| 1. |
- Binder, Manfred, et al.
(författare)
-
Phylogenetic and phylogenomic overview of the Polyporales
- 2013
-
Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 105:6, s. 1350-1373
-
Tidskriftsartikel (refereegranskat)abstract
- We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000–49 900 00 bp and encode for 12 910–16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.
|
|
| 2. |
- Miettinen, Otto, et al.
(författare)
-
Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)
- 2012
-
Ingår i: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 28:3, s. 251-270
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogeny of the poroid and hydnoid genera Antrodia, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2 and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer that 15 genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinaceae in shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within Steccherinaceae.
|
|
| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
Rethinking taxon sampling in the light of environmental sequencing
- 2011
-
Ingår i: Cladistics. - : Wiley. - 1096-0031 .- 0748-3007. ; 27:2, s. 197-203
-
Tidskriftsartikel (refereegranskat)abstract
- Environmental DNA sequencing efforts of substrates such as soil, wood, and seawater have been found to present very different views of the underlying biological communities compared with efforts based on morphological examination and culture studies. The taxonomic affiliation of many of these environmental sequences cannot be settled with certainty due to the lack of proximate reference sequences in the corpus of public sequence data, and they are typically submitted to the international sequence databases without much indication of their relatedness. The scientific community has proved reluctant to include such unnamed sequences in phylogenetic analyses and taxonomic studies, but the present study shows such a position to be not only largely unwarranted but also potentially unsound. The sequences of 48 published fungal alignments of the nuclear ribosomal internal transcribed spacer region were subjected to similarity searches in the sequence databases to recover environmental sequences with a clear bearing on the respective ingroup. An average of 20 environmental sequences were added to each alignment, and upon rerunning the phylogenetic analyses of each study we found that topological rearrangements involving the original ingroup sequences were observed for no less than 29 (60%) of the studies. In nearly 20% of these cases, the rearrangements were large enough to question or even overthrow at least one conclusion presented in the original studies. The basal branching order was similarly subject to changes in 16% of the applicable studies. Environmental sequences are thus not only relevant in ecological research but form a requisite source of information also in systematics and taxonomy.
|
|
| 4. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
- 2009
-
Ingår i: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 296:1, s. 97-101
-
Tidskriftsartikel (refereegranskat)abstract
- The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.
|
|
| 5. |
- Ryberg, Martin, 1976, et al.
(författare)
-
An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity
- 2009
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 181:2, s. 471-477
-
Tidskriftsartikel (refereegranskat)abstract
- The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using BLAST. The results are made available as a biweekly updated web service that can be queried to retrieve all insufficiently identified sequences (IIS) associated with any fungal genus. The most commonly available annotation items in GenBank are isolation source (55%); country of origin (50%); and specific host (38%). The molecular sampling of fungi shows a bias towards North America, Europe, China, and Japan whereas vast geographical areas remain effectively unexplored. Mycorrhizal and parasitic genera are on average associated with more IIS than are saprophytic taxa. Glomus, Alternaria, and Tomentella are the genera represented by the highest number of insufficiently identified ITS sequences in GenBank. The web service presented (http://andromeda.botany.gu.se/emerencia.html#genus_search) offers new means, particularly for mycorrhizal and plant pathogenic fungi, to examine the IIS in GenBank in a taxon-oriented framework and to explore their metadata in an easily accessible and time-efficient manner.
|
|
| 6. |
- Sjökvist, Elisabet, 1982, et al.
(författare)
-
A multi-locus phylogeny of the Polyporales
- 2009
-
Ingår i: Abstract Book, Botany & Mycology, Snowbird, Utah, July 25-29. ; 2009
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The recently redefined order Polyporales consists of roughly 1800 species of primarily polyporoid and corticioid fungi. Previous studies on the polyporoid clade have only used sequences from one or a few rDNA genes, resulting in phylogenies with low support on branches. This study aims to identify higher-level relationships within Polyporales using multi-locus phylogenies. For this purpose two matrices were composed. One is a matrix with gene markers RPB2, EF1-α, nLSU, 5.8S and mtSSU, for 53 in-group taxa. The other a super-matrix with RPB2, EF1-α, SSU, nLSU, 5.8S, mtSSU, and ATP6, for 84 in-group taxa. Preliminary analyses on the smaller dataset result in a strong support for the order in Bayesian analysis, but with only moderate support in Jackknife analysis. Several high-support clades could be identified in both analyses, which we temporarily acknowledge as Byssomeruliaceae, Fomitopsidaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae and Steccherinaceae. However, several taxa remain that in Bayesian analysis show little affinity to other taxa, and in Jackknife analysis little or no affinity to other taxa. The commonly identified Antrodia clade, core polyporoid clade, phlebioid clade and residual polyporoid clade are discussed. This study is the first to present a comprehensive family-level multi-locus phylogeny of the Polyporales.
|
|
| 7. |
- Sjökvist, Elisabet, 1982
(författare)
-
Polyporales - försök till en ny klassificering
- 2009
-
Ingår i: Svensk Mykologisk Tidskrift. Redaktör Mikael Jeppson.. ; 30: 2009:3, s. 2-4
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- A new classification of Polyporales. The author gives a brief account of her on-going studies in Polyporales aiming at a new syste- matic classification based of molecular data.
|
|
| 8. |
- Sjökvist, Elisabet, 1982, et al.
(författare)
-
Stereopsidales - a new order of mushroom-forming fungi
- 2014
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4
-
Tidskriftsartikel (refereegranskat)abstract
- One new order, one new family, and one new combination are presented, as the result of molecular phylogenetic analyses. The new order Stereopsidales and the new family Stereopsidaceae are described incorporating Stereopsis radicans and S. globosa, formerly Clavulicium globosum. We show that not only do these species represent an old overlooked lineage, but both species harbor cryptic diversity. In addition, a third species, C. macounii, appears as a plausible sister to the new lineage, but there is conflict in the data. All specimens of S. radicans and S. globosa analysed here are from the South and Central Americas; several records of S. radicans have been made also from tropical Asia. We expect the true diversity in this group to be a lot higher than presented in this paper. Stereopsis radicans was formerly included in Polyporales, but a placement within that order is rejected by our data through SH tests. The dataset consisted of four nuclear markers: rpb2, tef1, LSU and SSU, each of which was analysed separately using maximum likelihood and Bayesian inference. Recombination detection tests indicate no plausible recombinations. The potential of S. radicans, S. globosa and C. macounii being amphitallic is briefly discussed.
|
|
| 9. |
- Sjökvist, Elisabet, 1982, et al.
(författare)
-
Stipitate stereoid basidiocarps have evolved multiple times
- 2012
-
Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 104:5, s. 1046-1055
-
Tidskriftsartikel (refereegranskat)abstract
- Stipitate stereoid fungi are Basidiomycetes with a stipe, a spathulate- to funnel-shaped pileus, a smooth hymenophore, and hyaline, smooth spores. Representatives of the genera Cotylidia, Cymatoderma, Muscinupta, Podoscypha and Stereopsis were subjected to molecular phylogenetic analyses based on nuclear ribosomal large subunit, 5.8S and ITS sequences. For four of the genera the type species was included in analyses. Stereopsis radicans, the type species of Stereopsis, forms a lineage with the corticioid species Clavulicium globosum but could not be placed in any of the presently accepted orders within Agaricomycotina. Stereopsis vitellina falls within the Atheliales, making it the first pileus- and stipe-forming fungus recovered in this order. Cotylidia and Muscinupta again are shown to be members of the Hymenochaetales, whereas Cymatoderma and Podoscypha belong in the Polyporales. Cymatoderma is polyphyletic and Cymatoderma sensu stricto is separated from other stipitate stereoid fungi in the Polyporales, whereas the remaining Cymatoderma species are nested within a well supported clade holding all Podoscypha species but also Abortiporus biennis.
|
|
