| 1. |
- Beier, Sebastian, et al.
(författare)
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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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| 2. |
- Houben, Janne, et al.
(författare)
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The emotional well-being of parents with children at genetic risk for type 1 diabetes before and during participation in the POInT-study
- 2022
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Ingår i: Pediatric Diabetes. - : Hindawi Limited. - 1399-543X .- 1399-5448. ; 23:8, s. 1707-1716
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: This study examined the emotional impact that parents experience when confronted with an increased genetic risk of type 1 diabetes (T1D) in their child. Population-based screening of neonates for genetic risk of chronic disease carries the risk of increased emotional burden for parents. Methods: Information was collected using a well-being questionnaire for parents of infants identified as having an increased risk for T1D in a multinational research study. Parents were asked to complete this questionnaire after they were told their child had an increased risk for T1D (Freder1k-study) and at several time points during an intervention study (POInT-study), where oral insulin was administered daily. Results: Data were collected from 2595 parents of 1371 children across five countries. Panic-related anxiety symptoms were reported by only 4.9% after hearing about their child having an increased risk. Symptoms of depression were limited to 19.4% of the parents at the result-communication visit and declined over time during the intervention study. When thinking about their child's risk for developing T1D (disease-specific anxiety), 47.2% worried, felt nervous and tense. Mothers and parents with a first-degree relative (FDR) with T1D reported more symptoms of depression and disease-specific anxiety (p < 0.001) than fathers and parents without a FDR. Conclusion: Overall, symptoms of depression and panic-related anxiety are comparable with the German population. When asked about their child's risk for T1D during the intervention study, some parents reported disease-specific anxiety, which should be kept in mind when considering population-based screening. As certain subgroups are more prone, it will be important to continue psychological screening and, when necessary, to provide support by an experienced, multidisciplinary team.
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| 3. |
- Jacobs, Philipp, et al.
(författare)
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A Rietveld refinement method for angular- and wavelength-dispersive neutron time-of-flight powder diffraction data.
- 2015
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Ingår i: Journal of Applied Crystallography. - 1600-5767. ; 48:Pt 6, s. 1627-1636
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Tidskriftsartikel (refereegranskat)abstract
- This paper introduces a two-dimensional extension of the well established Rietveld refinement method for modeling neutron time-of-flight powder diffraction data. The novel approach takes into account the variation of two parameters, diffraction angle 2θ and wavelength λ, to optimally adapt to the varying resolution function in diffraction experiments. By doing so, the refinement against angular- and wavelength-dispersive data gets rid of common data-reduction steps and also avoids the loss of high-resolution information typically introduced by integration. In a case study using a numerically simulated diffraction pattern of Rh0.81Fe3.19N taking into account the layout of the future POWTEX instrument, the profile function as parameterized in 2θ and λ is extracted. As a proof-of-concept, the resulting instrument parameterization is then utilized to perform a typical refinement of the angular- and wavelength-dispersive diffraction pattern of CuNCN, yielding excellent residuals within feasible computational efforts. Another proof-of-concept is carried out by applying the same approach to a real neutron diffraction data set of CuNCN obtained from the POWGEN instrument at the Spallation Neutron Source in Oak Ridge. The paper highlights the general importance of the novel approach for data analysis at neutron time-of-flight diffractometers and its possible inclusion within existing Rietveld software packages.
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| 4. |
- Jacobs, Philipp, et al.
(författare)
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Instrumental resolution as a function of scattering angle and wavelength as exemplified for the POWGEN instrument
- 2017
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Ingår i: Journal of Applied Crystallography. - 0021-8898. ; 50:3, s. 866-875
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Tidskriftsartikel (refereegranskat)abstract
- The method of angular- and wavelength-dispersive (e.g. two-dimensional) Rietveld refinement is a new and emerging tool for the analysis of neutron diffraction data measured at time-of-flight instruments with large area detectors. Following the approach for one-dimensional refinements (using either scattering angle or time of flight), the first step at each beam time cycle is the calibration of the instrument including the determination of instrumental contributions to the peak shape variation to be expected for diffraction patterns measured by the users. The aim of this work is to provide the users with calibration files and - for the later Rietveld refinement of the measured data - with an instrumental resolution file (IRF). This article will elaborate on the necessary steps to generate such an IRF for the angular- and wavelength-dispersive case, exemplified for the POWGEN instrument. A dataset measured on a standard diamond sample is used to extract the profile function in the two-dimensional case. It is found that the variation of reflection width with 2gθ and λ can be expressed by the standard equation used for evaluating the instrumental resolution, which yields a substantially more fundamental approach to the parameterization of the instrumental contribution to the peak shape. Geometrical considerations of the POWGEN instrument and sample effects lead to values for Δgθ, Δt and ΔL that yield a very good match to the extracted FWHM values. In a final step the refinement results are compared with the one-dimensional, i.e. diffraction-focused, case.A fundamental description of the instrument resolution file is elaborated for the angular- and wavelength-dispersive cases of Rietveld refinement, exemplified for the POWGEN instrument. It is shown how to refine the necessary profile function parameters from a dataset measured on a diamond reference sample. The analysis is performed in a two-dimensional refinement space based on the convenient variables d and d?.
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| 5. |
- Ma, Wei, et al.
(författare)
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Rye B chromosomes encode a functional Argonaute-like proteinwith in vitro slicer activities similar to its A chromosome paralog
- 2017
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Ingår i: New Phytologist. - : Wiley-Blackwell. - 0028-646X .- 1469-8137. ; 213:2, s. 904-916
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Tidskriftsartikel (refereegranskat)abstract
- B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, whichappear in many different species of eukaryote. So far, Bs have been considered to be geneti-cally inert elements without any functional genes.Our comparative transcriptome analysis and the detection of active RNA polymerase II(RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) con-tribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open read-ing frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts withoutdetectable similarity to known proteins and gene fragments from A chromosomes (As) werefound, suggesting an ongoing gene erosion process.In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that bothpossess RNA slicer activity. These data demonstrate unambiguously the presence of a func-tional AGO4B gene on Bs and that these Bs carry both functional protein coding genes andpseudogene copies.Thus, B-encoded genes may provide an additional level of gene control and complexity incombination with their related A-located genes. Hence, physiological effects, associated withthe presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.
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| 6. |
- Ma, Wei, et al.
(författare)
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The distribution of alpha-kleisin during meiosis in the holocentromeric plant Luzula elegans
- 2016
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Ingår i: Chromosome Research. - : SPRINGER. - 0967-3849 .- 1573-6849. ; 24:3, s. 393-405
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Tidskriftsartikel (refereegranskat)abstract
- Holocentric chromosomes occur in a number of independent eukaryotic lineages, and they form holokinetic kinetochores along the entire poleward chromatid surfaces. Due to this alternative chromosome structure, Luzula elegans sister chromatids segregate already in anaphase I followed by the segregation of the homologues in anaphase II. However, not yet known is the localization and dynamics of cohesin and the structure of the synaptonemal complex (SC) during meiosis. We show here that the alpha-kleisin subunit of cohesin localizes at the centromeres of both mitotic and meiotic metaphase chromosomes and that it, thus, may contribute to assemble the centromere in L. elegans. This localization and the formation of a tripartite SC structure indicate that the prophase I behaviour of L. elegans is similar as in monocentric species.
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| 7. |
- Mascher, Martin, et al.
(författare)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 8. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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