. In this study, the b-tubulin gene was used for species identification by direct DNA sequencing and as marker in a species-specific PCR assay. The results showed that all examined W. anomalus strains were clearly distinguished from the closely related species by comparative sequence analysis of the b-tubulin gene. In addition, the species-specific primers were also developed based on the b-tubulin gene, which was employed for polymerase chain reaction with the template DNA of Wickerhamomyces strains. A single 218 bp species-specific band was found only in W. anomalus. Our data indicate that the phylogenetic relationships between these strains are easily resolved by sequencing of the b-tubulin gene and combined with species-specific PCR assay.

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The β-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex

Cited by 17 publications

References 42 publications

Multi-loci Molecular Characterisation of Endophytic Fungi Isolated from Five Medicinal Plants of Meghalaya, India

Multi-loci Molecular Characterisation of Endophytic Fungi Isolated from Five Medicinal Plants of Meghalaya, India

Testing the phylogenetic utility of MCM7 in the Ascomycota

Species identification ofWickerhamomyces anomalusand related taxa usingβ‐tubulin(β‐tub) DNA barcode marker

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