| 1. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Binder, Manfred, et al.
(författare)
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Phylogenetic and phylogenomic overview of the Polyporales
- 2013
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 105:6, s. 1350-1373
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Tidskriftsartikel (refereegranskat)abstract
- We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000–49 900 00 bp and encode for 12 910–16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.
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| 3. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 4. |
- 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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| 5. |
- Eshghi Sahraei, Shadi, et al.
(författare)
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Evolution and genomic signatures of arbuscular mycorrhizal fungi
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungi include at least two lineages of mutualistic plant symbionts, the arbuscular mycorrhizal fungi and the mycorrhizal fungi in Endogonales, as well as fungi with saprotrophic, pathogenic and endophytic life styles. Their evolutionary relationships remained enigmatic and the taxonomic rank is currently fluid. We recognize three phyla and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as the sister to Mucoromycota and Mortierellomycota. Analysis of gene family contractions and expansions indicate that arbuscular mycorrhizae (AM) fungi and Endogonales represent two independent transitions to mutualistic plant symbiosis and that these occurred early in the divergence of these lineages.
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| 6. |
- Floudas, Dimitrios, et al.
(författare)
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Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
- 2015
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 76, s. 78-92
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. (C) 2015 Elsevier Inc. All rights reserved.
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| 7. |
- Grigoriev, Igor A., et al.
(författare)
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A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation
- 2013
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 25:10, s. 105112-
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Tidskriftsartikel (refereegranskat)abstract
- The explicit algebraic Reynolds stress model of Wallin and Johansson [J. Fluid Mech. 403, 89 (2000)] is extended to compressible and variable-density turbulent flows. This is achieved by correctly taking into account the influence of the mean dilatation on the rapid pressure-strain correlation. The resulting model is formally identical to the original model in the limit of constant density. For two-dimensional mean flows the model is analyzed and the physical root of the resulting quartic equation is identified. Using a fixed-point analysis of homogeneously sheared and strained compressible flows, we show that the new model is realizable, unlike the previous model. Application of the model together with a K - omega model to quasi one-dimensional plane nozzle flow, transcending from subsonic to supersonic regime, also demonstrates realizability. Negative "dilatational" production of turbulence kinetic energy competes with positive "incompressible" production, eventually making the total production negative during the spatial evolution of the nozzle flow. Finally, an approach to include the baroclinic effect into the dissipation equation is proposed and an algebraic model for density-velocity correlations is outlined to estimate the corrections associated with density fluctuations. All in all, the new model can become a significant tool for CFD (computational fluid dynamics) of compressible flows.
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| 8. |
- Grigoriev, Igor A., et al.
(författare)
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Capturing turbulent density flux effects in variable density flow by an explicit algebraic model
- 2015
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:4
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Tidskriftsartikel (refereegranskat)abstract
- The explicit algebraic Reynolds stress model of Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25, 105112 (2013)] is extended to account for the turbulent density flux in variable density flows. The influence of the mean dilatation and the variation of mean density on the rapid pressure-strain correlation are properly accounted for introducing terms balancing a so-called "baroclinic" production in the Reynolds stress tensor equation. Applying the weak-equilibrium assumption leads to a self-consistent formulation of the model. The model together with a K - ω model is applied to a quasi-one-dimensional plane nozzle flow transcending from subsonic to supersonic regimes. The model remains realizable with constraints put on the model parameters. When density fluxes are taken into account, the model is less likely to become unrealizable. The density variance coupled with a "local mean acceleration" also can influence the model acting to increase anisotropy. The general trends of the behaviour of the anisotropy and production components under the variation of model parameters are assessed. We show how the explicit model can be applied to two- and three-dimensional mean flows without previous knowledge of a tensor basis to obtain the general solution. Approaches are proposed in order to achieve an approximate solution to the consistency equation in cases when analytic solution is missing. In summary, the proposed model has the potential to significantly improve simulations of variable-density flows.
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| 9. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Algebraic Reynolds stress modeling of turbulence subject to rapid homogeneous and non-homogeneous compression or expansion
- 2016
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Ingår i: Physics of fluids. - : American Institute of Physics (AIP). - 1070-6631 .- 1089-7666. ; 28:2, s. 026101-
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Tidskriftsartikel (refereegranskat)abstract
- A recently developed explicit algebraic Reynolds stress model (EARSM) by Grigoriev et al. ["A realizable explicit algebraic Reynolds stress model for compressible turbulent flow with significant mean dilatation," Phys. Fluids 25(10), 105112 (2013)] and the related differential Reynolds stress model (DRSM) are used to investigate the influence of homogeneous shear and compression on the evolution of turbulence in the limit of rapid distortion theory (RDT). The DRSM predictions of the turbulence kinetic energy evolution are in reasonable agreement with RDT while the evolution of diagonal components of anisotropy correctly captures the essential features, which is not the case for standard compressible extensions of DRSMs. The EARSM is shown to give a realizable anisotropy tensor and a correct trend of the growth of turbulence kinetic energy K, which saturates at a power law growth versus compression ratio, as well as retaining a normalized strain in the RDT regime. In contrast, an eddy-viscosity model results in a rapid exponential growth of K and excludes both realizability and high magnitude of the strain rate. We illustrate the importance of using a proper algebraic treatment of EARSM in systems with high values of dilatation and vorticity but low shear. A homogeneously compressed and rotating gas cloud with cylindrical symmetry, related to astrophysical flows and swirling supercritical flows, was investigated too. We also outline the extension of DRSM and EARSM to include the effect of non-homogeneous density coupled with "local mean acceleration" which can be important for, e.g., stratified flows or flows with heat release. A fixed-point analysis of direct numerical simulation data of combustion in a wall-jet flow demonstrates that our model gives quantitatively correct predictions of both streamwise and cross-stream components of turbulent density flux as well as their influence on the anisotropies. In summary, we believe that our approach, based on a proper formulation of the rapid pressure-strain correlation and accounting for the coupling with turbulent density flux, can be an important element in CFD tools for compressible flows.
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| 10. |
- Grigoriev, Igor, 1984-, et al.
(författare)
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Unified explicit algebraic Reynolds stress model for compressible, heat-releasing and supercritical flowswith large density variation
- 2016
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- An explicit algebraic model (EARSM) for variable denstiy turbulent flow developed by Grigoriev et al. [Phys. Fluids (2015)] is revisited here. We apply it to a quasi one-dimensional nozzle flow, a wall-jet flow with combustion and large density variation and a supercritical flow of carbon dioxide with heat transfer and buoyancy. It is confirmed that the coupling between strong mean density gradient due to high speed, heat release or thermodynamic variations and the 'local mean acceleration' of the flow produces strong turbulent density and heat fluxes, which strongly affect the turbulence. The possible calibration branches are identified and analyzed. We show that a simple and unified calibration of the model gives good predictions for all cases considered. Therefore, the model is a reliable tool for the computation of compressible flows with large density variation.
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