| 1. |
- Hepworth, Jo, et al.
(författare)
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Absence of warmth permits epigenetic memory of winter in Arabidopsis
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Plants integrate widely fluctuating temperatures to monitor seasonal progression. Here, we investigate the temperature signals in field conditions that result in vernalisation, the mechanism by which flowering is aligned with spring. We find that multiple, distinct aspects of the temperature profile contribute to vernalisation. In autumn, transient cold temperatures promote transcriptional shutdown of Arabidopsis FLOWERING LOCUS C (FLC), independently of factors conferring epigenetic memory. As winter continues, expression of VERNALIZATION INSENSITIVE3 (VIN3), a factor needed for epigenetic silencing, is upregulated by at least two independent thermosensory processes. One integrates long-term cold temperatures, while the other requires the absence of daily temperatures above 15 °C. The lack of spikes of high temperature, not just prolonged cold, is thus the major driver for vernalisation. Monitoring of peak daily temperature is an effective mechanism to judge seasonal progression, but is likely to have deleterious consequences for vernalisation as the climate becomes more variable.
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| 2. |
- Kohler, Annegret, et al.
(författare)
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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| 3. |
- Carlsson, Fredrik, 1974-, et al.
(författare)
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Strong clustering in a SNP study of Phlebiopsis gigantea in sweden
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The population structures of wood decaying basidomycetes depend on several factors; one is dispersal pattern of spores, another is age structure including lifespan and also environmental impacts like forest fires. Phlebiopsis gigantea has been shown to be in the group of basidomycetes that have a well developed tolerance to heat, is long-distance wind dispersed and whose fruit body show up early in succession on fallen logs. In a study of 132 individuals from 3 pairs of locations, 350 km apart, in middle to northern Sweden we used 26 SNP-markers in 6 loci to make a genetic clustering study using STRUCTURE (v. 2.3.4.). The hypothesis; first, clustering should follow the geographic sampling locations with more gene flow between geographically close locations, second; that genetic distance between different clusters should be low due to the long distance dispersal of spores, third; as markers are random we don’t expect to find a correlation between locations affected by forest fires and locations not affected by forest fires. In the study we found 5 clusters (Pr[K= 1]) with moderate to high Fst values (0,0697-03939). Clusters had a poor geographical correlation to sampled populations indicating a complicated population structure. Out of 132 individuals 119 had a private genotype showing a large genetic variation over the total area and a low level of clones in the field.
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| 4. |
- Carlsson, Fredrik, 1974-, et al.
(författare)
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Testing the probability of finding major decomposing basidiomycetes in logs with T-RFLP - implications for field sampling
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In this article we examine the limitations and potential of T-RFLP for the accurate detection of fungal species in dead wood. We collected cross-sections of decayed logs to evaluate the number of fungal species domains that are likely to be hit when drilling a sawdust sample from a log. We used these estimates to simulate the number of species that would be found using a certain number of samples. We found that in 99% of the simulations, 4 or fewer species would be contained in a sample. Based on these results we tested the probability of detecting two species of wood-decaying basidiomycetes at three different DNA concentration ratios: 1:1, 1:5 and 1:20. An additional experiment was done with 3-5 species. It was possible to detect all species at ratios higher than 1:20 but lower than 1:5; in this range all peaks were easily detected. We were able to detect all species in the mixtures of 3-5 species, with extracts from both pure cultures and wood.
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| 5. |
- de Vries, Ronald P, et al.
(författare)
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Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
- 2017
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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| 6. |
- Gaskell, George, et al.
(författare)
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Europeans and biotechnology in 2002 - Eurobarometer 58.0 : A report to the EC Directorate General for Research from the project "Life Sciences in European Society"
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This is the fifth in a series of Eurobarometer surveys on biotechnology and the life sciences. The surveys have been conducted in 1991, 1993, 1996, 1999 and in 2002. The survey is based on a representative sample of 16 500 respondents, approximately 1 000 in each EU member state (see report for exceptions). Survey design and analysis was conducted by an international research group ‘Life Sciences in European Society’ supported by DG Research. In a year when many European countries are involved in public discussions on aspects of biotechnology, this survey stands as a contribution to the informed debate.
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| 7. |
- Hepworth, Jo, et al.
(författare)
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Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes
- 2020
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Ingår i: eLIFE. - 2050-084X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- In Arabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor FLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the FLC repression mechanism is most important for adaptation to different environments is unclear. By analysing FLC dynamics in natural variants and mutants throughout winter in three field sites, we find that autumnal FLC expression, rather than epigenetic silencing, is the major variable conferred by the distinct Arabidopsis FLChaplotypes. This variation influences flowering responses of Arabidopsis accessions resulting in an interplay between promotion and delay of flowering in different climates to balance survival and, through a post-vernalization effect, reproductive output. These data reveal how expression variation through non-coding cis variation at FLC has enabled Arabidopsis accessions to adapt to different climatic conditions and year-on-year fluctuations.
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| 8. |
- Novikova, P. Y., et al.
(författare)
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Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
- 2016
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 48:9, s. 1077-1082
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Tidskriftsartikel (refereegranskat)abstract
- The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection. © 2016 Nature America, Inc. All rights reserved.
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| 9. |
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| 10. |
- Temrin, Hans, et al.
(författare)
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Is the higher rate of parental child homicide in stepfamilies an effect of non-genetic relatedness?
- 2011
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Ingår i: Current Zoology. - : Oxford University Press (OUP). - 1674-5507 .- 2396-9814. ; 57:3, s. 253-259
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Tidskriftsartikel (refereegranskat)abstract
- In an evolutionary perspective individuals are expected to vary the degree of parental love and care in relation to the fitness value that a child represents. Hence, stepparents are expected to show less solicitude than genetically related parents, and this lack of genetic relatedness has been used to explain the higher frequencies of child abuse and homicide found in stepfamilies. However, other factors than non-genetic relatedness may cause this over-representation in stepfamilies. Here we use a 45-year data set of parental child homicides in Sweden to test two hypotheses related to the higher incidence in stepfamilies: 1) adults in different types of family differ in their general disposition to use violence, and 2) parents are more likely to kill stepchildren than genetically related children. Of the 152 perpetrators in biparental families there was an overrepresentation of perpetrators in stepfamilies (n=27) compared with the general population. We found support for the first hypothesis in that both general and violent crime rates were higher in stepfamilies, both in the general population and among perpetrators of child homicide. However, we found no support for the second hypothesis because of the 27 perpetrators in stepfamilies the perpetrator killed a genetically related child in 13 cases, a stepchild in 13 cases and both types of children in one case. Moreover, out of the 12 families where the perpetrator lived with both stepchildren and genetic children, there was no bias towards killing stepchildren. Thus, we found no evidence for an effect of non-genetic relatedness per se.
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