| 1. |
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| 2. |
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| 3. |
- Adomas, Aleksandra, et al.
(författare)
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Comparative analysis of transcript abundance in Pinus sylvestris after challenge with a saprotrophic, pathogenic or mutualistic fungus
- 2008
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Ingår i: Tree Physiology. - : Oxford University Press (OUP). - 0829-318X .- 1758-4469. ; 28:6, s. 885-897
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Tidskriftsartikel (refereegranskat)abstract
- To investigate functional differences in the recognition and response mechanisms of conifer roots to fungi with different trophic strategies, Pinus sylvestris L. was challenged with a saprotrophic fungus Trichoderma aureoviride Rifai. The results were compared with separate studies investigating pine interactions with a pathogen, Heterobasidion annosum (Fr.) Bref. sensu stricto and an ectomycorrhizal symbiont, Laccaria bicolor Maire (Orton). Global changes in the expression of 2109 conifer genes were assayed 1, 5 and 15 days after inoculation. Gene expression data from a cDNA microarray were analyzed by the 2-interconnected mixed linear model statistical approach. The total number of genes differentially expressed compared with the uninfected control was similar after challenge with the pathogen and the ectomycorrhizal symbiont, but the number of differentially expressed genes increased over time, for H. annosum, and decreased for L. bicolor. Inoculation of pine roots with T aureoviride resulted overall in a much lower number of genes with changed transcript levels compared with inoculation with H. annosum or L. bicolor. Functional classification of the differentially expressed genes revealed that the ectomycorrhizal fungus triggered transient induction of defence-related genes. The response and induction of defence against the pathogen was delayed and the magnitude increased over time. Thus, there were specific transcriptional responses depending on whether the conifer roots were challenged with mutualistic, saprotrophic or pathogenic fungi. This suggests that pine trees are able to recognize diverse fungal species and specifically distinguish whether they are pathogenic, neutral or beneficial microbial agents.
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| 4. |
- Andersson, Ulrika, et al.
(författare)
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Germline rearrangements in families with strong family history of glioma and malignant melanoma, colon, and breast cancer
- 2014
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Ingår i: Neuro-Oncology. - : Oxford University Press. - 1522-8517 .- 1523-5866. ; 16:10, s. 1333-1340
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Tidskriftsartikel (refereegranskat)abstract
- Background: Although familial susceptibility to glioma is known, the genetic basis for this susceptibility remains unidentified in the majority of glioma-specific families. An alternative approach to identifying such genes is to examine cancer pedigrees, which include glioma as one of several cancer phenotypes, to determine whether common chromosomal modifications might account for the familial aggregation of glioma and other cancers. Methods: Germline rearrangements in 146 glioma families (from the Gliogene Consortium; http://www.gliogene.org/) were examined using multiplex ligation-dependent probe amplification. These families all had at least 2 verified glioma cases and a third reported or verified glioma case in the same family or 2 glioma cases in the family with at least one family member affected with melanoma, colon, or breast cancer. The genomic areas covering TP53, CDKN2A, MLH1, and MSH2 were selected because these genes have been previously reported to be associated with cancer pedigrees known to include glioma. Results: We detected a single structural rearrangement, a deletion of exons 1-6 in MSH2, in the proband of one family with 3 cases with glioma and one relative with colon cancer. Conclusions: Large deletions and duplications are rare events in familial glioma cases, even in families with a strong family history of cancers that may be involved in known cancer syndromes.
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| 5. |
- Arnerup, Jenny, et al.
(författare)
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The pathogenic white-rot fungus Heterobasidion parviporum triggers non-specific defence responses in the bark of Norway spruce
- 2011
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Ingår i: Tree Physiology. - : Oxford University Press. - 0829-318X .- 1758-4469. ; 31:11, s. 1262-1272
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Tidskriftsartikel (refereegranskat)abstract
- Norway spruce [Picea abies (L.) Karst.] is one of the economically most important conifer species in Europe. The major pathogen on Norway spruce is Heterobasidion parviporum (Fr.) Niemelä & Korhonen. To achieve a better understanding of Norway spruce's defence mechanisms, transcriptional responses in bark to H. parviporum infection were compared with the response to wounding using cDNA-amplified fragment length polymorphism. The majority of the recovered transcript-derived fragments (TDFs) showed a similar expression pattern for infection and wounding treatment, although inoculated samples showed an enhanced reaction. Genes related to systemic acquired resistance, e.g., PR1, accumulated after H. parviporum infection. Simultaneously, several transcripts involved in various aspects of jasmonic acid (JA)- and ethylene (ET)-mediated signalling accumulated. Genes involved in the ubiquitin/proteasome system were also regulated. Expression patterns have been confirmed by quantitative polymerase chain reaction. The expression patterns of the isolated TDFs suggest that infection with H. parviporum in Norway spruce induces a broad defence, with many similarities to non-specific defence responses in angiosperms. The parallel induction of salicylic acid- and JA/ET-mediated pathways implies spatially separated responses in different cell layers, with and without hyphal contact. A set of TDFs were analysed in an independent experiment with unrelated material treated with wounding or with inoculation with H. parviporum or Phlebiopsis gigantea, verifying the original observations and underlining the non-specific defence responses. In addition, our data suggest that rerouting of carbon in secondary metabolism is an integral part of Norway spruce induced defence. We report the sequences of three 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase genes (PaDAHP1, PaDAHP2 and PaDAHP3) and their relative expression in response to wounding and infection with H. parviporum and P. gigantea. The results clearly indicate differential regulation of the three DAHPs in the induced defence responses in Norway spruce. This study gives insights into the central mechanisms in the induced defences in Norway spruce.
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| 6. |
- Berlin, Anna, et al.
(författare)
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Scientific evidence for sustainable plant disease protection strategies for the main arable crops in Sweden. A systematic map protocol
- 2018
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Ingår i: Environmental Evidence. - : Springer Science and Business Media LLC. - 2047-2382. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Efficient and sustainable plant protection is of great economic and ecological significance for global crop production. A number of challenges, e.g. climate change, population growth and global trade, put increasing demands on future crop production and crop protection. This necessitates an increase in crop productivity with less environmental impact while maintaining good food quality and food security. To meet these challenges, it is essential that the recommendations provided to growers are efficient and correct, which can only be ensured by evidence-based recommendations based on outcomes from scientific studies.Methods and output: The aim of these systematic maps is to compile scientific evidence for different plant disease protection strategies for the main arable crops grown in Sweden. Six major crops (wheat, barley, oat, potato, sugar beet and oilseed rape) have been selected based on the area under production, the annual production, the economic importance, and the amount of pesticide used against diseases in these crops in Sweden. All methods to manage diseases will be considered, including cropping system, pesticide application, biological control methods, as well as combinations of methods and integrated pest management. These systematic maps will only deal with field studies of relevance for agricultural practices in Sweden, although we expect that the results will be applicable for northern Europe as a whole. The main outcome to be used will be productivity measured as yield per area. Plant health and pathogen reduction will be included as a proxy for potential increase in crop quality and yield. This will provide a systematic overview of the plant disease protection measures that have been reported in the scientific literature. The study will result in one searchable database per crop that may be used as a catalogue of evidence for researchers and stakeholders, especially authorities and advisory organizations. The systematic maps will aid in the identification of areas that need further research and guide funding agencies and policymakers when deciding where research resources should be allocated. It will also help to select topics for future systematic reviews and meta-studies within the field of plant protection.
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| 7. |
- Borg, Åke, et al.
(författare)
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Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study.
- 2010
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 31, s. 1200-1240
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Tidskriftsartikel (refereegranskat)abstract
- BRCA1 and BRCA2 screening in women at high-risk of breast cancer results in the identification of both unambiguously defined deleterious mutations and sequence variants of unknown clinical significance (VUS). We examined a population-based sample of young women with contralateral breast cancer (CBC, n=705) or unilateral breast cancer (UBC, n=1398). We identified 470 unique sequence variants, of which 113 were deleterious mutations. The remaining 357 VUS comprised 185 unique missense changes, 60% were observed only once, while 3% occurred with a frequency of >10%. Deleterious mutations occurred three times more often in women with CBC (15.3%) than in women with UBC (5.2%), whereas combined, VUS were observed in similar frequencies in women with CBC and UBC. A protein alignment algorithm defined 16 rare VUS, occurring at highly conserved residues and/or conferring a considerable biochemical difference, the majority located in the BRCA2 DNA-binding domain. We confirm a multiplicity of BRCA1 and BRCA2 VUS that occur at a wide range of allele frequencies. Although some VUS inflict chemical differences at conserved residues, suggesting a deleterious effect, the majority are not associated with an increased risk of CBC. (c) 2010 Wiley-Liss, Inc.
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| 8. |
- Bödeker, Inga, et al.
(författare)
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ClassII peroxidase-encoding genes are present in a phylogenetically wide range of ectomycorrhizal fungi
- 2009
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 3, s. 1387-1395
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Tidskriftsartikel (refereegranskat)abstract
- Fungal peroxidases (ClassII) have a key role in degrading recalcitrant polyphenolic compounds in boreal forest wood, litter and humus. To date, their occurrence and activity have mainly been studied in a small number of white-rot wood decomposers. However, peroxidase activity is commonly measured in boreal forest humus and mineral soils, in which ectomycorrhizal fungi predominate. Here, we used degenerate PCR primers to investigate whether peroxidase-encoding genes are present in the genomes of a wide phylogenetic range of ectomycorrhizal taxa. Cloning and sequencing of PCR products showed that ectomycorrhizal fungi from several different genera possess peroxidase genes. The new sequences represent four major homobasidiomycete lineages, but the majority is derived from Cortinarius, Russula and Lactarius. These genera are ecologically important, but consist mainly of non-culturable species from which little ecophysiological information is available. The amplified sequences contain conserved active sites, both for folding and substrate oxidation. In some Cortinarius spp., there is evidence for gene duplications during the evolution of the genus. ClassII peroxidases seem to be an ancient and a common feature of most homobasidiomycetes, including ectomycorrhizal fungi. Production of extracellular peroxidases may provide ectomycorrhizal fungi with access to nitrogen sequestered in complex polyphenolic sources. The ISME Journal (2009) 3, 1387-1395; doi: 10.1038/ismej.2009.77; published online 2 July 2009
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| 9. |
- Bödeker, Inga, et al.
(författare)
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Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems
- 2014
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 203, s. 245-256
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Tidskriftsartikel (refereegranskat)abstract
- In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N.In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed.We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases - a number comparable to many white-rot wood decomposers.These results support the hypothesis that some ectomycorrhizal fungi - Cortinarius species in particular - may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.
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| 10. |
- Bödeker, Inga, et al.
(författare)
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Mycorrhizal and saprotrophic fungal guilds compete for the same organic substrates but affect decomposition differently
- 2016
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 30, s. 1967-1978
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Tidskriftsartikel (refereegranskat)abstract
- 1. Communities of litter saprotrophic and root-associated fungi are vertically separated within boreal forest soil profiles. It is unclear whether this depth partitioning is maintained exclusively by substrate-mediated niche partitioning (i.e. distinct fundamental niches), or by competition for space and resources (i.e. distinct realized niches). Improved understanding of the mechanisms driving spatial partitioning of these fungal guilds is critical, as they modulate carbon and nutrient cycling in different ways.2. Under field settings, we tested the effects of substrate quality and the local fungal species pool at various depths in determining the potential of saprotrophic and mycorrhizal fungi to colonize and exploit organic matter. Natural substrates of three qualities-fresh or partly decomposed litter or humus -were incubated in the corresponding organic layers of a boreal forest soil profile in a fully factorial design. After one and two growing seasons, fungal community composition in the substrates was determined by 454-pyrosequencing and decomposition was analyzed.3. Fungal community development during the course of the experiment was determined to similar degrees by vertical location of the substrates (24% of explained variation) and by substrate quality (20%), indicating that interference competition is a strong additional driver of the substrate-dependent depth partitioning of fungal guilds in the system. During the first growing season, litter substrates decomposed slower when colonized by root-associated communities than when colonized by communities of litter saprotrophs, whereas humus was only slightly decomposed by both fungal guilds. During the second season, certain basidiomycetes from both guilds were particularly efficient in localizing and exploiting their native organic substrates although displaced in the vertical profile. This validates that fungal community composition, rather than microclimatic factors, were responsible for observed depth-related differences in decomposer activities during the first season.4. In conclusion, our results suggest that saprotrophic and root-associated fungal guilds have overlapping fundamental niches with respect to colonization of substrates of different qualities, and that their substrate-dependent depth partitioning in soils of ectomycorrhiza-dominated ecosystems is reinforced by interference competition. Through competitive interactions, mycorrhizal fungi can thus indirectly regulate litter decomposition rates by restraining activities of more efficient litter saprotrophs.
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| 11. |
- Capador-Barreto, Hernán Dario, et al.
(författare)
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Development of microsatellite markers for Thekopsora areolata, the causal agent of cherry spruce rust
- 2018
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 48
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Tidskriftsartikel (refereegranskat)abstract
- Cherry spruce rust is a fungal disease of Norway spruce cones caused by Thekopsora areolata and responsible for significant losses in seed production in Sweden and Finland. Here, we report the first set of nine microsatellites, which will allow an effective genetic fingerprinting of T.areolata. The markers were isolated using the FIASCO method and were characterized using DNA from 49 single aecia sampled from spruce cones in three different seed orchards in Sweden. Eight of the nine markers were shown to be polymorphic among the aecia. The markers were unlinked and are therefore suitable for future population genetic studies.
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| 12. |
- Capador-Barreto, Hernán Dario, et al.
(författare)
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Genetic evidence for sexual reproduction and multiple infections of Norway spruce cones by the rust fungus Thekopsora areolata
- 2020
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10, s. 7389-7403
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Tidskriftsartikel (refereegranskat)abstract
- Rust fungi are obligate parasites, of plants, with complex and in many cases poorly known life cycles which may include host alteration and up to five spore types with haploid, diploid, and dikaryotic nuclear stages. This study supports thatThekopasora areolata, the causal agent of cherry-spruce rust in Norway spruce, is a macrocyclic heteroecious fungus with all five spore stages which uses two host plantsPrunus padusandPicea abiesto complete its life cycle. High genotypic diversity without population structure was found, which suggests predominantly sexual reproduction, random mating and a high gene flow within and between the populations in Fennoscandia. There was no evidence for an autoecious life cycle resulting from aeciospore infection of pistillate cones that would explain the previously reported rust epidemics without the alternate host. However, within cones and scales identical multilocus genotypes were repeatedly sampled which can be explained by vegetative growth of the fertilized mycelia or repeated mating of mycelium by spermatia of the same genotype. The high genotypic diversity within cones and haplotype inference show that each pistillate cone is infected by several basidiospores. This study provides genetic evidence for high gene flow, sexual reproduction, and multiple infections of Norway spruce cone by the rust fungusT. areolatawhich expands the general understanding of the biology of rust fungi.
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| 13. |
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| 14. |
- Castaño Soler, Carles, et al.
(författare)
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Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities
- 2020
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 228, s. 1149-1158
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
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| 15. |
- Chen, Zhi‑Qiang, et al.
(författare)
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Early selection for resistance to Heterobasidion parviporum in Norway spruce is not likely to adversely affect growth and wood quality traits in late-age performance
- 2018
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Ingår i: European Journal of Forest Research. - : Springer Science and Business Media LLC. - 1612-4669 .- 1612-4677. ; 137:4, s. 517-525
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Tidskriftsartikel (refereegranskat)abstract
- Infections with Heterobasidion parviporum devalue the Norway spruce timber as the decayed wood does not meet the necessary quality requirements for sawing. To evaluate the incorporation of disease resistance in the Norway spruce breeding strategy, an inoculation experiment with H. parviporum on 2-year-old progenies of 466 open-pollinated families was conducted under greenhouse (nursery) conditions. Lesion length in the phloem (LL), fungal growth in sapwood (FG) and growth (D) were measured on an average of 10 seedlings for each family. The genetic variation and genetic correlations between both LL, FG and growth in the nursery trial and wood quality traits measured previously from 21-year old trees in two progeny trials, including solid-wood quality traits (wood density, and modulus of elasticity) and fiber properties traits (radial fiber width, tangential fiber width, fiber wall thickness, fiber coarseness, microfibril angle and fiber length). For both LL and FG, large coefficients of phenotypic variation (> 26%) and genetic variation (> 46%) were detected. Heritabilities of LL and FG were 0.33 and 0.42, respectively. We found no significant correlations between wood quality traits and growth in the field progeny trials with neither LL nor FG in the nursery trial. Our data suggest that the genetic gains may reach 41 and 52% from mass selection by LL and FG, respectively. Early selection for resistance to H. parviporum based on assessments of fungal spread in the sapwood in nursery material, FG, will not adversely affect growth and wood quality traits in late-age performance.
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| 16. |
- Clergeot, Pierre-Henri, et al.
(författare)
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Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle : A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum
- 2019
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 211:3, s. 963-976
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Tidskriftsartikel (refereegranskat)abstract
- Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance-a measure that accounts for these two effects-should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum-a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.
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| 17. |
- Coignard, J, et al.
(författare)
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A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 1078-
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Tidskriftsartikel (refereegranskat)abstract
- Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.
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| 18. |
- Couch, Fergus J., et al.
(författare)
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AURKA F31I polymorphism and breast cancer risk in BRCA1 and BRCA2 mutation carriers: A consortium of investigators of modifiers of BRCA1/2 study
- 2007
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Ingår i: Cancer Epidemiology Biomarkers & Prevention. - 1538-7755. ; 16:7, s. 1416-1421
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Tidskriftsartikel (refereegranskat)abstract
- The AURKA oncogene is associated with abnormal chromosome segregation and aneuploidy and predisposition to cancer. Amplification of AURKA has been detected at higher frequency in tumors from BRCA1 and BRCA2 mutation carriers than in sporadic breast tumors, suggesting that overexpression of AURKA and inactivation of BRCA1 and BRCA2 cooperate during tumor development and progression. The F31I polymorphism in AURKA has been associated with breast cancer risk in the homozygous state in prior studies. We evaluated whether the AURKA F31I polymorphism modifies breast cancer risk in BRCA1 and BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2. Consortium of Investigators of Modifiers of BRCA1/2 was established to provide sufficient statistical power through increased numbers of mutation carriers to identify polymorphisms that act as modifiers of cancer risk and can refine breast cancer risk estimates in BRCA1 and BRCA2 mutation carriers. A total of 4,935 BRCA1 and 2,241 BRCA2 mutation carriers and 11 individuals carrying both BRCA1 and BRCA2 mutations was genotyped for F31I. Overall, homozygosity for the 311 allele was not significantly associated with breast cancer risk in BRCA1 and BRCA2 carriers combined [hazard ratio (HR), 0.91; 95% confidence interval (95% CI), 0.77-1.061. Similarly, no significant association was seen in BRCA1 (HR, 0.90; 95% Cl, 0.75-1.08) or BRCA2 carriers (HR, 0.93; 95% CI, 0.67-1.29) or when assessing the modifying effects of either bilateral prophylactic oophorectomy or menopausal status of BRCA1 and BRCA2 carriers. In summary, the F31I polymorphism in AURKA is not associated with a modified risk of breast cancer in BRCA1 and BRCA2 carriers.
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| 19. |
- Dalman, Kerstin, et al.
(författare)
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A genome-wide association study identifies genomic regions for virulence in Heterobasidion annosum s.s
- 2012
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Heterobasidion annosum (Fr.) Bref. sensu lato (s.l.) is a necrotrophic pathogen that causessevere damage to coniferous forests in the Northern Hemisphere. A genome-wide association studyanalysing the virulence of H. annosum sensu stricto (s.s.) on spruce (Picea abies) and pine (Pinussylvestris) using 23 homokaryotic haploid isolates was performed. The virulence of the isolates wasmeasured as lesion length in the phloem and fungal growth within the sapwood followinginoculations in the stem of 2-year-old pine and spruce seedlings. The fungal isolates were sequencedto between 2.6× and 12.6× coverage using the Illumina Genome Analyzer. This data set yielded33,018 single nucleotide polymorphisms (SNPs), with a minor allelic frequency of at least two out of23. These loci were present in all isolates. SNPs and mean values for each virulence trait were usedfor the association study. Twelve SNP markers distributed on seven contigs were found to besignificantly associated with fungal virulence (P< 0.0001). These regions were characterized forlinkage disequilibrium (LD) and gene contents. The LD blocks in these regions ranged between 1.2and 31.2 kb when present. Nine genes encoding calcineurin, acetylglutamate kinase/synthase,cytochrome P450 monooxygenase, serine carboxypeptidase, quinone oxidoreductase (ToxD), twoflavin-containing monooxygenases, exopolyphosphatase and a Swi5 transcription factor wereidentified as candidates for virulence.
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| 20. |
- Dalman, Kerstin, et al.
(författare)
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A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum ss
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- The dense single nucleotide polymorphisms (SNP) panels needed for genome wide association (GWA) studies have hitherto been expensive to establish and use on non-model organisms. To overcome this, we used a next generation sequencing approach to both establish SNPs and to determine genotypes. We conducted a GWA study on a fungal species, analysing the virulence of Heterobasidion annosum s.s., a necrotrophic pathogen, on its hosts Picea abies and Pinus sylvestris. From a set of 33,018 single nucleotide polymorphisms (SNP) in 23 haploid isolates, twelve SNP markers distributed on seven contigs were associated with virulence (P,0.0001). Four of the contigs harbour known virulence genes from other fungal pathogens and the remaining three harbour novel candidate genes. Two contigs link closely to virulence regions recognized previously by QTL mapping in the congeneric hybrid H. irregulare6H. occidentale. Our study demonstrates the efficiency of GWA studies for dissecting important complex traits of small populations of non-model haploid organisms with small genomes.
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| 21. |
- Dalman, Kerstin, et al.
(författare)
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Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato
- 2012
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Ingår i: Proceedings e report. ; 93, s. 67-70
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We investigated two hypotheses for the origin of the root rot fungus Heterobasidionannosum species complex: (i) that geology has been an important factor for the speciation (ii) that coevolutionaryprocesses with the hosts drove the divergence of the pathogen species. The H. annosumspecies complex consists of five species: three occur in Europe, H. annosum s.s., Heterobasidionparviporum and Heterobasidion abietinum, and two in North America, Heterobasidion irregulare andHeterobasidion occidentale; all with different but partially overlapping host preferences. Theevolution of the H. annosum species complex was studied using six partially sequenced genes,between 10 and 30 individuals of each species were analysed. Neighbour-joining trees wereconstructed for each gene, and a Bayesian tree was built for the combined data set. In addition,haplotype networks were constructed to illustrate the species relationships. For three of the genes, H.parviporum and H. abietinum share haplotypes supporting recent divergence and⁄or possible geneflow. We propose that the H. annosum species complex originated in Laurasia and that the H.annosum s.s.⁄H. irregulare and H. parviporum⁄H. abietinum⁄H. occidentale ancestral species emergedbetween 45 and 60 Ma in the Palaearctic, well after the radiation of the host genera. Our data implythat H. irregulare and H. occidentale were colonizing North America via different routes. Inconclusion, plate tectonics are likely to have been the main factor influencing Heterobasidionspeciation and biogeography.
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| 22. |
- Dalman, Kerstin, et al.
(författare)
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Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato
- 2010
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19, s. 4979-4993
-
Tidskriftsartikel (refereegranskat)abstract
- We investigated two hypotheses for the origin of the root rot fungus Heterobasidion annosum species complex: (i) that geology has been an important factor for the speciation (ii) that co-evolutionary processes with the hosts drove the divergence of the pathogen species. The H. annosum species complex consists of five species: three occur in Europe, H. annosum s.s., Heterobasidion parviporum and Heterobasidion abietinum, and two in North America, Heterobasidion irregulare and Heterobasidion occidentale; all with different but partially overlapping host preferences. The evolution of the H. annosum species complex was studied using six partially sequenced genes, between 10 and 30 individuals of each species were analysed. Neighbour-joining trees were constructed for each gene, and a Bayesian tree was built for the combined data set. In addition, haplotype networks were constructed to illustrate the species relationships. For three of the genes, H. parviporum and H. abietinum share haplotypes supporting recent divergence and/or possible gene flow. We propose that the H. annosum species complex originated in Laurasia and that the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 and 60 Ma in the Palaearctic, well after the radiation of the host genera. Our data imply that H. irregulare and H. occidentale were colonizing North America via different routes. In conclusion, plate tectonics are likely to have been the main factor influencing Heterobasidion speciation and biogeography.
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| 23. |
- Davydenko, Kateryna, et al.
(författare)
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Invasion of Emerald Ash Borer Agrilus planipennis and Ash Dieback Pathogen Hymenoscyphus fraxineus in Ukraine-A Concerted Action
- 2022
-
Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- Emerald Ash Borer (EAB), Agrilus planipennis, is a beetle that originates from East Asia. Upon invasion to North America in the early 2000s, it killed untold millions of ash trees. In European Russia, EAB was first detected in Moscow in 2003 and proved to have the potential to also kill native European ash (Fraxinus excelsior). The beetle has since spread in all geographic directions, establishing itself in eastern Ukraine by 2019 and possessing potential for further westward spread towards the EU. Apart from the approaching EAB, F. excelsior is currently threatened by the dieback disease (ADB) caused by the invasive ascomycete fungus Hymenoscyphus fraxineus. The infestation by EAB combined with ADB infection is expected to be more lethal than either of them alone, yet the potential consequences are unknown. To date, eastern Ukraine represents the geographic area in which both invasions overlap, thus providing the opportunity for related investigations. The aims of the study were to investigate: (i) the EAB expansion range in Ukraine, (ii) the relative susceptibility of F. excelsior and American ash (Fraxinus pennsylvanica) to EAB and ADB, and (iii) the combined effect/impact on ash condition imposed by both the pest and disease in the area subjected to the invasion. The results have demonstrated that (i) the invasion of EAB is currently expanding both in terms of newly infested trees and invaded geographic area; (ii) F. excelsior is more resistant to EAB than F. pennsylvanica, while F. excelsior is more susceptible to ADB than F. pennsylvanica; and (iii) the infection by ADB is likely to predispose F. excelsior to the infestation by EAB. It was concluded that inventory and mapping of surviving F. excelsior, affected by both ADB and EAB, is necessary to acquire genetic resources for the work on strategic, long-term restoration of F. excelsior in devastated areas, thereby tackling a possible invasion of EAB to the EU.
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| 24. |
- Edin, Eva, et al.
(författare)
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Fungicide sensitivity in Swedish isolates of Phaeosphaeria nodorum
- 2009
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Ingår i: Plant Pathology. - : Wiley. - 0032-0862 .- 1365-3059. ; 58, s. 655-664
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Tidskriftsartikel (refereegranskat)abstract
- This is the first report of variability in sensitivity of Phaeosphaeria nodorum to the fungicide azoxystrobin, and also reports on sensitivity to propiconazole, prothioconazole and cyprodinil. An in vitro sensitivity test of 42 isolates from five Swedish winter wheat fields, collected in 2003-2005, was performed on malt extract agar amended with six concentrations of each fungicide. Four isolates collected during the early 1990s, before azoxystrobin had been commercially used in agriculture, were used as references. Fragments of DNA from 231 isolates, including the reference isolates, were sequenced for the genes of cytochrome b and CYPS1 in search for amino acid substitutions known to cause loss of sensitivity to strobilurins and triazoles, respectively. The majority of the P. nodorum isolates possessed the amino acid substitution G143A, associated with loss of sensitivity in fungi to strobilurins, except in one field where only half of the isolates had the substitution. The EC(50) values varied between 0.66 mg L(-1) to estimations far above 1000 mg L(-1), with an estimated median value of 366 mg L(-1). The EC, values of the reference isolates ranged from 0.02 to 80.72 mg L(-1). The P. nodorum population is still sensitive to propiconazole, prothioconazole and cyprodinil, even though some isolates varied in sensitivity to triazoles. Part of the CYP51 gene, a possible target for triazole sensitivity, was sequenced but no nonsynonymous substitutions were found.
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| 25. |
- Edin, Eva, et al.
(författare)
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Spatiotemporal variation in the fungal community associated with wheat leaves showing symptoms similar to stagonospora nodorum blotch
- 2010
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Ingår i: European Journal of Plant Pathology. - : Springer Science and Business Media LLC. - 0929-1873 .- 1573-8469. ; 126, s. 373-386
-
Tidskriftsartikel (refereegranskat)abstract
- The fungal communities on wheat leaves showing symptoms similar to stagonospora nodorum blotch were analysed using terminal restriction fragment length polymorphism (T-RFLP). Collection of diseased leaves was carried out in eleven winter wheat fields located in three regions of Sweden during mid-July in 2003-2005. Fourteen different fungal species were found on the leaves out of which thirteen were identified to the species level and one to the genus level. The majority of the samples had between one and four species present of which at least one was a pathogen. Among the analysed leaves three major leaf pathogens were found: Phaeosphaeria nodorum was common during 2003 and 2004, Mycosphaerella graminicola dominated during 2005. Pyrenophora tritici-repentis was present in all fields, but sometimes in just a few samples. Phaeosphaeria nodorum and P. tritici-repentis often co-occurred on the same leaf. In addition, seven species of yeast and three saprophytes frequently occurred on the leaves every year. The variation in fungal community was largest between the different years while the region of Uppland diverged from the other two regions in species composition. No significant differences in fungal communities were found within a single field, indicating a uniform community at the lowest spatial level.
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| 26. |
- Elfstrand, Malin, et al.
(författare)
-
Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance
- 2020
-
Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 43, s. 1779-1791
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Tidskriftsartikel (refereegranskat)abstract
- It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot.In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.
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| 27. |
- Elfstrand, Malin, et al.
(författare)
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Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds
- 2020
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29, s. 199-213
-
Tidskriftsartikel (refereegranskat)abstract
- The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.
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| 28. |
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| 29. |
- Elfstrand, Malin, et al.
(författare)
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Root Rot Resistance Locus PaLAR3 Is Delivered by Somatic Embryogenesis (SE) Pipeline in Norway Spruce (Picea abies (L.) Karst.)
- 2021
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5% of the studied elite trees carry the PaLAR3B allele (45% are heterozygous and 2.5% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2% to 32.1% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.
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| 30. |
- Fang, Jun, et al.
(författare)
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Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Genome wide association studies (GWAS) have mapped multiple independent cancer susceptibility loci to chr5p15.33. Here, we show that fine-mapping of pancreatic and testicular cancer GWAS within one of these loci (Region 2 in CLPTM1L) focuses the signal to nine highly correlated SNPs. Of these, rs36115365-C associated with increased pancreatic and testicular but decreased lung cancer and melanoma risk, and exhibited preferred protein-binding and enhanced regulatory activity. Transcriptional gene silencing of this regulatory element repressed TERT expression in an allele-specific manner. Proteomic analysis identifies allele-preferred binding of Zinc finger protein 148 (ZNF148) to rs36115365-C, further supported by binding of purified recombinant ZNF148. Knockdown of ZNF148 results in reduced TERT expression, telomerase activity and telomere length. Our results indicate that the association with chr5p15.33-Region 2 may be explained by rs36115365, a variant influencing TERT expression via ZNF148 in a manner consistent with elevated TERT in carriers of the C allele.
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| 31. |
- Finlay, Roger, et al.
(författare)
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Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
- 2024
-
Ingår i: New Phytologist. - 0028-646X .- 1469-8137. ; 242, s. 1676-1690
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Tidskriftsartikel (refereegranskat)abstract
- Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils.We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls.Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling.Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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| 32. |
- Himmelstrand, Kajsa, et al.
(författare)
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Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes
- 2014
-
Ingår i: Current Genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 60, s. 303-313
-
Tidskriftsartikel (refereegranskat)abstract
- Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.
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| 33. |
- Hu, Yang, et al.
(författare)
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Characterization of a Heterobasidion irregulare endo-rhamnogalacturonase that mediate growth on pectin
- 2018
-
Ingår i: Journal of Phytopathology. - : Wiley. - 0931-1785 .- 1439-0434. ; 166, s. 34-43
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Tidskriftsartikel (refereegranskat)abstract
- Heterobasidion irregulare is one of five Heterobasidion annosum sensu lato (s.l.) species, which are destructive pathogens in boreal and temperate forests of the northern hemisphere that causes root and butt rot in conifer. A gene encoding endo-rhamnogalacturonase (HIRHG), which belongs to the glycoside hydrolase family 28 (GH28), was found in a quantitative trait loci (QTL) region for virulence in Heterobasidion. In this study, we showed that HIRHG is highly upregulated during necrotrophic infection of Norway spruce compared with growth in liquid culture and that the HIRHG encoded protein is produced during fungal growth on complex carbon sources. Phylogenetic analysis of endo-rhamnogalacturonases revealed that rhamnogalacturonase genes have been lost in most of the biotrophic and hemibiotrophic plant pathogens investigated but were common in necrotrophic pathogens and saprophytic fungi. Heterologous expression of the HIRHG gene in the hemibiotrophic fungus Magnaporthe oryzae increased its capacity to grow on pectin; however, the transformed M.oryzae isolates showed significant less infection of rice leaves compared to the wild type.
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| 34. |
- Hu, Yang, et al.
(författare)
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Evolution of RNA interference proteins dicer and argonaute in Basidiomycota
- 2013
-
Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 105, s. 1489-1498
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Tidskriftsartikel (refereegranskat)abstract
- RNA interference (RNAi) refers to a mechanism in which cells control gene expression, protect the genome against mobile repetitive DNA sequences, retro elements and transposons, and defend themself against viruses. Two core components, dicer and argonaute, are central in the RNAi machinery. In this study the evolution of argonaute and dicer genes were analyzed with 43 fungal genomes, with the focus on Basidiomycota. Argonaute and dicer genes are widely represented in Basidiomycota as well as in other fungal groups, but the number of copies of them vary. However, in certain lineages, argonaute or dicer is missing. Our results suggest an ancient duplication of dicer and argonaute genes concurrently with early diversification of the Basidiomycota followed by additional species-specific duplications and losses of more recent origin. Several distinct RNAi pathways exist in fungi, based on structural similarity and phylogenetic relationship, our results indicate that quelling possibly exists in most Basidiomycota, while we could not find any evidence for the MSUD (meiotic-silencing) pathway in Basidiomycota. RNAi has been developed to be an important tool for reverse genetics studies. Because both argonaute and dicer are present in almost all Basidiomycota our results indicate that it should be possible to develop RNAi as a tool for functional studies of genes in most Basidiomycota species.
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| 35. |
- Hu, Yang, et al.
(författare)
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The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce
- 2020
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Heterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.
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| 36. |
- James, Timothy Y., et al.
(författare)
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Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum
- 2008
-
Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 62:9, s. 2279-2296
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Tidskriftsartikel (refereegranskat)abstract
- Many fungi have heterokaryotic life stages in which genetically different nuclei inhabit the same cell. In basidiomycetes, the heterokaryon is the product of mating and represents a genomic union very similar to a diploid thallus, yet the maintenance of unfused nuclei suggests a more complex association of the two genomes relative to diploidy. In species with variable numbers of nuclei per heterokaryotic cell, nuclear ratios within a mycelium may possibly become imbalanced (differ from 1:1) due to nuclear competition. In this study, heterokaryons of the basidiomycete Heterobasidion parviporum were examined to determine the effects of genotype and environment on nuclear ratios within vegetative mycelia. The data reveal that nuclear ratios are frequently imbalanced, generally stable over time, and genetically determined. The nuclear ratios were affected by environment, but the observed nuclear ratios did not follow the expectations of strong selection acting on a population of nuclei. Instead, these ratios were largely driven by genetic effects and epigenetic effects. Finally, the data suggest that nuclear ratio imbalance also affects both gene transcription and growth rate, implying that heterokaryotic basidiomycetes are not functionally equivalent to diploid individuals and have a higher potential for genotypic and phenotypic variation.
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| 37. |
- Karlsson, Magnus, et al.
(författare)
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Two hydrophobin genes from the conifer pathogen Heterobasidion annosum are expressed in aerial hyphae.
- 2007
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 99:2, s. 227-231
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Tidskriftsartikel (refereegranskat)abstract
- Two hydrophobin genes (HAH1 and HAH2) have been identified in a Heterobasidion annosum infection-stage cDNA-library. Comparisons of their nucleotide and amino acid sequences show similarity to the coh1 hydrophobin from Coprinopsis cinerea and the sc3 hydrophobin from Schizophyllum commune. Both HAH1 and HAH2 display the amino acid consensus pattern of class I hydrophobins, including the spacing of eight conserved cysteine residues. Real-time quantitative RT-PCR showed high expression of both genes in aerial hyphae but low expression in submerged hyphae and during in vitro infection of pine seedlings. Segregation analysis of HAH1 and HAH2 in a defined cross of Heterobasidion annosum localised HAH1 to linkage group 3 but did not positioned HAH2 in the genetic linkage map. Sequence characteristics and expression patterns of HAH1 and HAH2 suggest a role in aerial growth of mycelia, but not during pathogenesis.
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| 38. |
- Karlsson, Niclas G., 1966, et al.
(författare)
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Identification of transient glycosylation alterations of sialylated mucin oligosaccharides during infection by the rat intestinal parasite Nippostrongylus brasiliensis.
- 2000
-
Ingår i: The Biochemical journal. - 0264-6021. ; 350 Pt 3, s. 805-14
-
Tidskriftsartikel (refereegranskat)abstract
- The sialylation of the oligosaccharides from small-intestinal mucins during a 13-day infectious cycle was studied in Sprague-Dawley rats with the parasite Nippostrongylus brasiliensis. Sialic acid analysis and release, permethylation and analysis by GC-MS of the sialylated oligosaccharides isolated from the 'insoluble' mucin complex revealed a relative decrease (4-7-fold) of N-glycolylneuraminic acid compared with N-acetylneuraminic acid just before parasite expulsion. Northern blots showed that this effect was due to the decreased expression of a hydroxylase converting CMP-N-acetylneuraminic acid into CMP-N-glycolylneuraminic acid. Analysis of other rat strains showed that this parasite infection also caused the same effect in these animals. Detailed analysis of infected Sprague-Dawley rats revealed four sialylated oligosaccharides not found in the uninfected animals. These new oligosaccharides were characterized in detail and all shown to contain the trisaccharide epitope NeuAc/NeuGcalpha2-3(GalNAcbeta1-4)Galbeta1 (where NeuGc is N-glycolyl neuraminic acid). This epitope is similar to the Sd(a)- and Cad-type blood-group antigens and suggests that the infection causes the induction of a GalNAcbeta1-4 glycosyltransferase. This model for an intestinal infection suggests that the glycosylation of intestinal mucins is a dynamic process being modulated by the expression of specific enzymes during an infection process.
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| 39. |
- Kälvö, David, et al.
(författare)
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Biosynthesis of fomannoxin in the root rotting pathogen Heterobasidion occidentale
- 2012
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Ingår i: Phytochemistry. - : Elsevier BV. - 0031-9422 .- 1873-3700. ; 84, s. 31-39
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Tidskriftsartikel (refereegranskat)abstract
- Fomannoxin is a biologically active benzohydrofuran, which has been suggested to be involved in the pathogenicity of the root rotting fungus Heterobasidion annosum sensu lato. The biosynthesis of fomannoxin was investigated through an isotopic enrichment study utilizing [1-C-13]glucose as metabolic tracer. C-13 NMR spectroscopic analysis revealed the labeling pattern and showed that the isoprene building block originates from the mevalonic acid pathway, whereas the aromatic motif is formed via the shikimic acid route by elimination of pyruvate from chorismic acid. A natural product, 4-hydroxy-3-(3-methylbut-2-enyl)benzaldehyde (1), was isolated and characterized, and was suggested to be a key intermediate in the biosynthesis of fomannoxin and related secondary metabolites previously identified from the H. annosum fungal species complex. (c) 2012 Elsevier Ltd. All rights reserved.
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| 40. |
- Kälvö, David, et al.
(författare)
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Secondary metabolite comparison of the species within the Heterobasidion annosum s.l. complex
- 2014
-
Ingår i: Phytochemistry. - : Elsevier BV. - 0031-9422 .- 1873-3700. ; 108, s. 243-251
-
Tidskriftsartikel (refereegranskat)abstract
- The metabolite production of the five members of the fungal species complex Heterobasidion annosum s.l., i.e. H. annosum s.s., H. abietinum, H. parviporum, H. occidentale and H. irregulare, was analyzed by LC-HAMS. The five members are described to have differences in host preferences: H. annosum s.s. and H. irregulare are pine infecting species, and H. parviporum, H. occidentale and H. abietinum are non-pine infecting. Principal component analysis (PCA) of the LC-HRMS data showed that samples from the five species could be separated into five groups and in accordance with the differences in host preferences. Twenty-three compounds, important to the observed PCA grouping, were isolated and identified. The main contributor to the separation of the pine infecting species from the non-pine infecting species in PC1 was the benzohydrofuran fomannoxin, which was only detected in the pine infecting species H. annosum s.s. and H. irregulare. These two species were further separated in PC3, and one major contributor here was the sesquiterpene deoxyfomannosin A. The three non-pine infecting species were separated in PC2, by epoxydrimenol that was detected in only two of the species and further in PC4, where a few fomannoxin related compounds were important for the grouping. During the work, three unknown compounds were isolated and described: 3-hydroxy-2-(1,3-dihydroxypropan-2-yl)-2,3-dihydrobenzofuran-5-carbaldehyde, 3-hydroxy-2-(1,2,3-trihydroxypropan-2-yl)-2,3-dihydrobenzofuran-5-carbaldehyde and 3-hydroxy-2,3-dihydrobenzofuran-5-carboxylic acid. (c) 2014 Elsevier Ltd. All rights reserved.
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| 41. |
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| 42. |
- Lankinen, Åsa, et al.
(författare)
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Challenges and opportunities for increasing the use of low-risk plant protection products in sustainable production. A review
- 2024
-
Ingår i: Agronomy for Sustainable Development. - : Springer. - 1774-0746 .- 1773-0155. ; 44:2
-
Forskningsöversikt (refereegranskat)abstract
- Plant production systems worldwide are struggling to meet the diverse and increasing needs of humankind while also facing challenges such as climate change and biodiversity loss. This, combined with the desirable transition from the use of conventional pesticides to more sustainable plant protection solutions, has led to an urgent, and increasing, need for low-risk plant protection products (PPPs) to be developed, applied, and integrated into management practices across all types of plant production systems. Despite a high demand from end users and consumers together with joint political goals at the EU level to replace conventional pesticides, the number of low-risk PPPs on the European market remains low, in comparison to synthetic agrochemicals. In this review, we summarize knowledge about the policy, technical, and administrative issues hampering the process of bringing new low-risk PPPs to the European market. We present an overview of the challenges in using the low-risk PPPs that are currently available within the EU agricultural, horticultural, and forestry sectors. We describe the variation in modes of action and the limitations associated with different application techniques and give concrete examples of problems and solutions from Swedish plant production sectors, in contrast to global perspectives as demonstrated by examples from African agriculture. Finally, we conclude that trans-sectoral, multi-actor approaches are required and provide suggestions on how to address the remaining knowledge gaps related to efficiency, application, and economics of low-risk PPP use in Integrated Pest Management (IPM) solutions for plant protection to improve future food security in Europe.
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| 43. |
- Larsson, Rebecca, et al.
(författare)
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Diplodia sapinea in Swedish forest nurseries
- 2021
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Ingår i: Plant Protection Science. - 1212-2580. ; 57, s. 66-69
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Tidskriftsartikel (refereegranskat)abstract
- Diplodia sapinea is a common forest pathogen on Pinus spp. in a large part of the world. In 2013, disease caused by this pathogen on Scots pine (Pinus sylvestris) trees in Sweden was reported for the first time. In this study, we report the first detection of D. sapinea on diseased seedlings of P. sylvestris from two Swedish forest nurseries. Infected seedlings were collected July-November 2019. Diplodia sapinea was identified by morphological characteristics of fungal structures on plant tissues and from culture grown on Hagem agar media, followed by sequencing of fungal ITS rDNA. The result emphasizes the susceptibility of P. sylvestris seedlings. More research is needed to better understand the risk for disease spreading within forest nurseries and into the forest through infected plant material.
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| 44. |
- Larsson, Rebecca, et al.
(författare)
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The development of foliar fungal communities of nursery-grown Pinus sylvestris seedlings
- 2023
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Ingår i: Scandinavian Journal of Forest Research. - 0282-7581 .- 1651-1891. ; 38, s. 513-528
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Tidskriftsartikel (refereegranskat)abstract
- In forest nurseries, foliar fungi play a key role in the health of tree seedlings. The aim of this study was to study the diversity and the development of foliar fungal species associated with nursery-grown Pinus sylvestris, and to evaluate the effect of two biological control products and two growth-stimulating products on seedling growth and disease control, as well as seedling associated fungal community. The study was conducted at four Swedish forest nurseries. Fungal communities were assessed from non-symptomatic needles using high-throughput sequencing of the ITS2 rRNA region. The fungal pathogens Cladosporium sp. (15.1%), Phoma herbarum (14.5%), and Alternaria alternata (5.5%) were among the most abundant fungi. Results showed that the nurseries and the development of fungal communities influenced the occurrence of dominant fungal taxa. Disease prevalence was low and microbial treatments had no significant impact on seedling growth and survival, nor on the number of fungal operational taxonomic units (OTUs), species diversity, and species evenness (p > 0.05). In conclusion, the results showed a dynamic change in foliar fungal community structure over the growing season. With appropriate nursery management strategies and under suitable climatic conditions, nursery seedlings can remain healthy even in the presence of fungal pathogens.
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| 45. |
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| 46. |
- Lind, Mårten, et al.
(författare)
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Heterobasidion annosum s.l. Genomics
- 2014
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Ingår i: Advances in Botanical Research. - 0065-2296. ; 70, s. 371-396
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Forskningsöversikt (refereegranskat)abstract
- The economically important forest pathogen H. irregulare represents one of the most complete sequenced genomes among Basidiomycota/Agaricomycotina, with few gaps and a low nucleotide error rate (1 per 100,000 bp). Ninety percent of the predicted genes have support from microarray analysis or cDNA sequencing although individual gene models would benefit from a curation supported by a high-coverage RNA-seq data. The sequencing of the H. irregulare genome has paved the way for many other genetic and genomic studies within the species complex and will be an invaluable resource for the research community for many years.
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| 47. |
- Liu, Bing, et al.
(författare)
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Biochemical studies of two lytic polysaccharide monooxygenases from the white-rot fungus Heterobasidion irregulare and their roles in lignocellulose degradation
- 2017
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Lytic polysaccharide monooxygenases (LPMO) are important redox enzymes produced by microorganisms for the degradation of recalcitrant natural polysaccharides. Heterobasidion irregulare is a white-rot phytopathogenic fungus that causes wood decay in conifers. The genome of this fungus encodes 10 putative Auxiliary Activity family 9 (AA9) LPMOs. We describe the first biochemical characterization of H. irregulare LPMOs through heterologous expression of two CBM-containing LPMOs from this fungus (HiLPMO9H, HiLPMO9I) in Pichia pastoris. The oxidization preferences and substrate specificities of these two enzymes were determined. The two LPMOs were shown to cleave different carbohydrate components of plant cell walls. HiLPMO9H was active on cellulose and oxidized the substrate at the C1 carbon of the pyranose ring at beta-1,4-glycosidic linkages, whereas HiLPMO9I cleaved cellulose with strict oxidization at the C4 carbon of glucose unit at internal bonds, and also showed activity against glucomannan. We propose that the two LPMOs play different roles in the plant-cell-wall degrading system of H. irregulare for degradation of softwood and that the lignocellulose degradation mediated by this white-rot fungus may require collective efforts from multi-types of LPMOs.
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| 48. |
- Liu, Bing, et al.
(författare)
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Side-by-side biochemical comparison of two lytic polysaccharide monooxygenases from the white-rot fungus Heterobasidion irregulare on their activity against crystalline cellulose and glucomannan
- 2018
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 13:9
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Tidskriftsartikel (refereegranskat)abstract
- Our comparative studies reveal that the two lytic polysaccharide monooxygenases HiLP-MO9B and HiLPMO9I from the white-rot conifer pathogen Heterobasidion irregulare display clear difference with respect to their activity against crystalline cellulose and glucomannan. HiLPMO9I produced very little soluble sugar on bacterial microcrystalline cellulose (BMCC). In contrast, HiLPMO9B was much more active against BMCC and even released more soluble sugar than the H. irregulare cellobiohydrolase I, HiCel7A. Furthermore, HiLPMO9B was shown to cooperate with and stimulate the activity of HiCel7A, both when the BMCC was first pretreated with HiLPMO9B, as well as when HiLPMO9B and HiCel7A were added together. No such stimulation was shown by HiLPMO9I. On the other hand, HiLPMO9I was shown to degrade glucomannan, using a C4-oxidizing mechanism, whereas no oxidative cleavage activity of glucomannan was detected for HiLPMO9B. Structural modeling and comparison with other glucomannan-active LPMOs suggest that conserved sugar-interacting residues on the L2, L3 and LC loops may be essential for glucomannan binding, where 4 out of 7 residues are shared by HiLPMO9I, but only one is found in HiLPMO9B. The difference shown between these two H. irregulare LPMOs may reflect distinct biological roles of these enzymes within deconstruction of different plant cell wall polysaccharides during fungal colonization of softwood.
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| 49. |
- Nemesio Gorriz, Miguel, et al.
(författare)
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Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies
- 2016
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 171:4, s. 2671-2681
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Tidskriftsartikel (refereegranskat)abstract
- Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.
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| 50. |
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