A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach

Sung, Gi‐Ho; Sung, Jae-Mo; Hywel‐Jones, Nigel L.; Spatafora, Joseph W.

doi:10.1016/j.ympev.2007.03.011

Cited by 476 publications

(240 citation statements)

References 79 publications

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“…Spribille et al (2011) also showed a higher level of transition-saturation at the third codon position for MCM7 gene in their phylogenetic analyses. Substitution saturation appears to be a common problem among protein-coding genes routinely used for inferring phylogenetic relationships among fungi (Liu et al 1999, Hansen et al 2005, Miller and Huhndorf 2005, Sung et al 2007). There are currently two schools of thought regarding the inclusion or exclusion of third codon positions from saturated protein-coding genes and their method of utilization for phylogenetic analyses.…”

Section: Mcm7 Codon Saturationmentioning

confidence: 99%

“…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%

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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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Section: Mcm7 Codon Saturationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Testing the phylogenetic utility of MCM7 in the Ascomycota

Raja¹,

Schoch²,

Hustad³

et al. 2011

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show abstract

“…Primes for amplifying and sequencing were: ITS5 and ITS4 for the internal transcribed spacer (ITS) (White et al 1990), NS1 and NS4 for the ribosomal small subunit (18S) (Vilgalys & Hester 1990), 983F and 2218R for partial elongation Factor 1-Alpha (TEF1) (Sung et al 2007b) and CRPB1A and RPB1Cr (Castlebury et al 2004) for partial second largest RNA polymerase subunit I (RPB1). PCR conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 35 cycles at 95 °C for 50s, 50-53 °C for 50 s, 72 °C for 80 s, and a final extension of 72 °C for 10 min.…”

Section: Dna Extraction Pcr Amplification and Determination Of Dna Smentioning

confidence: 99%

Multigene phylogeny and morphology reveal that the Chinese medicinal mushroom ‘Cordyceps gunnii’ is Metacordyceps neogunnii sp. nov.

Wen

Xiao²,

Han

et al. 2017

Phytotaxa

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Morphological and molecular phylogenetic analyses of an entomogenous fungus associated with larvae of Lepidoptera in Guizhou and Anhui, China showed it to be a new species, Metacordyceps neogunnii. It differs from similar species in having longer asci and wider ascospores. Multigene analysis of ITS, 18S, TEF1 and RPB1 sequence data also confirmed the distinctiveness of this species. This species has been wrongly regarded in China as 'Cordyceps gunnii' for more than 30 years. Cordyceps gunnii from Tasmania is considered to be in the family Ophiocordycipitaceae based on its multigene phylogeny and morphological analysis.

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“…The internal transcribed spacer region of ribosomal DNA (ITS1-5.8S-ITS2), the small subunits of the rDNA (SSU) and two protein genes the transcription elongation factor-1α (TEF), and the first largest subunits of RNA polymerase II (RPB1) loci were amplified and sequenced (Sung et al 2007b).…”

Section: Dna Extraction Pcr Amplification and Determination Of Dna Smentioning

confidence: 99%

Multigene phylogeny and morphology reveal a new species, Ophiocordyceps tettigonia, from Guizhou Province, China

et al. 2016

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A species of Cordyceps sensu lato associated with an adult of Tettigonia was collected in Chishui Danxia natural world heritage site, Guizhou Province, China. Following morpho-phylogenetic studies it was found to be a new species and is described as Ophiocordyceps tettigonia sp. nov. It differs from similar Ophiocordyceps species in having a unique host insect, and wide secondary ascospores. Combined sequence data from the ITS, SSU, TEF, and RPB1 gene loci also confirmed the distinctiveness of this new species.

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A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): Identification of localized incongruence using a combinational bootstrap approach

Cited by 476 publications

References 79 publications

Testing the phylogenetic utility of MCM7 in the Ascomycota

Testing the phylogenetic utility of MCM7 in the Ascomycota

Multigene phylogeny and morphology reveal that the Chinese medicinal mushroom ‘Cordyceps gunnii’ is Metacordyceps neogunnii sp. nov.

Multigene phylogeny and morphology reveal a new species, Ophiocordyceps tettigonia, from Guizhou Province, China

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