| 1. |
- Abarenkov, Kessy, et al.
(författare)
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PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences
- 2010
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Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 189-196
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.
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| 2. |
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| 3. |
- Ihrmark, Katarina, et al.
(författare)
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Comparative Molecular Evolution of Trichoderma Chitinases in Response to Mycoparasitic Interactions
- 2010
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Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 6, s. 1-25
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Tidskriftsartikel (refereegranskat)abstract
- Certain species of the fungal genus Trichoderma are potent mycoparasites and are used for biological control of fungal diseases on agricultural crops. In Trichoderma, whole-genome sequencing reveal between 20 and 36 different genes encoding chitinases, hydrolytic enzymes that are involved in the mycoparasitic attack. Sequences of Trichoderma chitinase genes chi18-5, chi18-13, chi18-15 and chi18-17, which all exhibit specific expression during mycoparasitism-related conditions, were determined from up to 13 different taxa and studied with regard to their evolutionary patterns. Two of them, chi18-13 and chi18-17, are members of the B1/B2 chitinase subgroup that have expanded significantly in paralog number in mycoparasitic Hypocrea atroviridis and H. virens. Chi18-13 contains two codons that evolve under positive selection and seven groups of co-evolving sites. Chi18-15 displays a unique codon-usage and contains five codons that evolve under positive selection and three groups of co-evolving sites. Regions of high amino acid variability are preferentially localized to substrate-or product side of the catalytic clefts. Differences in amino acid diversity/conservation patterns between different Trichoderma clades are observed. These observations show that Trichoderma chitinases chi18-13 and chi18-15 evolve in a manner consistent with rapid co-evolutionary interactions and identifies putative target regions involved in determining substrate-specificity.
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| 4. |
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| 5. |
- Neumann, Nadja, et al.
(författare)
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Outsourcing the Nucleus : Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes
- 2006
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Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 2, s. 23-34
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Tidskriftsartikel (refereegranskat)abstract
- The nuclear pore complex (NPC) facilitates transport between nucleus and cytoplasm. The protein constituents of the NPC, termed nucleoporins (Nups), are conserved across a wide diversity of eukaryotes. In apparent exception to this, no nucleoporin genes have been identified in nucleomorph genomes. Nucleomorphs, nuclear remnants of once free-living eukaryotes, took up residence as secondary endosymbionts in cryptomonad and chlorarachniophyte algae. As these genomes are highly reduced, Nup genes may have been lost, or relocated to the host nucleus. However, Nup genes are often poorly conserved between species, so absence may be an artifact of low sequence similarity. We therefore constructed an evolutionary bioinformatic screen to establish whether the apparent absence of Nup genes in nucleomorph genomes is due to genuine absence or the inability of current methods to detect homologues. We searched green plant (Arabidopsis and rice), green alga (Chlamydomonas reinhardtii) and red alga (Cyanidioschyzon merolae) genomes, plus two nucleomorph genomes (Bigelowiella natans and Guillardia theta) with profile hidden Markov models (HMMs) from curated alignments of known vertebrate/yeast Nups. Since the plant, algal and nucleomorph genomes all belong to the kingdom Plantae, and are evolutionarily distant from the outgroup (vertebrate/yeast) training set, we use the plant and algal genomes as internal positive controls for the sensitivity of the searches in nucleomorph genomes. We find numerous Nup homologues in all plant and free-living algal species, but none in either nucleomorph genome. BLAST searches using identified plant and algal Nups also failed to detect nucleomorph homologues. We conclude that nucleomorph Nup genes have either been lost, being replaced by host Nup genes, or, that nucleomorph Nup genes have been transferred to the host nucleus twice independently; once in the evolution of the red algal nucleomorph and once in the green algal nucleomorph.
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| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification
- 2008
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Ingår i: Evolutionary Bioinformatics. - 1176-9343. ; 2008:4, s. 193-201
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Tidskriftsartikel (refereegranskat)abstract
- The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequencebased mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3 % threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITSbased species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
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| 7. |
- Norrström, Niclas, et al.
(författare)
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Coevolution of exploiter specialization and victim mimicry can be cyclic and saltational
- 2007
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Ingår i: Evolutionary Bioinformatics. - : Libertas Academica. - 1176-9343. ; 2, s. 35-43
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Tidskriftsartikel (refereegranskat)abstract
- Darwin’s Principle of Divergence explains sympatric speciation as gradual and directional. Contradicting evidence suggests that species’ traits evolve saltationally. Here, we model coevolution in exploiter-victim systems. Victims (resource population) have heritable, mutable cue phenotypes with different levels of defense. Exploiters have heritable, mutable perceptual phenotypes. Our simulations reveal coevolution of victim mimicry and exploiter spe-cialization in a saltational and reversible cycle. Evolution is gradual and directional only in the specialization phase of the cycle. Once linked to assortative mating, exploiter specialization provides conditions for speciation.
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| 8. |
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