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81.
Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes 下载免费PDF全文
Sebastian Beier Axel Himmelbach Thomas Schmutzer Marius Felder Stefan Taudien Klaus F. X. Mayer Matthias Platzer Nils Stein Uwe Scholz Martin Mascher 《Plant biotechnology journal》2016,14(7):1511-1522
Hierarchical shotgun sequencing remains the method of choice for assembling high‐quality reference sequences of complex plant genomes. The efficient exploitation of current high‐throughput technologies and powerful computational facilities for large‐insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole‐genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high‐quality assemblies of a large number of clones to assemble map‐based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path. 相似文献
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Sigbjrn Grini Kostiantyn V. Sopiha Nils Ross Xin Liu Tor S. Bjrheim Charlotte Platzer‐Bjrkman Clas Persson Lasse Vines 《Liver Transplantation》2019,9(27)
Sodium and oxygen are prevalent impurities in kesterite solar cells. Both elements are known to strongly impact performance of the kesterite devices and can be connected to efficiency improvements seen after heat treatments. The sodium distribution in the kesterite absorber is commonly reported, whereas the oxygen distribution has received less attention. Here, a direct relationship between sodium and oxygen in kesterite absorbers is established using secondary ion mass spectrometry and explained by defect analyses within the density functional theory. The calculations reveal a binding energy of 0.76 eV between the substitutional defects NaCu and OS in the nearest neighbor configuration, indicating an abundance of Na? O complexes in kesterite absorbers at relevant temperatures. Oxygen incorporation is studied by introducing isotopic 18O at different stages of the Cu2ZnSnS4/Mo/soda‐lime glass baseline processing. It is observed that oxygen from the Mo back contact and contaminations during the sulfurization are primary contributors to the oxygen distribution. Indeed, unintentional oxygen incorporation leads to immobilization of sodium. This results in a strong correlation between sodium and oxygen, in excellent agreement with the theoretical calculations. Consequently, oxygen availability should be monitored to optimize postdeposition heat treatments to control impurities in kesterite absorbers and ultimately, the solar cell efficiency. 相似文献
84.
Maga Daniel Thonemann Nils Hiebel Markus Sebastião Diogo Lopes Tiago F. Fonseca César Gírio Francisco 《The International Journal of Life Cycle Assessment》2019,24(2):266-280
The International Journal of Life Cycle Assessment - The use of bagasse and trash from sugarcane fields in ethanol production is supposed to increase the ethanol yield per hectare, to reduce the... 相似文献
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Daniela Bustos‐Korts Ian K. Dawson Joanne Russell Alessandro Tondelli Davide Guerra Chiara Ferrandi Francesco Strozzi Ezequiel L. Nicolazzi Marta Molnar‐Lang Hakan Ozkan Maria Megyeri Peter Miko Esra akr Enes Yakr Noemi Trabanco Stefano Delbono Stylianos Kyriakidis Allan Booth Davide Cammarano Martin Mascher Peter Werner Luigi Cattivelli Laura Rossini Nils Stein Benjamin Kilian Robbie Waugh Fred A. van Eeuwijk 《The Plant journal : for cell and molecular biology》2019,99(6):1172-1191
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi‐environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype‐by‐environment (G×E) modelling. Sub‐populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock‐related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large‐effect alleles. Our analysis supports a gene‐level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses. 相似文献
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Joanna Melonek Ruonan Zhou Philipp E. Bayer David Edwards Nils Stein Ian Small 《The Plant journal : for cell and molecular biology》2019,97(2):281-295
Nuclear restorer of fertility (Rf) genes suppress the effects of mitochondrial genes causing cytoplasmic male sterility (CMS), a condition in which plants fail to produce viable pollen. Rf genes, many of which encode RNA‐binding pentatricopeptide repeat (PPR) proteins, are applied in hybrid breeding to overcome CMS used to block self‐pollination of the seed parent. Here, we characterise the repertoire of restorer‐of‐fertility‐like (RFL) PPR genes in barley (Hordeum vulgare). We found 26 RFL genes in the reference genome (‘Morex’) and an additional 51 putative orthogroups (POGs) in a re‐sequencing data set from 262 barley genotypes and landraces. Whereas the sequences of some POGs are highly conserved across hundreds of barley accessions, the sequences of others are much more variable. High sequence variation strongly correlates with genomic location – the most variable genes are found in a cluster on chromosome 1H. A much higher likelihood of diversifying selection was found for genes within this cluster than for genes present as singlets. This work includes a comprehensive analysis of the patterns of intraspecific variation of RFL genes. The RFL sequences characterised in this study will be useful for the development of new markers for fertility restoration loci. 相似文献
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The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule. To test whether this crystal contact introduces a structural perturbation into the catalytic core, we have analyzed approximately 200 ns of molecular dynamics (MD) simulations. In the absence of crystal packing, the simulated G76 fluctuates between several conformations, including one wherein G76 establishes a perpendicular base quadruplet in the major groove of the adjacent P1 stem. Second-site mutagenesis experiments suggest that the identity of the nucleotide in position 76 (N76) indeed contributes to the catalytic activity of a trans-acting HDV ribozyme through its capacity for hydrogen bonding with P1. By contrast, in the cis-cleaving genomic ribozyme the functional relevance of N76 is less pronounced and not correlated with the P1 sequence. Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross-correlations in the trefoil turn. 相似文献