Efficient COI barcoding using high throughput single-end 400 bp sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Efficient \u3ci\u3eCOI\u3c/i\u3e Barcoding Using High Throughput Single-End 400 bp Sequencing

Background Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current highthroughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (for example, a maximum read length of 300 bp for the Illumina’s MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio’s SEQUEL II system). Results Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5′ and 3′ ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly, and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. Conclusions The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications

Genetic Management of Virus Diseases in Peanut

Peanut, also known as groundnut (Arachis hypogaea L.) is a major oilseed crop in the world. About 31 viruses representing 14 genera are reported to naturally infe.ct peanut in different parts of the world, although only a few of these are of economic importance. These include groundnutrosette disease in Africa, tomato spotted wilt-disease in the United States, peanut bud necrosis disease in south Asia, and peanut stripe virus disease in east and southeast Asia. Cucumber mosaic virus disease in China and Argentina and peanut stem necrosis disease in certain -pockets in southern India are also economically important. Host plant resistance provides the most effective and economic option to manage virus diseases. However, for many virus diseases, effective resistance gene(s) in cultivated peanut have not been identified. With a few exceptions, the virus resistance breeding work has received little attention in peanut improvement programs. Transgenic resistance offers another option in virus resistance breeding. This review focuses on the status of genetic resistance to various economically important groundnut viruses and'use of transgenic-technology for the improvement of virus resistance

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Investigating the jamming of particles in a three-dimensional fluid-driven flow via coupled CFD–DEM simulations

The clogging of a dense stream of particles when passing through an orifice occurs ubiquitously in both natural and industrial fields. Since most of the jamming phenomena lead to the negative effects, studying and preventing jamming is of great importance. There are two typical types of jamming due to different types of driving force: (a) gravity-driven jamming and (b) fluid-driven jamming. Among these two types of jamming, the fluid-driven jamming occurs in fluid-driven particle flows, and the initial solid concentration, the fluid velocity, and the orifice-particle size ratio has been demonstrated to have effects on the occurrence of this jamming. Although the individual influence of the initial solid concentration and orifice-particle size ratio on jamming has been studied, the coupled effects of these two factors on jamming are little known. In addition, the complex effects of the fluid velocity on jamming have not been fully discussed. To address these problems, this work performs a three-dimensional simulation of the fluid-driven jamming using the coupled Computational Fluid Dynamics–Discrete Element Method (CFD–DEM) model. At first, the jamming probability under different initial conditions is studied. The jamming probability is displayed on the solid concentration–orifice size ratio plane to illustrate the coupled effects of these two factors on jamming. The simulation results show that the critical solid concentration, at which the jamming probability increases to 1, increases with the orifice-particle size ratio. This is because an orifice with a larger orifice size ratio has a greater particle discharge capacity, which allows more particles to pass through without jamming. Then, we reveal the influence of fluid velocity over a wide range on the fluid-driven jamming type, jamming probability and shape of the jamming dome. To the author’s knowledge, this is the first time that the shape of the jamming dome has been related to the fluid velocity. The jamming dome formed in the higher-speed flow has a greater curvature due to the greater fluid drag acting on the particles

Story Generation Using Knowledge Graph under Psychological States

Story generation, aiming to generate a story that people could understand easily, captures increasing researchers’ attention in recent years. However, a good story usually requires interesting and emotional plots. Previous works only consider a specific or binary emotion like positive or negative. In our work, we propose a Knowledge-Aware Generation framework under Controllable CondItions (K-GuCCI). The model assigns a change line of psychological states to story characters, which makes the story develop following the setting. Besides, we incorporate the knowledge graph into the model to facilitate the coherence of the story. Moreover, we investigate a metric AGPS to evaluate the accuracy of generated stories’ psychological states. Experiments exhibit that the proposed model improves over standard benchmarks, while also generating stories reliable and valid