Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory

Reeb, Valérie; Lutzoni, François; Roux, Claude

doi:10.1016/j.ympev.2004.04.012

Cited by 398 publications

(212 citation statements)

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“…We analyzed the single-locus data sets within a maximum likelihood (ML) framework (Mason-Gamer and Kellogg 1996; Reeb et al 2004) and the combined data set using both ML and Bayesian approaches. The combined data set was partitioned by individual locus, nuclear 28S and 18S and mitochondrial 16S, in both ML and Bayesian analyses.…”

Section: Methodsmentioning

confidence: 99%

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

et al. 2017

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The genus Cheiromycina is one of the few genera of lichenized hyphomycetes for which no sexual reproductive stages have been observed. The genus includes species from boreal to temperate regions of the Northern Hemisphere where it is found growing on bark or wood. Congeners in Cheiromycina are characterized by a noncorticate thallus, nearly immersed in the substrate and presenting powdery unpigmented sporodochia, and containing chlorococcoid photobionts. The relationships of members of Cheiromycina with other fungi are not known. Here we inferred the phylogenetic placement of Cheiromycina using three loci (nuSSU, nuLSU, and mtSSU) representing C. flabelliformis, the type species for the genus, C. petri, and C. reimeri. Our results revealed that the genus Cheiromycina is found within the family Malmideaceae (Lecanorales) where members formed a monophyletic clade sister to the genera Savoronala and Malmidea. This phylogenetic placement and the relationships of Cheiromycina with other lichenized hyphomycetous taxa are here discussed.

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Section: Methodsmentioning

confidence: 99%

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

et al. 2017

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“…A more recent phylogeny produced from protein gene coding data (Liu and Hall 2004) was inferred as supporting the taxonomic concepts for a monophyletic lineage for ascostromatic taxa, but the ontogenetic designations were considered oversimplified by some (Lumbsch et al 2005). Other studies combining data from protein-coding genes and the ribosomal operon have shown the paraphyly of ascostromatic, bitunicate lineages , Reeb et al 2004. An example is the group of fungi that recently were transferred to the Eurotiomycetes based on nuclear small subunit ribosomal sequences, the ''black yeasts'' of the Chaetothyriales (Winka et al 1998).…”

Section: Introductionmentioning

confidence: 98%

“…An example is the group of fungi that recently were transferred to the Eurotiomycetes based on nuclear small subunit ribosomal sequences, the ''black yeasts'' of the Chaetothyriales (Winka et al 1998). Together with the Verrucariales and Pyrenulales these bitunicate taxa have been placed within a separate subclass, the Chaetothyriomycetidae (Miadlikowska and Lutzoni 2004), which is sister of the Eurotiomycetidae , Reeb et al 2004 in the class Eurotiomycetes (also see Geiser et al in this issue).…”

Section: Introductionmentioning

confidence: 99%

A multigene phylogeny of the Dothideomycetes using four nuclear loci

Schoch

Shoemaker²,

Seifert³

et al. 2006

Mycologia

248

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We present an expanded multigene phylogeny of the Dothideomycetes. The final data matrix consisted of four loci (nuc SSU rDNA, nuc LSU rDNA, TEF1, RPB2) for 96 taxa, representing five of the seven orders in the current classification of Dothideomycetes and several outgroup taxa representative of the major clades in the Pezizomycotina. The resulting phylogeny differentiated two main dothideomycete lineages comprising the pseudoparaphysate Pleosporales and aparaphysate Dothideales. We propose the subclasses Pleosporomycetidae (order Pleosporales) and Dothideomycetidae (orders Dothideales, Capnodiales and Myriangiales). Furthermore we provide strong molecular support for the placement of Mycosphaerellaceae and Piedraiaceae within the Capnodiales and introduce Davidiellaceae as a new family to accommodate species of Davidiella with Cladosporium anamorphs. Some taxa could not be placed with certainty (e.g. Hysteriales), but there was strong support for new groupings. The clade containing members of the genera Botryosphaeria and Guignardia resolved well but without support for any relationship to any other described orders and we hereby propose the new order Botryosphaeriales. These data also are consistent with the removal of Chaetothyriales and Coryneliales from the Dothideomycetes and strongly support their placement in the Eurotiomycetes.

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“…These fungi were included in this study. The class Pezizomycetes is the earliest diverging lineage in the Pezizomycotina Reeb et al, 2004). Tuber melanosporum belongs to the Pezizomycetes.…”

Section: Methodsmentioning

confidence: 99%

The early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages

Nishida

Matsumoto

Kondo

et al. 2014

J. Gen. Appl. Microbiol.

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We sequenced the genomic DNA and the transcribed RNA of the ascomycetous budding yeast Saitoella complicata, which belongs to the earliest lineage (Taphrinomycotina) of ascomycetes. We found 3 protein-coding regions similar to Clr6 of Schizosaccharomyces (a member of Taphrinomycotina). Clr6 has a structure similar to that of Rpd3 and Hos2 of Saccharomyces. These proteins belong to the class 1 histone deacetylase (HDAC) family. The phylogenetic tree showed that the Clr6, Hos2, and Rpd3 lineages are separated in fungal HDACs. Basidiomycetes have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. On the other hand, whereas ascomycetes except for Schizosaccharomyces have the Hos2 and Rpd3 homologs, and lack the Clr6 homolog, Schizosaccharomyces has the Clr6 and Hos2 homologs, and lacks the Rpd3 homolog. Interestingly, Pneumocystis and Saitoella have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. Thus, these fungi are the first ascomycete found to possess all 3 types. Our findings indicated that Taphrinomycotina has conserved the Clr6 protein, suggesting that the ancestor of Dikarya (ascomycetes and basidiomycetes) had 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. During ascomycete evolution, Pezizomycotina and Saccharomycotina appear to have lost their Clr6 homologs and Schizosaccharomyces to have lost its Rpd3 homolog.Key words: ascomycetes; basidiomycetes; histone deacetylase; Saitoella complicata; Schizosaccharomyces IntroductionThe subphylum Taphrinomycotina ( Archiascomycetes ) is the earliest ascomycetous lineage that diverged before the separation of the subphyla Pezizomycotina ( Euascomycetes ) and Saccharomycotina ( Hemiascomycetes ) (Nishida and Sugiyama, 1993;An et al., 2002;Liu et al., 2009;Schoch et al., 2009). Genome analyses of ascomycetes belonging to Taphrinomycotina are central to the elucidation of ascomycetes evolution. At present, genome information on Taphrinomycotina is limited to that of species belonging to the genus Schizosaccharomyces (Wood et al., 2002;Rhind et al., 2011). The anamorphic and saprobic yeast Saitoella complicata is a member of Taphrinomycotina which has been isolated from Himalayan soil . Although Schizosaccharomyces is a fission yeast, Saitoella is a budding yeast. Saitoella complicata shares some characteristics with both ascomycetous and basidiomycetous yeasts (Sugiyama et al., 1985;Goto et al., 1987). For example, a negative diazonium blue B reaction and negative extracellular deoxyribonuclease activity are characteristics of ascomycetous yeasts, whereas positive urease activity, the major ubiquinone system Q-10, and enteroblastic budding are traits of basidiomycetous yeasts (Sugiyama et al., 1985;Goto et al., 1987). Based on 18S ribosomal DNA sequence comparison, Saitoella complicata forms a monophyletic lineage with Schizosaccharomyces pombe and Taphrina Full PaperThe early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages (Received July 17, 2013; Acc...

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Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory

Cited by 398 publications

References 74 publications

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

A multigene phylogeny of the Dothideomycetes using four nuclear loci

The early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages

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