Didymellaceae revisited

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The Didymellaceae is one of the most species-rich families in the fungal kingdom, and includes species that inhabit a wide range of ecosystems. The taxonomy of Didymellaceae has recently been revised on the basis of multi-locus DNA sequence data. In the present study, we investigated 108 Didymellaceae isolates newly obtained from 40 host plant species in 27 plant families, and various substrates from caves, including air, water and carbonatite, originating from Argentina, Australia, Canada, China, Hungary, Israel, Italy, Japan, South Africa, the Netherlands, the USA and former Yugoslavia. Among these, 68 isolates representing 32 new taxa are recognised based on the multi-locus phylogeny using sequences of LSU, ITS, rpb2 and tub2, and morphological differences. Within the Didymellaceae, five genera appeared to be limited to specific host families, with other genera having broader host ranges. In total 19 genera are recognised in the family, with Heracleicola being reduced to synonymy under Ascochyta. This study has significantly improved our understanding on the distribution and biodiversity of Didymellaceae, although the placement of several genera still need to be clarified.

Related collections

Most cited references 38

Record: found
Abstract: found
Article: not found

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.

0 comments Cited 4045 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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

M.M. Aveskamp, J. de Gruyter, J.H.C. Woudenberg … (2010)

Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the β-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.

0 comments Cited 157 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach.

Deuk Sung, Joseph Spatafora, Jace W. Jones … (2007)

Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). These data were analyzed in a complete 66-taxon matrix and 91-taxon supermatrix that included some missing data. Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e., Clavicipitaceae clade A, B, and C), whereas the tree obtained from mtATP6 is in strong conflict with the monophyly of Clavicipitaceae clade B and the sister-group relationship of Hypocreaceae and Clavicipitaceae clade C. The distribution of relative contribution of nodal support for each gene partition was assessed using both partitioned Bremer support (PBS) values and combinational bootstrap (CB) analyses, the latter of which analyzed bootstrap proportions from all possible combinations of the seven gene partitions. These results suggest that CB analyses provide a more consistent estimate of nodal support than PBS and that combining heterogeneous gene partitions, which individually support a limited number of nodes, results in increased support for overall tree topology. Analyses of the 91-taxa supermatrix data sets revealed that some nodes were more strongly supported by increased taxon sampling. Identifying the localized incongruence of mtATP6 and analyses of complete and supermatrix data sets strengthen the evidence for rejecting the monophyly of Clavicipitaceae and much of the current subfamilial classification of the family. Although the monophyly of the grass-associated subfamily Clavicipitoideae (e.g., Claviceps, Balansia, and Epichloë) is strongly supported, the subfamily Cordycipitoideae (e.g., Cordyceps and Torrubiella) is not monophyletic. In particular, species of the genus Cordyceps, which are pathogens of arthropods and truffles, are found in all three clavicipitaceous clades. These results imply that most characters used in the current familial classification of Clavicipitaceae are not diagnostic of monophyly.

0 comments Cited 152 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

P.W. Crous

L. Cai

Journal

Journal ID (nlm-ta): Stud Mycol

Journal ID (iso-abbrev): Stud. Mycol

Title: Studies in Mycology

Publisher: CBS Fungal Biodiversity Centre

ISSN (Print): 0166-0616

ISSN (Electronic): 1872-9797

Publication date PMC-release: 09 June 2017

Publication date (Print): June 2017

Publication date (Electronic): 09 June 2017

Volume: 87

Pages: 105-159

Affiliations

[1 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

[2 ]College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China

[3 ]Ningbo Academy of Inspection and Quarantine, Ningbo 315012, China

[4 ]Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands

[5 ]Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

Author notes

[∗ ] Correspondence: P.W. Crous; L. Cai p.crous@ 123456westerdijkinstitute.nl cail@ 123456im.ac.cn

Article

Publisher ID: S0166-0616(17)30025-8

DOI: 10.1016/j.simyco.2017.06.002

PMC ID: 5498420

PubMed ID: 28706324

SO-VID: 1e4f1a50-7d1f-406e-adb7-6acbbece0e5c

License:

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

History

Categories

Subject: Research Paper

ScienceOpen disciplines: Plant science & Botany

Data availability:

ScienceOpen disciplines: Plant science & Botany

Didymellaceae revisited

Read this article at

Abstract

Related collections

Plant MYBs

Most cited references 38

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

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

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach.

Author and article information

Contributors

Journal

Affiliations

Author notes

Article

History

Categories

Comments

Comment on this article

Similar content 11

Cited by 77

Most referenced authors 1,182