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Sökning: WFRF:(Ahrén Dag)

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1.
  • Ahrén, Dag, et al. (författare)
  • Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum
  • 2005
  • Ingår i: Microbiology. - : Microbiology Society. - 1465-2080 .- 1350-0872. ; 151:3, s. 789-803
  • 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)
  • Evolution of parasitism in nematode-trapping fungi
  • 2003
  • Ingår i: Journal of Nematology. - 0022-300X. ; 35:2, s. 194-197
  • 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)
  • Genomic Diversity and Evolution of Parasitism in Nematode-trapping Fungi
  • 2001
  • 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)
  • Low genetic diversity among isolates of the nematode-trapping fungus Duddingtonia flagrans: evidence for recent worldwide dispersion from a single common ancestor
  • 2004
  • Ingår i: Mycological Research. - 0953-7562. ; 108, s. 1205-1214
  • 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)
  • PHOREST: a web-based tool for comparative analyses of expressed sequence tag data
  • 2004
  • Ingår i: Molecular Ecology Notes. - : Wiley. - 1471-8278 .- 1471-8286. ; 4:2, s. 311-314
  • 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)
  • Phylogeny of nematode-trapping fungi based on 18S rDNA sequences
  • 1998
  • Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 158:2, s. 179-184
  • 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)
  • Interspecific and host-related gene expression patterns in nematode-trapping fungi.
  • 2014
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15:1
  • 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)
  • Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
  • 2013
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 79:16, s. 4993-5004
  • 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)
  • Delineating closely related dinoflagellate lineages using phylotranscriptomics
  • 2018
  • Ingår i: Journal of Phycology. - : Wiley. - 0022-3646. ; 54:4, s. 571-576
  • 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)
  • Geography and environmental pressure are predictive of class-specific radioresistance in black fungi
  • 2023
  • Ingår i: Environmental Microbiology. - 1462-2920. ; 25:12, s. 2931-2942
  • 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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11.
  • Belfiori, Lautaro Francisco, et al. (författare)
  • Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson's disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration
  • 2024
  • Ingår i: Frontiers in Aging Neuroscience. - 1663-4365. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • INTRODUCTION: Parkinson's disease (PD) is the second most common neurodegenerative disorder, increasing both in terms of prevalence and incidence. To date, only symptomatic treatment is available, highlighting the need to increase knowledge on disease etiology in order to develop new therapeutic strategies. Hemizygosity for the gene Engrailed-1 ( En1), encoding a conserved transcription factor essential for the programming, survival, and maintenance of midbrain dopaminergic neurons, leads to progressive nigrostriatal degeneration, motor impairment and depressive-like behavior in SwissOF1 (OF1 -En1 +/-). The neurodegenerative phenotype is, however, absent in C57Bl/6j (C57 -En1 +/-) mice. En1 +/- mice are thus highly relevant tools to identify genetic factors underlying PD susceptibility. METHODS: Transcriptome profiles were defined by RNAseq in microdissected substantia nigra from 1-week old OF1, OF1- En1 +/-, C57 and C57- En1 +/- male mice. Differentially expressed genes (DEGs) were analyzed for functional enrichment. Neurodegeneration was assessed in 4- and 16-week old mice by histology. RESULTS: Nigrostriatal neurodegeneration was manifested in OF1- En1 +/- mice by increased dopaminergic striatal axonal swellings from 4 to 16 weeks and decreased number of dopaminergic neurons in the SNpc at 16 weeks compared to OF1. In contrast, C57- En1 +/- mice had no significant increase in axonal swellings or cell loss in SNpc at 16 weeks. Transcriptomic analyses identified 198 DEGs between OF1- En1 +/- and OF1 mice but only 52 DEGs between C57- En1 +/- and C57 mice. Enrichment analysis of DEGs revealed that the neuroprotective phenotype of C57- En1 +/- mice was associated with a higher expression of oxidative phosphorylation-related genes compared to both C57 and OF1- En1 +/- mice. DISCUSSION: Our results suggest that increased expression of genes encoding mitochondrial proteins before the onset of neurodegeneration is associated with increased resistance to PD-like nigrostriatal neurodegeneration. This highlights the importance of genetic background in PD models, how different strains can be used to model clinical and sub-clinical pathologies and provides insights to gene expression mechanisms associated with PD susceptibility and progression.
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12.
  • Dong, Yiran, et al. (författare)
  • Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats
  • 2019
  • Ingår i: Astrobiology. - : MARY ANN LIEBERT, INC. - 1531-1074 .- 1557-8070. ; 19:12
  • Tidskriftsartikel (refereegranskat)abstract
    • The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O-2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.
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13.
  • Ellström, Magnus, et al. (författare)
  • The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus.
  • 2015
  • Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941. ; 91:4
  • Tidskriftsartikel (refereegranskat)abstract
    • The amounts of carbon allocated to the fungal partner in ectomycorrhizal associations can vary substantially depending on the plant growth and the soil nutrient conditions, and the fungus may frequently be confronted with limitations in carbon. We used chemical analysis and transcriptome profiling to examine the physiological response of the ectomycorrhizal fungus Paxillus involutus to carbon starvation during axenic cultivation. Carbon starvation induced a decrease in the biomass. Concomitantly, ammonium, cell-wall material (chitin) and proteolytic enzymes were released into the medium, which suggest autolysis. Compared with the transcriptome of actively growing hyphae, about 45% of the transcripts analyzed were differentially regulated during C-starvation. Induced during starvation were transcripts encoding extracellular enzymes such as peptidases, chitinases, and laccases. In parallel, transcripts of N-transporters were upregulated, which suggest that some of the released nitrogen compounds were re-assimilated by the mycelium. The observed changes suggest that the carbon-starvation response in P. involutus is associated with complex cellular changes that involves autolysis, recycling of intracellular compounds by autophagy and reabsorption of the extracellular released material. The study provides molecular markers that can be used to examine the role of autolysis for the turnover and survival of the ectomycorrhizal mycelium in soils.
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14.
  • Fekete, Csaba, et al. (författare)
  • Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans
  • 2008
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 10:2, s. 364-375
  • Tidskriftsartikel (refereegranskat)abstract
    • The transcriptional response in the parasitic fungus Monacrosporium haptotylum and its nematode host Caenorhabditis elegans were analyzed during infection using cDNA microarrays. The array contained 2,684 fungal and 372 worm gene reporters. Dramatic shifts occurred in the transcriptome of M. haptotylum during the different stages of the infection. An initial transcriptional response was recorded after 1h of infection when the traps adhered to the cuticle, but before immobilization of the captured nematodes. Among the differentially expressed genes were two serine proteases (spr1 and spr2), and several homologues to genes known to be regulated in other pathogenic fungi. After 4 hours, when approximately 40 % of the nematodes were paralyzed, we identified an up-regulated cluster of 372 fungal genes which were not regulated during the other phases of the infection. This cohort contained a large proportion (79%) of genes that appear to be specific for M. haptotylum and closely related species. These genes were of two different classes; those translating into presumably functional peptides and those with no apparent protein coding potential (noncoding RNAs). Among the infection-induced C. elegans genes were those encoding antimicrobial peptides, protease inhibitors and lectins.
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15.
  • Floudas, Dimitrios, et al. (författare)
  • Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi
  • 2020
  • Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 14:8, s. 2046-2059
  • Tidskriftsartikel (refereegranskat)abstract
    • Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.
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16.
  • Gollnisch, Raphael, et al. (författare)
  • Calcium and pH interaction limits bloom formation and expansion of a nuisance microalga
  • 2021
  • Ingår i: Limnology and Oceanography. - : Wiley. - 1939-5590 .- 0024-3590.
  • Tidskriftsartikel (refereegranskat)abstract
    • Microalgal range expansions are increasing in frequency and magnitude but generally remain unnoticed until mass development occurs. Gonyostomum semen is a freshwater raphidophyte that causes nuisance blooms in lakes and has recently expanded its distribution across Europe. G. semen was considered to mainly occur in humic lakes in the boreal region but is now found in high density also in other freshwater habitats on a larger geographic scale with growing incidence. In this study, we focused on which environmental factors limit its expansion. Our hypothesis was that G. semen occurs in many different lake types, except for high alkalinity lakes, in which high pH in combination with high calcium concentration would inhibit its growth. Results from our field study illustrate the environmental heterogeneity of G. semen bloom sites across Europe and the United States. Nevertheless, none of these sites combined high pH and high calcium concentration. In a mesocosm study, as well as a laboratory experiment, we further demonstrated that growth of G. semen is inhibited in conditions combining both high pH and high calcium concentration. We also discuss the function of Sphagnum peat mosses in rendering an alkaline habitat suitable to G. semen growth. Our study highlights that high alkalinity environments act as a major colonization barrier to G. semen. While this finding explains which environmental filters limit G. semen distribution it also helps in understanding its current expansion. With globally decreasing calcium concentrations in freshwater ecosystems, new habitats have and will become conducive to G. semen growth.
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17.
  • Gollnisch, Raphael, et al. (författare)
  • Sag-rad : A Method for Single-Cell Population Genomics of Unicellular Eukaryotes
  • 2023
  • Ingår i: Molecular biology and evolution. - 0737-4038. ; 40:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.
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18.
  • Gollnisch, Raphael, et al. (författare)
  • Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents
  • 2024
  • Ingår i: The Isme Journal. - 1751-7362. ; 18:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.
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19.
  • Hüttner, Silvia, 1984, et al. (författare)
  • Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea
  • 2017
  • Ingår i: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834 .- 1754-6834. ; 10:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The information obtained enables the investigation and discovery of genes encoding proteins involved in plant cell wall degradation, which are crucial for saccharification of lignocellulosic biomass in second-generation biorefinery applications. The thermophilic fungus Malbranchea cinnamomea is an efficient producer of many industrially relevant enzymes and a detailed analysis of its genomic content will considerably enhance our understanding of its lignocellulolytic system and promote the discovery of novel proteins. Results: The 25-million-base-pair genome of M. cinnamomea FCH 10.5 was sequenced with 225x coverage. A total of 9437 protein-coding genes were predicted and annotated, among which 301 carbohydrate-active enzyme (CAZyme) domains were found. The putative CAZymes of M. cinnamomea cover cellulases, hemicellulases, chitinases and pectinases, equipping the fungus with the ability to grow on a wide variety of biomass types. Upregulation of 438 and 150 genes during growth on wheat bran and xylan, respectively, in comparison to growth on glucose was revealed. Among the most highly upregulated CAZymes on xylan were glycoside hydrolase family GH10 and GH11 xylanases, as well as a putative glucuronoyl esterase and a putative lytic polysaccharide monooxygenase (LPMO). AA9-domain-containing proteins were also found to be upregulated on wheat bran, as well as a putative cutinase and a protein harbouring a CBM9 domain. Several genes encoding secreted proteins of unknown function were also more abundant on wheat bran and xylan than on glucose. Conclusions: The comprehensive combined genome and transcriptome analysis of M. cinnamomea provides a detailed insight into its response to growth on different types of biomass. In addition, the study facilitates the further exploration and exploitation of the repertoire of industrially relevant lignocellulolytic enzymes of this fungus.
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20.
  • Ipcho, Simon V S, et al. (författare)
  • Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability.
  • 2012
  • Ingår i: Molecular Plant Pathology. - : Wiley. - 1464-6722. ; 13:6, s. 531-545
  • Tidskriftsartikel (refereegranskat)abstract
    • The wheat pathogen Stagonospora nodorum, causal organism of the wheat disease Stagonospora nodorum blotch, has emerged as a model for the Dothideomycetes, a large fungal taxon that includes many important plant pathogens. The initial annotation of the genome assembly included 16 586 nuclear gene models. These gene models were used to design a microarray that has been interrogated with labelled transcripts from six cDNA samples: four from infected wheat plants at time points spanning early infection to sporulation, and two time points taken from growth in artificial media. Positive signals of expression were obtained for 12 281 genes. This represents strong corroborative evidence of the validity of these gene models. Significantly differential expression between the various time points was observed. When infected samples were compared with axenic cultures, 2882 genes were expressed at a higher level in planta and 3630 were expressed more highly in vitro. Similar numbers were differentially expressed between different developmental stages. The earliest time points in planta were particularly enriched in differentially expressed genes. A disproportionate number of the early expressed gene products were predicted to be secreted, but otherwise had no obvious sequence homology to functionally characterized genes. These genes are candidate necrotrophic effectors. We have focused attention on genes for carbohydrate metabolism and the specific biosynthetic pathways active during growth in planta. The analysis points to a very dynamic adjustment of metabolism during infection. Functional analysis of a gene in the coenzyme A biosynthetic pathway showed that the enzyme was dispensable for growth, indicating that a precursor is supplied by the plant.
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21.
  • Johansson, Tomas, et al. (författare)
  • Transcriptional responses of Paxillus involutus and Betula pendula during formation of ectomycorrhizal root tissue
  • 2004
  • Ingår i: Molecular Plant-Microbe Interactions. - 0894-0282 .- 1943-7706. ; 17:2, s. 202-215
  • Tidskriftsartikel (refereegranskat)abstract
    • In order to obtain information on genes specifically expressed in the ectomycorrhizal symbiosis, 3,555 expressed sequence tags (ESTs) were analyzed from a cDNA library constructed from ectomycorrhiza formed between the basidiomycete Paxillus involutus and birch (Betula pendula). cDNA libraries from saprophytically growing fungus (3,964 ESTs) and from axenic plants (2,532 ESTs) were analyzed in parallel. By clustering all the EST obtained, a nonredundant set of 2,284 unique transcripts of either fungal or plant origin were identified. The expression pattern of these genes was analyzed using cDNA microarrays. The analyses showed that the plant and fungus responded to the symbiosis by altering the expression levels of a number of enzymes involved in carbon metabolism. Several plant transcripts with sequence similarities to genes encoding enzymes in the tricarboxylic cycle and electron transport chain were down regulated as compared with the levels in free-living roots. In the fungal partner, a number of genes encoding enzymes in the lipid and secondary metabolism were down regulated in mycorrhiza as compared with the saprophytically growing mycelium. A substantial number of the ESTs analyzed displayed significant sequence similarities to proteins involved in biotic stress responses, but only a few of them showed differential expression in the mycorrhizal tissue, including plant and fungal metallothioneins and a plant defensin homologue. Several of the genes that were differentially expressed in the mycorrhizal root tissue displayed sequence similarity to genes that are known to regulate growth and development of plant roots and fungal hyphae, including transcription factors and Rho-like GTPases.
  •  
22.
  • Kalbskopf, Victor, et al. (författare)
  • Shifts in Gene Expression Variability in the blood-stage of Plasmodium relictum
  • 2021
  • Ingår i: Gene. - : Elsevier BV. - 0378-1119. ; 792
  • Tidskriftsartikel (refereegranskat)abstract
    • Avian malaria is a common and widespread disease of birds caused by a diverse group of pathogens of the genera Plasmodium. We investigated the transcriptomal profiles of one of the most common species, Plasmodium relictum, lineage SGS1, at multiple timepoints during the blood stages of the infection under experimental settings. The parasite showed well separated overall transcriptome profiles between day 8 and 20 after the infection, shown by well separated PCA profiles. Moreover, gene expression becomes more heterogenous within the experimental group late in the infection, either due to adaptations to individual differences between the experimental hosts, or due to desynchronisation of the life-cycle of the parasite. Overall, this study shows how the avian malaria system can be used to study gene expression of the avian Plasmodium parasite under controlled experimental settings, thus allowing for future comparative analysis of gene responses of parasite with different life-history traits and host effects.
  •  
23.
  • Kozjek, Katja, et al. (författare)
  • Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought
  • 2021
  • Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393. ; 168
  • Tidskriftsartikel (refereegranskat)abstract
    • Agricultural management practices and extreme weather events associated with climate change can influence the diversity and abundance of arbuscular mycorrhizal fungi (AMF) with potential consequences for crop production. However, the importance of the interactive effects of long-term agricultural management and extreme weather events on AMF communities in agricultural soils is not yet fully explored. A short-term drought experiment with rainout-shelters was performed in winter wheat fields in a long-term agricultural trial with organic (biodynamic) and conventional management practices. During four months of the winter wheat growing period (March–June 2017), the rainout-shelters reduced the ambient precipitation by 65% on average. At two sampling dates, the AMF diversity and community composition were assessed using a single-molecule real-time (SMRT) DNA sequencing. A total of 955 amplicon sequence variants (ASVs), belonging to twelve genera were identified. The long-term farming systems and the short-term experimental drought did not affect AMF ASV diversity levels. The AMF community composition at the genus level differed between the organic and the conventional farming systems, but no distinctive communities were found in response to the experimental drought. The three most abundant genera Acaulospora, Paraglomus and Funneliformis were correlated to the two farming practices. Our study demonstrates that AMF communities in agricultural soils are responsive to long-term farming systems, and are resistant to one short-term summer drought event.
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24.
  • Kozjek, Katja, et al. (författare)
  • Microbial functional genes influenced by short-term experimental drought across European agricultural fields
  • 2022
  • Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 168
  • Tidskriftsartikel (refereegranskat)abstract
    • Agricultural intensification and extreme weather events can represent considerable stress to soil microorganisms and their functions by influencing the key players behind the degradation of soil organic matter. A better understanding of the diversity and abundance of microbial functional genes that predict the functional potential of soils, can link the microbial communities to their key ecosystem functions. As there are still gaps in understanding how the functional genetic diversity behind microbial extracellular enzymes is influenced by events like drought and soil carbon management, an agricultural experiment over a range of different climatic conditions and soil properties was set-up across Europe. In Sweden, Germany and Spain, fields with varying levels of soil organic carbon were subjected to a short-term experimental drought. The diversity and composition of genes encoding for carbohydrate-related extracellular enzymes were determined using a ‘captured metagenomics' technique. Functional gene diversity differed among the European regions and to a range of soil factors such as organic carbon and water content. The functional and taxonomic gene composition significantly differed between the climatic regions, while an effect of short-term drought was only observed in Germany. The results indicate that some soil microbial communities and their functional genes displayed a certain degree of resistance. The results suggest that soil microbial communities respond differently to short-term drought mainly due to regional adaptations to already dry environments and differences in their soil physicochemical properties.
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25.
  • Kozjek, Katja, et al. (författare)
  • Microbial gene activity in straw residue amendments reveals carbon sequestration mechanisms in agricultural soils
  • 2023
  • Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 179
  • Tidskriftsartikel (refereegranskat)abstract
    • Land-use practices and their intensity along with climatic conditions alter amounts of soil organic carbon content and consequently influence soil microorganisms. However, land-use management, such as crop residue incorporation to soils has a potential to mitigate losses of soil organic carbon and thereafter promote the diversity of soil microorganisms. To gain insight of microbial functional diversity and activity under organic soil amendments, a glasshouse experiment with arable and grassland soils was performed. Straw was added as a crop residue and microbial activity in the soils was monitored using a captured metatranscriptomics technique. The overall expression of genes related to soil organic matter degradation differed between the two land-use systems. Straw addition enhanced the expression of genes involved in the degradation of organic material, particularly in arable soils. After a month of the amendment, the overall gene expression in arable soils had a similar pattern to that of the grasslands. The straw addition triggered the upregulation of a set of enzyme families catalysing the organic matter degradation in both land-uses but downregulated a higher number of enzyme families in grasslands. However, in the grasslands, the gene families involved in the biosynthesis of carbohydrates were upregulated at straw addition. These findings indicate that arable soils with a low organic carbon content have a potential to get a higher and more active microbial diversity with amendments. In soils such as grasslands the amendments trigger a carbon sequestration process from the added organic material to the soil and can significantly contribute to enhanced soil carbon sequestration.
  •  
26.
  • Kunin, Victor, et al. (författare)
  • Measuring genome conservation across taxa: divided strains and united kingdoms
  • 2005
  • Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962. ; 33:2, s. 616-621
  • Tidskriftsartikel (refereegranskat)abstract
    • Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation—a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: .
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27.
  • Kushwaha, Sandeep, et al. (författare)
  • MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
  • 2015
  • Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.
  •  
28.
  • Kushwaha, Sandeep, et al. (författare)
  • NBSPred: A support vector machine-based high throughput pipeline for plant resistance protein NBSLRR prediction.
  • 2015
  • Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:8, s. 1223-1225
  • Tidskriftsartikel (refereegranskat)abstract
    • The nucleotide binding site-leucine-rich repeats (NBSLRR) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time consuming task. Therefore, we have developed a support vector machine (SVM) based high throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from 3 dicot and 2 monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays.
  •  
29.
  • Manoharan, Lokeshwaran, et al. (författare)
  • Agricultural land use determines functional genetic diversity of soil microbial communities
  • 2017
  • Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 115, s. 423-432
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial communities play a major role in the degradation of soil organic matter (SOM) in soils. Despite its significance, the functional diversity of the highly diverse microbial communities is poorly understood. To address this, we applied a recently developed technique, captured metagenomics, to determine the effects of land-use on the functional genetic diversity of genes involved in the carbon degradation of SOM in five pairs of agricultural soils with either winter wheat or grass as management. In addition, 16S rRNA based amplicon sequencing was used to study the taxonomic composition in the same soils. The functional genes resulting from the captured metagenomes had a higher abundance and diversity of sequences coding for enzymes degrading SOM in the grasslands compared to the wheat soils. Though the taxonomic diversity did not correlate with the land use. Amounts of C and N (organic matter content) in the soils affected both functional and taxonomic diversity of the microbial communities, where N was highly correlated to their functions and C was highly correlated to their taxonomy. Captured metagenomic analyses of the functional genes may provide a measure of the potential SOM degradation capacity by soil microbial communities at a high resolution. This can be used for assessments of how agricultural management affects the functioning of soil communities.
  •  
30.
  • Manoharan, Lokeshwaran, et al. (författare)
  • Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.
  • 2015
  • Ingår i: DNA Research. - : Oxford University Press (OUP). - 1756-1663 .- 1340-2838. ; 22:6, s. 451-460
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.
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31.
  • Martin, Francis, et al. (författare)
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
  • 2008
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7183, s. 7-88
  • Tidskriftsartikel (refereegranskat)abstract
    • Mycorrhizal symbioses -- the union of roots and soil fungi -- are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate, and montane forests all depend upon ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of 2 ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here, we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-million-base genome assembly contains ~ 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features most notably a battery of effector-type small secreted proteins (SSP) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific proteins likely play a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell walls, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus which enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
  •  
32.
  • McDonald, Megan, et al. (författare)
  • The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana
  • 2017
  • Ingår i: Molecular Plant Pathology. - : Wiley. - 1464-6722 .- 1364-3703. ; , s. 1-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.
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33.
  • Meerupati, Tejashwari, et al. (författare)
  • Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi
  • 2013
  • Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 9:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Orbiliomycetes is one of the earliest diverging branches of the filamentous ascomycetes. The class contains nematode-trapping fungi that form unique infection structures, called traps, to capture and kill free-living nematodes. The traps have evolved differently along several lineages and include adhesive traps (knobs, nets or branches) and constricting rings. We show, by genome sequencing of the knob-forming species Monacrosporium haptotylum and comparison with the net-forming species Arthrobotrys oligospora, that two genomic mechanisms are likely to have been important for the adaptation to parasitism in these fungi. Firstly, the expansion of protein domain families and the large number of species-specific genes indicated that gene duplication followed by functional diversification had a major role in the evolution of the nematode-trapping fungi. Gene expression indicated that many of these genes are important for pathogenicity. Secondly, gene expression of orthologs between the two fungi during infection indicated that differential regulation was an important mechanism for the evolution of parasitism in nematode-trapping fungi. Many of the highly expressed and highly upregulated M. haptotylum transcripts during the early stages of nematode infection were species-specific and encoded small secreted proteins (SSPs) that were affected by repeat-induced point mutations (RIP). An active RIP mechanism was revealed by lack of repeats, dinucleotide bias in repeats and genes, low proportion of recent gene duplicates, and reduction of recent gene family expansions. The high expression and rapid divergence of SSPs indicate a striking similarity in the infection mechanisms of nematode-trapping fungi and plant and insect pathogens from the crown groups of the filamentous ascomycetes (Pezizomycotina). The patterns of gene family expansions in the nematode-trapping fungi were more similar to plant pathogens than to insect and animal pathogens. The observation of RIP activity in the Orbiliomycetes suggested that this mechanism was present early in the evolution of the filamentous ascomycetes.
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34.
  • Rajashekar, Balaji, et al. (författare)
  • Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases.
  • 2009
  • Ingår i: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 183:2, s. 365-379
  • Tidskriftsartikel (refereegranskat)abstract
    • * The ectomycorrhizal fungus Laccaria bicolor has the largest genome of all fungi yet sequenced. The large genome size is partly a result of an expansion of gene family sizes. Among the largest gene families are protein kinases and RAS small guanosine triphosphatases (GTPases), which are key components of signal transduction pathways. * Comparative genomics and phylogenetic analyses were used to examine the evolution of the two largest families of protein kinases and RAS small GTPases in L. bicolor. Expression levels in various tissues and growth conditions were inferred from microarray data. * The two families possessed a large number of young duplicates (paralogs) that had arisen in the Laccaria lineage following the separation from the saprophyte Coprinopsis cinerea. The protein kinase paralogs were dispersed in many small clades and the majority were pseudogenes. By contrast, the RAS paralogs were found in three large groups of RAS1-, RAS2- and RHO1-like GTPases with few pseudogenes. * Duplicates of protein kinases and RAS small GTPase have either retained, gained or lost motifs found in the coding regions of their ancestors. Frequent outcomes during evolution were the formation of pseudogenes (nonfunctionalization) or proteins with novel structures and expression patterns (neofunctionalization).
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35.
  • Rengefors, Karin, et al. (författare)
  • Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species
  • 2021
  • Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:4, s. 912-925
  • Tidskriftsartikel (refereegranskat)abstract
    • Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.
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36.
  • Rengefors, Karin, et al. (författare)
  • Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist
  • 2024
  • Ingår i: Scientific Reports. - 2045-2322. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.
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37.
  • Salmón, Pablo, et al. (författare)
  • Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe
  • 2021
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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38.
  • Sekar, Vaishnovi, et al. (författare)
  • Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector
  • 2021
  • Ingår i: Genomics. - : Elsevier BV. - 1089-8646 .- 0888-7543. ; 113:4, s. 2327-2337
  • Tidskriftsartikel (refereegranskat)abstract
    • The malaria parasite Plasmodium relictum is one of the most widespread species of avian malaria. As in the case of its human counterparts, bird Plasmodium undergoes a complex life cycle infecting two hosts: the arthropod vector and the vertebrate host. In this study, we examined transcriptomes of P. relictum (SGS1) during crucial timepoints within its vector, Culex pipiens quinquefasciatus. Differential gene-expression analyses identified genes linked to the parasites life-stages at: i) a few minutes after the blood meal is ingested, ii) during peak oocyst production phase, iii) during peak sporozoite phase and iv) during the late-stages of the infection. A large amount of genes coding for functions linked to host-immune invasion and multifunctional genes was active throughout the infection cycle. One gene associated with a conserved Plasmodium membrane protein with unknown function was upregulated throughout the parasite development in the vector, suggesting an important role in the successful completion of the sporogonic cycle. Gene expression analysis further identified genes, with unknown functions to be significantly differentially expressed during the infection in the vector as well as upregulation of reticulocyte-binding proteins, which raises the possibility of the multifunctionality of these RBPs. We establish the existence of highly stage-specific pathways being overexpressed during the infection. This first study of gene-expression of a non-human Plasmodium species in its vector provides a comprehensive insight into the molecular mechanisms of the common avian malaria parasite P. relictum and provides essential information on the evolutionary diversity in gene regulation of the Plasmodium's vector stages.
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39.
  •  
40.
  • Stajich, Jason E., et al. (författare)
  • Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
  • 2010
  • Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 107:26, s. 11889-11894
  • Tidskriftsartikel (refereegranskat)abstract
    • The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
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41.
  • Strandh, Maria, et al. (författare)
  • Transcriptional analysis of the pheromone gland of the turnip moth, Agrotis segetum (Noctuidae), reveals candidate genes involved in pheromone production.
  • 2008
  • Ingår i: Insect Molecular Biology. - : Wiley. - 1365-2583 .- 0962-1075. ; 17:1, s. 73-85
  • Tidskriftsartikel (refereegranskat)abstract
    • Moths generally rely on pheromone communication for mate finding. The pheromone components of most moths are produced by a common pathway of fatty-acid biosynthesis coupled with species-specific modifications of the final products. Some genes involved in moth pheromone production have previously been described, whereas others remain to be characterized and thus the molecular mechanisms accounting for the production of species-specific blends are far from understood. The turnip moth, Agrotis segetum, has a multicomponent pheromone, consisting of at least four components derived from palmitic and stearic acid. Different populations produce and respond to different pheromone blends, which makes this species an excellent model for research on genes and molecular mechanisms involved in moth pheromone production. For this purpose, we performed an expressed sequence tag (EST) analysis of two cDNA libraries, one representing the female pheromone gland and the other representing the remainder of the insect body. Among 2285 ESTs analysed altogether, we identified a unigene set of 707 putative gene representatives. The comparative distribution of those in the two libraries showed the transcriptomes of the tissues to be clearly different. One third of the gene representatives were exclusively found in the pheromone gland. From sequence homology to public database information we assigned putative functional roles for a majority of the unigenes and then compared functional profiles of the two tissues. In the set of ESTs more abundant in the pheromone gland library, we found homologues of an acyl-CoA Delta11-desaturase, a G-protein subunit, a chemosensory protein as well as a juvenile hormone binding protein.
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42.
  • Svennerholm, Kristina, 1981, et al. (författare)
  • DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning
  • 2016
  • Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 11:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Extracellular vesicles (EV) are nano-sized membranous structures released from most cells. They have the capacity to carry bioactive molecules and gene expression signals between cells, thus mediating intercellular communication. It is believed that EV confer protection after ischemic preconditioning (IPC). We hypothesize that myocardial ischemic preconditioning will lead to rapid alteration of EV DNA content in EV collected from coronary venous effluent. In a porcine myocardial ischemic preconditioning model, EV were isolated from coronary venous blood before and after IPC by differential centrifugation steps culminating in preparative ultracentrifugation combined with density gradient ultracentrifugation. The EV preparation was validated, the DNA was extracted and further characterized by DNA sequencing followed by bioinformatics analysis. Porcine genomic DNA fragments representing each chromosome, including mitochondrial DNA sequences, were detected in EV isolated before and after IPC. There was no difference detected in the number of sequenced gene fragments (reads) or in the genomic coverage of the sequenced DNA fragments in EV isolated before and after IPC. Gene ontology analysis showed an enrichment of genes coding for ion channels, enzymes and proteins for basal metabolism and vesicle biogenesis and specific cardiac proteins. This study demonstrates that porcine EV isolated from coronary venous blood plasma contain fragments of DNA from the entire genome, including the mitochondria. In this model we did not find specific qualitative or quantitative changes of the DNA content in EV collected immediately after an in vivo myocardial IPC provocation. This does not rule out the possibility that EV DNA content changes in response to myocardial IPC which could occur in a later time frame.
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43.
  • Troein, Carl, et al. (författare)
  • Is Transcriptional Regulation of Metabolic Pathways and Optimal Strategy for Fitness?
  • 2007
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 2:9
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. The lac operon of E. coli is but one example of how enzyme and transporter production can be made conditional on the presence of a nutrient to catabolize. Methodology With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. This in silico model, which is based on biochemical rate equations, does not describe a specific organism, but the magnitudes of its parameters are chosen to match realistic values. Optimizing the parameters of the regulatory system allows us to quantify the fitness benefit of regulation. When a second nutrient and its metabolic pathway are introduced, the system must further decide whether and how to activate both pathways. Conclusions Even the crudest transcriptional network is shown to substantially increase the fitness of the organism, and this effect persists even when the range of nutrient levels is kept very narrow. We show that maximal growth is achieved when pathway activation is a more or less steeply graded function of the nutrient concentration. Furthermore, we predict that bistability of the system is a rare phenomenon in this context, but outline a situation where it may be selected for.
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44.
  • Tsardakas Renhuldt, Nikos, et al. (författare)
  • Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa)
  • 2024
  • Ingår i: Frontiers in Plant Science. - 1664-462X. ; 15
  • Tidskriftsartikel (refereegranskat)abstract
    • In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.
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45.
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46.
  • Vasileiou, Dimitrios, et al. (författare)
  • CGG toolkit : Software components for computational genomics
  • 2023
  • Ingår i: PLoS Computational Biology. - 1553-734X. ; 19:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.
  •  
47.
  • Videvall, Elin, et al. (författare)
  • The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression
  • 2017
  • Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X.
  • Tidskriftsartikel (refereegranskat)abstract
    • Malaria parasites (Plasmodium spp.) include some of the world's most widespread and virulent pathogens. Our knowledge of the molecular mechanisms these parasites use to invade and exploit hosts other than mice and primates is, however, extremely limited. It is therefore imperative to characterize transcriptome-wide gene expression from non-model malaria parasites and how this varies across host individuals. Here, we used high-throughput Illumina RNA-sequencing on blood from wild-caught Eurasian siskins experimentally infected with a clonal strain of the avian malaria parasite Plasmodium ashfordi (lineage GRW2). By using a multi-step approach to filter out host transcripts, we successfully assembled the blood-stage transcriptome of P. ashfordi. A total of 11 954 expressed transcripts were identified, and 7 860 were annotated with protein information. We quantified gene expression levels of all parasite transcripts across three hosts during two infection stages – peak and decreasing parasitemia. Interestingly, parasites from the same host displayed remarkably similar expression profiles during different infection stages, but showed large differences across hosts, indicating that P. ashfordi may adjust its gene expression to specific host individuals. We further show that the majority of transcripts are most similar to the human parasite Plasmodium falciparum, and a large number of red blood cell invasion genes were discovered, suggesting evolutionary conserved invasion strategies between mammalian and avian Plasmodium. The transcriptome of P. ashfordi and its host-specific gene expression advances our understanding of Plasmodium plasticity and is a valuable resource as it allows for further studies analysing gene evolution and comparisons of parasite gene expression.
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48.
  • Wallace, Valeria, et al. (författare)
  • Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress
  • 2015
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved industrial Saccharomyces cerevisiae strain ISO12 that had acquired improved tolerance to grow and ferment in the presence of lignocellulose-derived inhibitors at high temperature (39 degrees C). In the current study, we used comparative genomics to uncover the extent of the genomic alterations that occurred during the evolution process and investigated possible associations between the mutations and the phenotypic traits in ISO12. Results: Through whole-genome sequencing and variant calling we identified a high number of strain-unique SNPs and INDELs in both ISO12 and the parental strain Ethanol Red. The variants were predicted to have 760 non-synonymous effects in both strains combined and were significantly enriched in Gene Ontology terms related to cell periphery, membranes and cell wall. Eleven genes, including MTL1, FLO9/FLO11, and CYC3 were found to be under positive selection in ISO12. Additionally, the FLO genes exhibited changes in copy number, and the alterations to this gene family were correlated with experimental results of multicellularity and invasive growth in the adapted strain. An independent lipidomic analysis revealed further differences between the strains in the content of nine lipid species. Finally, ISO12 displayed improved viability in undiluted spruce hydrolysate that was unrelated to reduction of inhibitors and changes in cell wall integrity, as shown by HPLC and lyticase assays. Conclusions: Together, the results of the sequence comparison and the physiological characterisations indicate that cell-periphery proteins (e.g. extracellular sensors such as MTL1) and peripheral lipids/membranes are important evolutionary targets in the process of adaptation to the combined stresses. The capacity of ISO12 to develop complex colony formation also revealed multicellularity as a possible evolutionary strategy to improve competitiveness and tolerance to environmental stresses (also reflected by the FLO genes). Although a panel of altered genes with high relevance to the novel phenotype was detected, this study also demonstrates that the observed long-term molecular effects of thermal and inhibitor stress have polygenetic basis.
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49.
  • Wirsel, SGR, et al. (författare)
  • Four or more species of Cladosporium sympatrically colonize Phragmites australis
  • 2002
  • Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 35:2, s. 99-113
  • Tidskriftsartikel (refereegranskat)abstract
    • A collection of Cladosporium has been recovered from common reed growing at Lake Constance (Germany). High-resolution cryo-scanning electron microscopy revealed that Cladosporium isolates from reed are diverse. Morphologically, we distinguished three species, viz. C. herbarum, C. oxysporum, and Cladosporium sp. Internal transcribed spacer (ITS) sequence analysis supported these results and, moreover, separated the most common species, C. oxysporum, into two subclades. Two additional phylogenies were generated to gain support for this finding. The first, differentiating fungi by their capacities to metabolize different carbon sources, showed correlation with morphology. The second, based on actin gene sequences, showed the same overall topology as that of the ITS tree, but resulted in a higher resolution indicating the existence of four or more species of Cladosporium on reed. A nested PCR assay targeting variable sequences within actin introns indicated that these four species sympatrically colonize reed. There was no evidence for mutual exclusion on or within the host or specialization for host habitats or organs.
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