| 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. |
- Cunningham, LK, et al.
(författare)
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Reconstructions of surface ocean conditions from the North East Atlantic and Nordic Seas during the last Millennium
- 2013
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 23:7, s. 921-935
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Tidskriftsartikel (refereegranskat)abstract
- We undertake the first comprehensive effort to integrate North Atlantic marine climate records for the last millennium, highlighting some key components common within this system at a range of temporal and spatial scales. In such an approach, careful consideration needs to be given to the complexities inherent to the marine system. Composites therefore need to be hydrographically constrained and sensitive to both surface water mass variability and three-dimensional ocean dynamics. This study focuses on the northeast (NE) North Atlantic Ocean, particularly sites influenced by the North Atlantic Current. A composite plus regression approach is used to create an inter-regional NE North Atlantic reconstruction of sea surface temperature (SST) for the last 1000 years. We highlight the loss of spatial information associated with large-scale composite reconstructions of the marine environment. Regional reconstructions of SSTs off the Norwegian and Icelandic margins are presented, along with a larger-scale reconstruction spanning the NE North Atlantic. The latter indicates that the ‘Medieval Climate Anomaly’ warming was most pronounced before ad 1200, with a long-term cooling trend apparent after ad 1250. This trend persisted until the early 20th century, while in recent decades temperatures have been similar to those inferred for the ‘Medieval Climate Anomaly’. The reconstructions are consistent with other independent records of sea-surface and surface air temperatures from the region, indicating that they are adequately capturing the climate dynamics of the last millennium. Consequently, this method could potentially be used to develop large-scale reconstructions of SSTs for other hydrographically constrained regions.
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| 3. |
- 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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