| 1. |
- Ahrén, Dag, et al.
(författare)
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Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum
- 2005
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Ingår i: Microbiology. - : Microbiology Society. - 1465-2080 .- 1350-0872. ; 151:3, s. 789-803
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Tidskriftsartikel (refereegranskat)abstract
- Nematode-trapping fungi enter the parasitic stage by developing specific morphological structures called traps. The global patterns of gene expression in traps and mycelium of the fungus Monacrosporium haptotylum were compared. The trap of this fungus is a unicellular spherical structure called the knob, which develops on the apex of a hyphal branch. RNA was isolated from knobs and mycelium and hybridized to a cDNA array containing probes of 2822 EST clones of M. haptotylum. Despite the fact that the knobs and mycelium were grown in the same medium, there were substantial differences in the patterns of genes expressed in the two cell types. In total, 23(.)3% (657 of 2822) of the putative genes were differentially expressed in knobs versus mycelium. Several of these genes displayed sequence similarities to genes known to be involved in regulating morphogenesis and cell polarity in fungi. Among them were several putative homologues for small GTPases, such as rho1, rac1 and ras1, and a rho GDP dissociation inhibitor (rdi1). Several homologues to genes involved in stress response, protein synthesis and protein degradation, transcription, and carbon metabolism were also differentially expressed. In the last category, a glycogen phosphorylase (gph1) gene homologue, one of the most upregulated genes in the knobs as compared to mycelium, was characterized. A number of the genes that were clifferentially expressed in trap cells are also known to be regulated during the development of infection structures in plant-pathogenic fungi. Among them, a gas1 (mas3) gene homologue (designated gks1), which is specifically expressed in appressoria of the rice blast fungus, was characterized.
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| 2. |
- Ahrén, Dag, et al.
(författare)
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Evolution of parasitism in nematode-trapping fungi
- 2003
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Ingår i: Journal of Nematology. - 0022-300X. ; 35:2, s. 194-197
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Konferensbidrag (refereegranskat)abstract
- We are studying the evolution of parasitism in a group of soil-living ascomycetes that can grow as saprophytes as well as parasites by forming special morphological structures called traps. Analyses of 18S ribosomal DNA sequences have shown that these fungi form a monophyletic and isolated clade among the ascomycetes. The phylogenetic patterns within this clade are concordant with the morphology of the traps and separate species having adhesive traps (nets, knobs, and branches) from those having constricting rings. This suggests that these nematode-trapping fungi have a common ancestor, and that the ability to capture nematodes has been an important trait for further speciation and diversification within the clade. To obtain information on the genomic basis for this pattern, we recently started a large-scale sequencing project of the nematode-trapping fungus Monacrosporium haptotylum. This will allow the identification of genes uniquely expressed during the development of traps, and elucidate the molecular evolution Of Such genes within the nematode-trapping fungi clade.
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| 3. |
- Ahrén, Dag
(författare)
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Genomic Diversity and Evolution of Parasitism in Nematode-trapping Fungi
- 2001
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Nematode-trapping fungi are soil-living organisms that have the ability to form infection structures, traps to capture nematodes. Many nematode species are parasites on plants and animals, which have resulted in an interest to use the nematode-trapping fungi as biological control agents. In order to understand more about the genomic diversity and evolution of parasitism among these fungi, several studies based on DNA sequence analysis were conducted. First, a phylogenetic tree was reconstructed using 18S ribosomal DNA (rDNA) sequences in order to classify and identify phylogenetic relationships between different species of nematode-trapping fungi. The obtained data was congruent with the trap morphology and it was revealed that the nematode-trapping fungi form a monophyletic clade, i. e. they have a common ancestor. Second, a population study of Duddingtonia flagrans, one of the most promising species for biological control of animal parasitic nematodes, was undertaken. The divergence of isolates from a worldwide collection as well as the mode of reproduction, dispersion and biogeography was investigated by using various DNA markers. The divergence time was estimated to 44000 years ago. Furthermore, it was found that the species has a clonal reproduction. There was no geographic pattern in the distribution of various genotypes, which indicates that D. flagrans has dispersed multiple times. Finally, a comparative transcriptome analysis was started using the nematode-trapping fungus Monacrosporium haptotylum. In total 4767 expressed sequence tags (ESTs) representing 2000 tentatively unique genes were sequenced from three different cDNA libraries: vegetative mycelium, developed traps, and traps infecting the model nematode Caenorhabditis elegans. The patterns of genes expressed in the different growth stages was to a large extent unique, only 7.6% of the sequenced transcripts were detected in more then one cDNA library. To comprehensively analyze the sequences, a web-based bioinformatic tool was developed. The software stores, perform similarity searches against an automatically downloaded protein database (non-redundant, GenBank) and displays the result in images as well as tables. Comparative analyses of annotated sequences indicated a number of differences in metabolic and cellular functions between the vegetative mycelium, knobs and fungus infecting C. elegans.
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| 4. |
- Ahrén, Dag, et al.
(författare)
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Low genetic diversity among isolates of the nematode-trapping fungus Duddingtonia flagrans: evidence for recent worldwide dispersion from a single common ancestor
- 2004
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Ingår i: Mycological Research. - 0953-7562. ; 108, s. 1205-1214
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Tidskriftsartikel (refereegranskat)abstract
- The genetic variation of Duddingtonia flagrans, which has become a promising biocontrol agent of animal parasitic nematodes, was investigated in a worldwide collection of 22 isolates. We analysed the sequence variation in four nuclear genes, tubA (beta-tubulin), CMD1 (calmodulin), EF1alpha (translation elongation factor 1alpha), and PII (extracellular serine protease). 1428 aligned base pairs (bp) were analysed from the four genes, including 709 bp of introns. In addition, the variations in three anonymous genomic regions comprising 1155 bp were examined. Three single nucleotide polymorphisms (SNPs) were detected in the seven loci, none of them in the protein encoding genes. The genetic variation was significantly higher in the nematode-trapping fungus Arthrobotrys oligospora, the closest evolutionary relative to D. flagrans. Analysis of 12 isolates of A. oligospora revealed 30 SNPs in tub A, CMD1, EF1alpha and PII. The genetic variation in the isolates of D. flagrans was further examined using AFLP analysis. Five primer combinations were used to detect 159 bands, of which 94 (59.1%) were polymorphic. A neighbour-joining tree based on the AFLP data showed no clear association between genotype and geographical origin. Furthermore, the AFLP data suggest that D. flagrans is mainly clonal and no recombination could be detected, not even within the same country. The low genetic variation in D. flagrans suggests that this fungus has recently diverged from a single progenitor. Based on estimations of mutation rates, it was calculated that this most recent common ancestor lived about 16000-23000 years ago.
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| 5. |
- Ahrén, Dag, et al.
(författare)
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PHOREST: a web-based tool for comparative analyses of expressed sequence tag data
- 2004
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Ingår i: Molecular Ecology Notes. - : Wiley. - 1471-8278 .- 1471-8286. ; 4:2, s. 311-314
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of expressed sequence tags is becoming an important tool in molecular ecology for comparing gene expression in organisms grown in certain environments. Additionally, expressed sequence tag database information can be used for the construction of DNA microarrays and for the detection of single nucleotide polymorphisms. For such applications, we present PHOREST, a web-based tool for managing, analysing and comparing various collections of expressed sequence tags. It is written in PHP (PHP: Hypertext Preprocessor) and runs on UNIX, Microsoft Windows and Macintosh (Mac OS X) platforms.
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| 6. |
- 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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| 7. |
- Andersson, Karl-Magnus, et al.
(författare)
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Interspecific and host-related gene expression patterns in nematode-trapping fungi.
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii).
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| 8. |
- Andersson, Karl-Magnus, et al.
(författare)
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Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
- 2013
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Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 79:16, s. 4993-5004
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Tidskriftsartikel (refereegranskat)abstract
- Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called knob that develops at the apex of a hyphae. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and LC-MS/MS. The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 being expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown function and putative cell surface adhesins containing carbohydrate-binding domains including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs to experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection, and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.
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| 9. |
- Annenkova, Nataliia V., et al.
(författare)
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Delineating closely related dinoflagellate lineages using phylotranscriptomics
- 2018
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Ingår i: Journal of Phycology. - : Wiley. - 0022-3646. ; 54:4, s. 571-576
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Tidskriftsartikel (refereegranskat)abstract
- Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A. aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A. malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A. aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species’ relationships.
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| 10. |
- Aureli, Lorenzo, et al.
(författare)
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Geography and environmental pressure are predictive of class-specific radioresistance in black fungi
- 2023
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Ingår i: Environmental Microbiology. - 1462-2920. ; 25:12, s. 2931-2942
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Tidskriftsartikel (refereegranskat)abstract
- Black fungi are among the most resistant organisms to ionizing radiation on Earth. However, our current knowledge is based on studies on a few isolates, while the overall radioresistance limits across this microbial group and the relationship with local environmental conditions remain largely undetermined. To address this knowledge gap, we assessed the survival of 101 strains of black fungi isolated across a worldwide spatial distribution to gamma radiation doses up to 100 kGy. We found that intra and inter-specific taxonomy, UV radiation, and precipitation levels primarily influence the radioresistance in black fungi. Altogether, this study provides insights into the adaptive mechanisms of black fungi to extreme environments and highlights the role of local adaptation in shaping the survival capabilities of these extreme-tolerant organisms.
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