Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus

Novel Evolutionary Lineages Revealed in the Chaetothyriales (Fungi) Based on Multigene Phylogenetic Analyses and Comparison of ITS Secondary Structure

<div><p><i>Cyphellophora</i> and <i>Phialophora</i> (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (<i>mcm7</i>) and second largest subunit of RNA polymerase II (<i>rpb2</i>). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-<i>rpb2</i>-<i>mcm7</i>, define a robust clade containing eight species of <i>Cyphellophora</i> (including the type) and six species of <i>Phialophora</i>. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. <i>Cyphellophora</i> is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in <i>Cyphellophora</i> are proposed and a dichotomous key to species accepted in the genus is provided. <i>Cyphellophora eugeniae</i> and <i>C. hylomeconis</i>, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.</p></div

Partial secondary structure of ITS1 rRNA molecule showing three helices (H1–H3).

<p>A) Partial 2D structure of <i>Phialophora verrucosa</i>. All substitutions recorded among representatives of the Cyphellophoraceae, Herpotrichiellaceae and members of the <i>Vonarxia</i>-group are mapped on the 2D model. B) Partial 2D structure of <i>Cyphellophora laciniata</i>. Variability in the 2D structure among members of the <i>Cyphellophoraceae</i> and two other taxa, <i>A. eugeniae</i> and <i>C. hylomeconis</i>, segregated from <i>Cyphellophora</i>, is recorded on the 2D model. Abbreviations: HERP  =  Herpotrichiellaceae, CYPH  =  Cyphellophoraceae, VRXG  =  <i>Vonarxia</i>-group. Parts of hairpin loops highlighted with gray color represent regions with variable number of nucleotides. The legend to symbols and colors is included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0063547#pone-0063547-g006" target="_blank">Figure 6</a>.</p

<i>Camptophora hylomeconis</i>, a foliicolous species with sickle-shaped septate conidia.

<p>Living culture with a detail of the center of the colony having a yeast-like appearance (A, B), intercalary phialides with conidia (C, D), a detail of conspicuous phialidic loci that can proliferate percurrently above the collarette (arrows indicate the proliferation, E–F), anastomosing conidia (I, J), and sickle-shaped or sigmoid septate conidia (K, L). DIC (D–F, H–K), PC (C, G, L), bar  =  10 µm. CBS 113311 (ex-type).</p

Multilocus phylogenetic analysis of the nuc28S-nuc18S-<i>rpb2</i>-<i>mcm7</i> sequences of 45 members of the Chaetothyriales.

<p>Phylogram inferred from the ML analysis with RAxML using the Gtrcat model of evolution. Taxa in bold refer to new combinations or new taxonomic treatments.</p