A class-wide phylogenetic assessment of Dothideomycetes

@article{Schoch2009ACP,
  title={A class-wide phylogenetic assessment of Dothideomycetes},
  author={Conrad L. Schoch and Pedro W. Crous and J.Z. Groenewald and Eric W.A. Boehm and Treena I. Burgess and Johannes de Gruyter and G. Sybren de Hoog and Linley J. Dixon and Martin Grube and C{\'e}cile Gueidan and Yukio Harada and Satoshi Hatakeyama and Kazuyuki Hirayama and Tsuyoshi Hosoya and Sabine M. Huhndorf and Kevin David Hyde and Evan B. Gareth Jones and J. J. Kohlmeyer and {\AA}sa Kruys and Y.M. Li and Robert L{\"u}cking and H. Thorsten Lumbsch and Ludmila Marvanová and Joelle Mbatchou and Alfred McVay and Andrew N. Miller and George K. Mugambi and Lucia Muggia and Matthew P. Nelsen and P. Nelson and C A. Owensby and Alan J. L. Phillips and Souwalak Phongpaichit and Stephen Brian Pointing and Val{\'e}rie Pujade-Renaud and Huzefa A. Raja and Eimy Rivas Plata and Barbara Robbertse and Constantino Ruibal and Jariya Sakayaroj and Teruo Sano and Laura Selbmann and Carol A. Shearer and Takashi Shirouzu and Bernard Slippers and Satinee Suetrong and K. Tanaka and Brigitte Volkmann-Kohlmeyer and M. J. Wingfield and Alan R. Wood and Joyce H. C. Woudenberg and Hiroaki Yonezawa and Y. Zhang and Joseph W. Spatafora},
  journal={Studies in Mycology},
  year={2009},
  volume={64},
  pages={1 - 15-S10}
}
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… 

Figures and Tables from this paper

Macro- and microevolutionary perspectives on Seynesiella juniperi, a fungus in the Venturiales (Dothideomycetes, Ascomycota)

Combining phylogenetics and multi-locus delimitation analyses, together with more detailed measurements of ascospores, will be fundamental for a better understanding of species boundaries and the biogeographic history of the delimited species, as well as for revealing more specific fungal-plant association patterns.

Genomic and comparative analysis of the class Dothideomycetes

The class Dothideomycetes is a recently defined taxon within the phylum Ascomycota, with approximately 20 000 member species. Many species are important phytopathogens employing diverse pathogenicity

Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies

It is confirmed that most rock inhabiting-fungi (RIF) are highly polyphyletic among Dothideomycetidae, mainly within the order Capnodiales, an order otherwise incorporating several families of major plant pathological importance.

New Dothideomycetes from Freshwater Habitats in Spain

Six strains of plant debris collected from various freshwater locations in Spain were identified as new species to science and significantly increases the number of the coelomycetous fungi that have been described from freshwater habitats.

Wiesneriomyces a new lineage of Dothideomycetes (Ascomycota) basal to Tubeufiales

The Wiesneriomyces clade is elevated to a higher taxonomic rank, the family Wieseriomycetaceae, based on cultural, morphological and multi-gene phylogenetic evidence, and forms a sister lineage to Tubeufiales with strong support.

Dark septate endophytic pleosporalean genera from semiarid areas

This study investigates three unidentified DSE lineages belonging to Pleosporales that were found previously in semiarid sandy grasslands, and manages for the first time to induce several DSE to form their sexual morphs.

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

A phylogenomic approach is used to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages.

Evolution of lifestyles in Capnodiales

Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus Phoma to be highly polyphyletic.

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations.
...

References

SHOWING 1-10 OF 112 REFERENCES

A class-wide phylogenetic assessment of Dothideomycetes Schoch,

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.

The search for the fungal tree of life.

Phylogenetic Relationships Among Taxa in the Jahnulales Inferred From 18S and 28S Nuclear Ribosomal DNA Sequences

A molecular study carried out using 18S and 28S rDNA sequence data from 15 species representing the four genera in the Jahnulales suggested that the presence of very wide, brown, septate hyphae is an important character defining the J Kahnulales.

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.

A 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi, and a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions support a terrestrial, saprobic ecology as ancestral are presented.

Phylogenomics reveal a robust fungal tree of life.

The single tree that is inferred from the dataset showed excellent nodal support for each branch, suggesting that it reflects the true phylogenetic relationships of the species involved, and is based on the analysis of full genomes.

Phylogenetic relationships and an assessment of traditionally used taxonomic characters in the Sporormiaceae (Pleosporales, Dothideomycetes, Ascomycota), utilising multi‐gene phylogenies

The aims of this study were to resolve the phylogenetic relationships within the Sporormiaceae, test the current generic classification, and study the utility of traditional characters for the taxonomy in the group.

Phylogenetic lineages in the Capnodiales

It is concluded that the strictly plant pathogenic, nectrotrophic families evolved from saprobic ancestors (Capnodiaceae), which is the more primitive state.

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.

The phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi and conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

Molecular data place Trypetheliaceae in Dothideomycetes.

...