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| 2. |
- Ahrén, Dag, et al.
(författare)
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Phylogeny of nematode-trapping fungi based on 18S rDNA sequences
- 1998
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 158:2, s. 179-184
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Tidskriftsartikel (refereegranskat)abstract
- The small subunit (SSU) ribosomal DNA (18S rDNA) from 15 species of nematode-trapping fungi and closely related non-parasitic species were sequenced. Phylogenetic analysis indicated that species within the genera of Arthrobotrys, Dactylaria, Dactylella, Monacrosporium and Duddingtonia formed a monophyletic and isolated clade among an unresolved cluster of apothecial ascomycetes. The phylogenetic patterns within this clade were not concordant with the morphology of the conidia nor the conidiophores, but rather with that of the infection structures. The results from the different methods of tree reconstruction supported three lineages; the species having constricting rings, the non-parasitic species and the species having various adhesive structures (nets, hyphae, knobs and non-constricting rings) to infect nematodes.
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| 3. |
- Kõljalg, Urmas, et al.
(författare)
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UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
- 2005
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 166:3, s. 1063-1068
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Tidskriftsartikel (refereegranskat)abstract
- Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using BLAST n, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a BLAST search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URLhttp://unite.zbi.ee.
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| 4. |
- 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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| 5. |
- Ursing, Björn M
(författare)
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Phylogeny of Artiodactyla and Cetacea - based on mitochondrial genomes
- 1998
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Artiodactyla (eved-toed ungulates) and Cetacea (whales) are two mammalian orders that are commonly recognised as sistergroups. Recently it has been suggested that Cetacea originated within Artiodactyla, but the relationships among the different artiodactyl lineages and Cetacea have not been conclusively established. In the present study the mitochondrial genome of the pig (Sus scrofa), the hippopotamus (Hippopotamus amphibius), the alpaca (Lama pacos) and the sperm whale (Physeter macrocephalus) have been analysed. These sequences have been used in phylogenetic analyses together with those of two baleen whales, two ruminants and several other eutherian mammals. The study is based on the concatenated nucleotide and amino acid sequences (10,554 and 3,518 characters respectively) of all the mitochondrial protein coding genes except NADH6. Analyses on both data sets identified a basal divergence of the recent artiodactyls into Ruminantia (bovids, deers, tragulids and giraffs), Tylopoda (camels and llamas) and Suina (pigs and peccaries). However, the order in which these lineages diverged was not conclusively resolved. A clade of Ruminatia, Hippopotamidae (hippopotamuses) and Cetacea was identified where the sistergroup relationship between Cetacea and Hippopotamidae was well supported, making both Artiodactyla and Suiformes (pigs, peccaries and hippopotamuses) paraphyletic. Molecular data in conjunction with the palaeontological record have suggested that the primary divergence between recent whales into Odontoceti (toothed whales) and Mysticeti (baleen whales) occured 32-34 million years before present (MYBP). This calibration point suggests that the primary split between Ruminantia, Tylopoda and Suina occured at =65 MYBP, the divergence between Ruminantia and Hippopotamidae/Cetacea at 60 MYBP and the divergence between Hippopotamidae and Cetacea at =55 MYBP.
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