Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, β-tubulin, and LSU rDNA

Hansen, Karen; LoBuglio, Katherine F.; Pfister, Donald H.

doi:10.1016/j.ympev.2005.03.010

Cited by 106 publications

(79 citation statements)

References 58 publications

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“…RPB2 gene ranks the next (16/19, 84.2%, Table 2). This result conforms to the previous studies in certain other fungal groups [38,[52][53][54]. The other two genes, β-tubulin and ITS, had undesirable intra-and inter-variations and exhibited relatively poor species resolution capacity (Table 2), which indicated that the partial β-tubulin gene and ITS gene are inadequate to identify closely related species.…”

Section: Discussionsupporting

confidence: 90%

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao

Luo

Zhuang

et al. 2011

Sci. China Life Sci.

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To determine a suitable DNA barcode for the genus Neonectria, the internal transcribed spacer rDNA, β-tubulin, EF-1α, and RPB2 genes were selected as candidate markers. A total of 205 sequences from 19 species of the genus were analyzed. Intraand inter-specific divergences and the ease of nucleotide sequence acquisition were treated as criteria to evaluate the feasibility of a DNA barcode. Our results indicated that any single gene among the candidate markers failed to serve as a successful barcode, while the combination of the partial EF-1α and RPB2 genes recognized all species tested. We tentatively propose the combined partial EF-1α and RPB2 genes as a DNA barcode for the genus. During this study, two cryptic species were discovered, based on the combined data of morphology and DNA barcode information. We described and named these two new species N. ditissimopsis and N. microconidia. intra-specific variation, inter-specific variation, morphology, DNA barcode, sequence analysis Citation:Zhao P, Luo J, Zhuang W Y, et al. DNA barcoding of the fungal genus Neonectria and the discovery of two new species . Sci China Life Sci, 2011, 54: 664 -674,

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Section: Discussionsupporting

confidence: 90%

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao

Luo

Zhuang

et al. 2011

Sci. China Life Sci.

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“…3) and increased nodal support for clades that were not strongly supported when analyzed separately (Table 4). Our data are in agreement with other Ascomycota studies that have shown that combining protein-coding data with nuclear ribosomal genes (either LSU or SSU) provides an increased number of supported nodes in phylogenetic analyses , Hansen et al 2005, Miller and Huhndorf 2005, Tang et al 2007). Hofstetter et al (2007) concluded that for better resolution and support of clades in phylogenetic analyses of fungi more characters and proteincoding genes in particular are important.…”

Section: Combine Gene Analysessupporting

confidence: 92%

“…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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“…These rDNA regions were amplified with rDNA primers ITS1 and ITS4 (White et al 1990) and LROR and LR5 (Moncalvo et al 2000). PCR amplification, purification and sequencing were carried out as described in Hansen et al (2005).…”

Section: Methodsmentioning

confidence: 99%

A Glomerella species phylogenetically related to Colletotrichum acutatum on Norway maple in Massachusetts

LoBuglio

Pfister

2008

Mycologia

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Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, β-tubulin, and LSU rDNA

Cited by 106 publications

References 58 publications

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Testing the phylogenetic utility of MCM7 in the Ascomycota

A Glomerella species phylogenetically related to Colletotrichum acutatum on Norway maple in Massachusetts

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