67 research outputs found
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic
A molecular phylogenetic reappraisal of the Hysteriaceae, Mytilinidiaceae and Gloniaceae (Pleosporomycetidae, Dothideomycetes) with keys to world species
A reappraisal of the phylogenetic integrity of bitunicate ascomycete fungi
belonging to or previously affiliated with the Hysteriaceae,
Mytilinidiaceae, Gloniaceae and Patellariaceae is
presented, based on an analysis of 121 isolates and four nuclear genes, the
ribosomal large and small subunits, transcription elongation factor 1 and the
second largest RNA polymerase II subunit. A geographically diverse and high
density taxon sampling strategy was employed, including multiple
isolates/species from the following genera: Anteaglonium (6/4),
Encephalographa (1/1), Farlowiella (3/1),
Gloniopsis (8/4), Glonium (4/2), Hysterium (12/5),
Hysterobrevium (14/3), Hysterographium (2/1),
Hysteropatella (2/2), Lophium (4/2), Mytilinidion
(13/10), Oedohysterium (5/3), Ostreichnion (2/2),
Patellaria (1/1), Psiloglonium (11/3), Quasiconcha
(1/1), Rhytidhysteron (8/3), and 24 outgroup taxa. Sequence data
indicate that although the Hysteriales are closely related to the
Pleosporales, sufficient branch support exists for their separation
into separate orders within the Pleosporomycetidae. The
Mytilinidiales are more distantly related within the subclass and
show a close association with the Gloniaceae. Although there are
examples of concordance between morphological and molecular data, these are
few. Molecular data instead support the premise of a large number of
convergent evolutionary lineages, which do not correspond to previously held
assumptions of synapomorphy relating to spore morphology. Thus, within the
Hysteriaceae, the genera Gloniopsis, Glonium,
Hysterium and Hysterographium are highly polyphyletic. This
necessitated the transfer of two species of Hysterium to
Oedohysterium gen. nov. (Od. insidens comb.
nov. and Od. sinense comb. nov.), the description of a new
species, Hysterium barrianum sp. nov., and the transfer of
two species of Gloniopsis to Hysterobrevium gen.
nov. (Hb. smilacis comb. nov. and Hb.
constrictum comb. nov.). While Hysterographium, with
the type Hg. fraxini, is removed from the Hysteriaceae, some
of its species remain within the family, transferred here to
Oedohysterium (Od. pulchrum comb. nov.),
Hysterobrevium (Hb. mori comb. nov.) and
Gloniopsis (Gp. subrugosa comb. nov.); the latter
genus, in addition to the type, Gp. praelonga, with two new species,
Gp. arciformis sp. nov. and Gp. kenyensis sp. nov.
The genus Glonium is now divided into Anteaglonium
(Pleosporales), Glonium (Gloniaceae), and
Psiloglonium (Hysteriaceae). The hysterothecium has evolved
convergently no less than five times within the Pleosporomycetidae
(e.g., Anteaglonium, Farlowiella, Glonium,
Hysterographium and the Hysteriaceae). Similarly,
thin-walled mytilinidioid (e.g., Ostreichnion) and patellarioid
(e.g., Rhytidhysteron) genera, previously in the
Mytilinidiaceae and Patellariaceae, respectively,
transferred here to the Hysteriaceae, have also evolved at least
twice within the subclass. As such, character states traditionally considered
to represent synapomorphies among these fungi, whether they relate to spore
septation or the ascomata, in fact, represent symplesiomorphies, and most
likely have arisen multiple times through convergent evolutionary processes in
response to common selective pressures
Molecular systematics of the marine Dothideomycetes
Phylogenetic analyses of four nuclear genes, namely the large and small subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha and the second largest RNA polymerase II subunit, established that the ecological group of marine bitunicate ascomycetes has representatives in the orders Capnodiales, Hysteriales, Jahnulales, Mytilinidiales, Patellariales and Pleosporales. Most of the fungi sequenced were intertidal mangrove taxa and belong to members of 12 families in the Pleosporales: Aigialaceae, Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae, Lophiostomataceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae, Testudinaceae and Trematosphaeriaceae. Two new families are described: Aigialaceae and Morosphaeriaceae, and three new genera proposed: Halomassarina, Morosphaeria and Rimora. Few marine species are reported from the Dothideomycetidae (e.g. Mycosphaerellaceae, Capnodiales), a group poorly studied at the molecular level. New marine lineages include the Testudinaceae and Manglicola guatemalensis in the Jahnulales. Significantly, most marine Dothideomycetes are intertidal tropical species with only a few from temperate regions on salt marsh plants (Spartina species and Juncus roemerianus), and rarely totally submerged (e.g. Halotthia posidoniae and Pontoporeia biturbinata on the seagrasses Posidonia oceanica and Cymodocea nodosum). Specific attention is given to the adaptation of the Dothideomycetes to the marine milieu, new lineages of marine fungi and their host specificity
Phylogeny of rock-inhabiting fungi related to Dothideomycetes
The class Dothideomycetes (along with Eurotiomycetes)
includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that
tolerates surprisingly well harsh conditions prevailing on rock surfaces.
Despite their convergent morphology and physiology, RIF are phylogenetically
highly diverse in Dothideomycetes. However, the positions of main
groups of RIF in this class remain unclear due to the lack of a strong
phylogenetic framework. Moreover, connections between rock-dwelling habit and
other lifestyles found in Dothideomycetes such as plant pathogens,
saprobes and lichen-forming fungi are still unexplored. Based on multigene
phylogenetic analyses, we report that RIF belong to Capnodiales
(particularly to the family Teratosphaeriaceae s.l.),
Dothideales, Pleosporales, and Myriangiales, as
well as some uncharacterised groups with affinities to
Dothideomycetes. Moreover, one lineage consisting exclusively of RIF
proved to be closely related to Arthoniomycetes, the sister class of
Dothideomycetes. The broad phylogenetic amplitude of RIF in
Dothideomycetes suggests that total species richness in this class
remains underestimated. Composition of some RIF-rich lineages suggests that
rock surfaces are reservoirs for plant-associated fungi or saprobes, although
other data also agree with rocks as a primary substrate for ancient fungal
lineages. According to the current sampling, long distance dispersal seems to
be common for RIF. Dothideomycetes lineages comprising lichens also
include RIF, suggesting a possible link between rock-dwelling habit and
lichenisation
Phylogenetic lineages in the Capnodiales
The Capnodiales incorporates plant and human pathogens,
endophytes, saprobes and epiphytes, with a wide range of nutritional modes.
Several species are lichenised, or occur as parasites on fungi, or animals.
The aim of the present study was to use DNA sequence data of the nuclear
ribosomal small and large subunit RNA genes to test the monophyly of the
Capnodiales, and resolve families within the order. We designed
primers to allow the amplification and sequencing of almost the complete
nuclear ribosomal small and large subunit RNA genes. Other than the
Capnodiaceae (sooty moulds), and the Davidiellaceae, which
contains saprobes and plant pathogens, the order presently incorporates
families of major plant pathological importance such as the
Mycosphaerellaceae, Teratosphaeriaceae and
Schizothyriaceae. The Piedraiaceae was not supported, but
resolves in the Teratosphaeriaceae. The Dissoconiaceae is
introduced as a new family to accommodate Dissoconium and
Ramichloridium. Lichenisation, as well as the ability to be saprobic
or plant pathogenic evolved more than once in several families, though the
taxa in the upper clades of the tree lead us to conclude that the strictly
plant pathogenic, nectrotrophic families evolved from saprobic ancestors
(Capnodiaceae), which is the more primitive state
Molecular systematics of the marine Dothideomycetes
Phylogenetic analyses of four nuclear genes, namely the large and small
subunits of the nuclear ribosomal RNA, transcription elongation factor 1-alpha
and the second largest RNA polymerase II subunit, established that the
ecological group of marine bitunicate ascomycetes has representatives in the
orders Capnodiales, Hysteriales, Jahnulales,
Mytilinidiales, Patellariales and Pleosporales.
Most of the fungi sequenced were intertidal mangrove taxa and belong to
members of 12 families in the Pleosporales: Aigialaceae,
Didymellaceae, Leptosphaeriaceae, Lenthitheciaceae,
Lophiostomataceae, Massarinaceae, Montagnulaceae,
Morosphaeriaceae, Phaeosphaeriaceae, Pleosporaceae,
Testudinaceae and Trematosphaeriaceae. Two new families are
described: Aigialaceae and Morosphaeriaceae, and three new
genera proposed: Halomassarina, Morosphaeria and
Rimora. Few marine species are reported from the
Dothideomycetidae (e.g. Mycosphaerellaceae,
Capnodiales), a group poorly studied at the molecular level. New
marine lineages include the Testudinaceae and Manglicola
guatemalensis in the Jahnulales. Significantly, most marine
Dothideomycetes are intertidal tropical species with only a few from
temperate regions on salt marsh plants (Spartina species and
Juncus roemerianus), and rarely totally submerged (e.g. Halotthia
posidoniae and Pontoporeia biturbinata on the seagrasses
Posidonia oceanica and Cymodocea nodosum). Specific
attention is given to the adaptation of the Dothideomycetes to the
marine milieu, new lineages of marine fungi and their host specificity
A class-wide phylogenetic assessment of Dothideomycetes
We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU
rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41
families (six newly described in this volume) in Dothideomycetes. All
currently accepted orders in the class are represented for the first time in
addition to numerous previously unplaced lineages. Subclass
Pleosporomycetidae is expanded to include the aquatic order
Jahnulales. An ancestral reconstruction of basic nutritional modes
supports numerous transitions from saprobic life histories to plant associated
and lichenised modes and a transition from terrestrial to aquatic habitats are
confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with
other fungi finds a high level of unique protein associated with the class,
supporting its delineation as a separate taxon
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress
- …