Background Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false-positive signals. Results We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false-positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30–40 times using HiFi sequencing is required for phasing of the leaf rust genome, with 0.7% heterozygosity, and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. Conclusions This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms.
Fungal diseases of plants are responsible for major losses in agriculture, highlighting the need for rapid and accurate identification of plant pathogens. Disease outcomes are often defined not only by the main pathogen but are influenced by diverse microbial communities known as the microbiome at sites of infection. Here we present the first use of whole genome shot-gun sequencing with a portable DNA sequencing device as a method for the detection of fungal pathogens from wheat (Triticum aestivum) in a standard molecular biology laboratory. The data revealed that our method is robust and applicable to the diagnosis of fungal diseases including wheat stripe rust (caused by Puccinia striiformis f. sp. tritici), Septoria tritici blotch (caused by Zymoseptoria tritici), and yellow leaf spot (caused by Pyrenophora tritici repentis). We also identified the bacterial genus Pseudomonas co-present with Puccinia and Zymoseptoria but not Pyrenophora infections. One limitation of the method is the over-representation of redundant wheat genome sequences from samples. This could be addressed by long-range amplicon-based sequencing approaches in future studies, which specifically target nonhost organisms. Our work outlines a new approach for detection of a broad range of plant pathogens and associated microbes using a portable sequencer in a standard laboratory, providing the basis for future development of an on-site disease monitoring system. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Different cupric oxide (CuO) structures have attracted intensive interest because of their promising applications in various fields. In this study, three kinds of CuO structures, namely, CuO microdisks, CuO nanoblocks, and CuO microspheres, are synthesized by solution-based synthetic methods. The morphologies and crystal structures of these CuO structures are characterized by field-emission scanning electron microscope and X-ray diffractometer, respectively. They are used as thermal conductive fillers to prepare silicone-based thermal greases, giving rise to great enhancement in thermal conductivity. Compared with pure silicone base, the thermal conductivities of thermal greases with CuO microdisks, CuO nanoblocks, and CuO microspheres are 0.283, 0256, and 0.239 W/mK, respectively, at filler loading of 9 vol.%, which increases 139%, 116%, and 99%, respectively. These thermal greases present a slight descendent tendency in thermal conductivity at elevated temperatures. These experimental data are compared with Nan's model prediction, indicating that the shape factor has a great influence on thermal conductivity improvement of thermal greases with different CuO structures. Meanwhile, due to large aspect ratio of CuO microdisks, they can form thermal networks more effectively than the other two structures, resulting in higher thermal conductivity enhancement.
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