109 research outputs found
A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved]
Length curves and volume functions for guadua bamboo (Guadua angustifolia Kunth) for the coffee region of Colombia
Variability of indices of macronutrient availability in soils at different spatial scales along an elevation transect in tropical moist forests (NE Ecuador)
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark
Plant-available P supply is not the main factor determining the benefit from arbuscular mycorrhiza to crop P nutrition and growth in contrasting cropping systems
CYP79D enzymes contribute to jasmonic acid-induced formation of aldoximes and other nitrogenous volatiles in two Erythroxylum species
The maize cytochrome P450 CYP79A61 produces phenylacetaldoxime and indole-3-acetaldoxime in heterologous systems and might contribute to plant defense and auxin formation
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