| 1. |
- Larsson, Karl-Henrik, 1948, et al.
(författare)
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High phylogenetic diversity among corticioid homobasidiomycetes
- 2004
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Ingår i: Mycological Research. - 0953-7562. ; 108:9, s. 983-1002
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Tidskriftsartikel (refereegranskat)abstract
- Homobasidiomycetes display a variety of fruit body morphologies. Examples include gilled mushrooms, coral fungi, polypores and puffballs but also species with simple crust-like basidiomata, usually called corticioid fungi. The latter group has largely been neglected in recent studies of homobasidiomycete evolution. The major goal of the present study was to explore the impact that the addition of a wide selection of species with crust-like basidiomata would have on homobasidiomycete phylogeny. Two genes, 5.8S and 28S in the nuclear rDNA repeats, were sequenced and a data set with 178 taxa analysed using neighbour-joining and maximum parsimony methods. Support for clades was evaluated by bootstrap. Basal nodes generally received weak support and branching order for major clades remained largely unresolved. Twelve major groups were recovered and corticioid fungi make up a major or important constituent in most of them. Nine groups are strongly supported but support for euagarics and polyporoid clades is poor. Phlebioid fungi were in earlier studies merged with the polyporoid clade but are here identified as a separate clade. Athelia is allied with ectomycorrhizal genera, inter alia Piloderma and Amphinema, in a separate clade forming a sister group to the boletes. We conclude that corticioid fungi hold a considerable share of the phylogenetic diversity displayed by homobasidiomycetes, and should always be considered when phylogenetic studies of larger basidiomycetes are designed.
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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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galaxie - CGI scripts for sequence identification through automated phylogenetic analysis
- 2004
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 20:9, s. 1447-1452
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Results: Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable.
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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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galaxieEST: addressing EST identity through automated phylogenetic analysis
- 2004
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Ingår i: Bmc Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Research involving expressed sequence tags ( ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. Results: galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download/local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. Conclusions: By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and additional information on the query EST is needed.
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| 4. |
- Parmasto, Erast, et al.
(författare)
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Cortbase version 2 – extensive updates of a nomenclatural database for corticioid fungi (Hymenomycetes)
- 2004
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Ingår i: PhyloInformatics. ; 5, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- Cortbase is a nomenclatural database for corticioid (resupinate) fungi (Corticiaceae s.l. and related hymenomycetes) with basionyms, synonyms, taxonomically correct names, data on name usage, literature references, and evaluation of nomenclatural status. It is available as an on-line service (http://andromeda.botany.gu.se/cortbase.html) and as an MS-DOS executable for local installation. The database includes 8112 species names; of the 4412 basionyms included, 2101 represent taxonomically acceptable species, 1434 are heterotypic synonyms, and 877 are of uncertain application. The improvements over the previous version include the new, platformindependent on-line search interface, some 800 more corticioid names, numerous additions to the existing data, and six new categories for searching, including searches for location of type specimens and for authors of species names.
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