| 1. |
- Berlin, Anna, et al.
(författare)
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Evolutionary history reveals two phylogenetically distinct species within Puccinia graminis
- 2013
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Ingår i: Acta Phytopathologica Sinica. - 0412-0914. ; 43, s. 486-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The cereal pathogen Puccinia graminis is considered to have high genetic diversity within the species. We hereby hypothesize that the different formae speciales of P. graminis have co-evolved with their various grass hosts. Elongation factor 1 alpha (EF-1α) and beta-tubulin (BT) genes, the internal transcribed spacer (ITS) region and mitochondrial cytochrome oxidase subunit I (COI) were sequenced from DNA isolated from Puccinia graminis collected from cereal and wild grasses to infer the phylogeny of the fungus. The related species Puccinia coronata, collected from both oats and wild grasses, were used as a reference throughout the analysis. Coalescence analysis showed that the time to the most recent common ancestor (TMRCA) for P. graminis and P. coronata were in all models further away in time than TMRCA for the two formae speciales. Within the species P. graminis, two main clades were formed; one including samples collected from Avena sativa, Avena fatua, Phleum pratense, and the other including samples collected from Triticum aestivum, Triticum monoccocum, Secale cereal and Hordeum vulgare, suggesting that P. graminis is to be divided into two different taxa. However, samples collected from the weed host Elytrigia repens, did not show any clear pattern, the samples equally grouped with either of the two groups. The phylogeny of P. graminis was thus congruent with its respective grass hosts, which confirm a co-evolution with the host.
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| 2. |
- Beste, Lisa, et al.
(författare)
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Synthesis of Hydroxylated Sterols in Transgenic Arabidopsis Plants Alters Growth and Steroid Metabolism
- 2011
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 157:1, s. 426-440
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Tidskriftsartikel (refereegranskat)abstract
- To explore mechanisms in plant sterol homeostasis, we have here increased the turnover of sterols in Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum) plants by overexpressing four mouse cDNA encoding cholesterol hydroxylases (CHs), hydroxylating cholesterol at the C-7, C-24, C-25, or C-27 positions. Compared to the wild type, the four types of Arabidopsis transformant showed varying degrees of phenotypic alteration, the strongest one being in CH25 lines, which were dark-green dwarfs resembling brassinosteroid-related mutants. Gas chromatography-mass spectrometry analysis of extracts from wild-type Arabidopsis plants revealed trace levels of alpha and beta forms of 7-hydroxycholesterol, 7-hydroxycampesterol, and 7-hydroxysitosterol. The expected hydroxycholesterol metabolites in CH7-, CH24-, and CH25 transformants were identified and quantified using gas chromatography-mass spectrometry. Additional hydroxysterol forms were also observed, particularly in CH25 plants. In CH24 and CH25 lines, but not in CH7 ones, the presence of hydroxysterols was correlated with a considerable alteration of the sterol profile and an increased sterol methyltransferase activity in microsomes. Moreover, CH25 lines contained clearly reduced levels of brassinosteroids, and displayed an enhanced drought tolerance. Equivalent transformations of potato plants with the CH25 construct increased hydroxysterol levels, but without the concomitant alteration of growth and sterol profiles observed in Arabidopsis. The results suggest that an increased hydroxylation of cholesterol and/or other sterols in Arabidopsis triggers compensatory processes, acting to maintain sterols at adequate levels.
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| 3. |
- Chaudhary, Rajiv, et al.
(författare)
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Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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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| 7. |
- Dalman, Kerstin, et al.
(författare)
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Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19, s. 4979-4993
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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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| 8. |
- Dalman, Kerstin
(författare)
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Heterobasidion root rot : genetic mapping of virulence and evolutionary history
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Heterobasidion annosum (Fr.) Bref. sensu lato (s.l.) is a necrotrophic pathogen causing damage to conifers in the Northern Hemisphere. H. annosum s.l. consists of five species: three European [H. annosum sensu stricto (s.s.), H. parviporum and H. abietinum] and two North American (H. irregulare and H. occidentale); all with different but partially overlapping host preferences. A multilocus phylogenetic tree was built and the divergence times were estimated. Plate tectonics is likely to have been the main factor influencing Heterobasidion speciation and biogeography. Along with the geographical separation, the Heterobasidion species have specialized on different host genera. The H. annosum species complex originated in Laurasia and the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 million–60 million years ago in the Palaearctic. The data imply that H. irregulare and H. occidentale colonized North America via different routes: H. irregulare colonizing from the east via Trans Atlantic land bridges and H. occidentale colonizing from the west via the Bering Land Bridge. Alternatively H. occidentale originated from North America. Identification of virulence factors is important for understanding the Heterobasidion–conifer pathosystem. Two studies of genetic mapping of virulence were performed. Virulence traits were measured as lesion length in the phloem and fungal growth in the sapwood of pine and spruce. Quantitative trait loci (QTL) were identified and positioned on a genetic linkage map for virulence of 102 progeny isolates from a cross between H. irregulare and H. occidentale. Both virulence traits in Picea abies identified significant QTLs on linkage group (LG) 15. Another QTL was positioned on LG 15 for the lesion length measurement in Pinus sylvestris. Moreover, QTLs on two separate smaller LGs were identified for fungal growth in sapwood and lesion length, respectively. The QTLs probably represent loci important for specific as well as general aspects of virulence on P. sylvestris and P. abies. A genome-wide association study was performed for virulence on 23 H. annosum s.s. isolates. Twelve SNP markers distributed on seven contigs were significantly associated with virulence. From these, three regions were characterized, two with one marker each with the lowest p-values and one region containing six markers. The linkage disequilibrium blocks in these regions ranged between 1.2 and 31.2 kb. Seven genes were identified as candidate virulence determinants encoding calcineurin, acetylglutamate kinase/synthase, cytochrome P450 monooxygenase, serine carboxypeptidase, quinone oxidoreductase (ToxD) and two flavin-containing monooxygenases.
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| 9. |
- Dalman, Kerstin, et al.
(författare)
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Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development
- 2017
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Ingår i: BMC Plant Biology. - : BioMed Central. - 1471-2229. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: The NAC family of transcription factors is one of the largest gene families of transcription factors in plants and the conifer NAC gene family is at least as large, or possibly larger, as in Arabidopsis. These transcription factors control both developmental and stress induced processes in plants. Yet, conifer NACs controlling stress induced processes has received relatively little attention. This study investigates NAC family transcription factors involved in the responses to the pathogen Heterobasidion annosum (Fr.) Bref. sensu lato. Results: The phylogeny and domain structure in the NAC proteins can be used to organize functional specificities, several well characterized stress-related NAC proteins are found in III-3 in Arabidopsis (Jensen et al. Biochem J 426: 183-196, 2010). The Norway spruce genome contain seven genes with similarity to subgroup III-3 NACs. Based on the expression pattern PaNAC03 was selected for detailed analyses. Norway spruce lines overexpressing PaNAC03 exhibited aberrant embryo development in response to maturation initiation and 482 misregulated genes were identified in proliferating cultures. Three key genes in the flavonoid biosynthesis pathway: a CHS, a F3'H and PaLAR3 were consistently down regulated in the overexpression lines. In accordance, the overexpression lines showed reduced levels of specific flavonoids, suggesting that PaNAC03 act as a repressor of this pathway, possibly by directly interacting with the promoter of the repressed genes. However, transactivation studies of PaNAC03 and PaLAR3 in Nicotiana benthamiana showed that PaNAC03 activated PaLAR3A, suggesting that PaNAC03 does not act as an independent negative regulator of flavan-3-ol production through direct interaction with the target flavonoid biosynthetic genes. Conclusions: PaNAC03 and its orthologs form a sister group to well characterized stress-related angiosperm NAC genes and at least PaNAC03 is responsive to biotic stress and appear to act in the control of defence associated secondary metabolite production.
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| 10. |
- Dauphinee, Adrian N., et al.
(författare)
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Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators
- 2019
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Ingår i: Plant Physiology. - : AMER SOC PLANT BIOLOGISTS. - 0032-0889 .- 1532-2548. ; 181:3, s. 855-866
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Tidskriftsartikel (refereegranskat)abstract
- Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.
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