The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Background: Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome. Findings: Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. Conclusions: The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity

Modelling of peristaltic pumps with respect to viscoelastic tube material properties and fatigue effects

Peristaltic pump technology is widely used wherever relatively low, highly accurately dosed volumetric flow rates are required and where fluid contamination must be excluded. Thus, typical fields of application include food, pharmaceuticals, medical technology, and analytics. In certain cases, when applied in conjunction with polymer-based tubing material, supplied peristaltic flow rates are reported to be significantly lower than the expected set flow rates. Said flow rate reductions are related to (i) the chosen tube material, (ii) tube material fatigue effects, and (iii) the applied pump frequency. This work presents a fast, dynamic, multiphysics, 1D peristaltic pump solver, which is demonstrated to capture all qualitatively relevant effects in terms of peristaltic flow rate reduction within linear peristaltic pumps. The numerical solver encompasses laminar fluid dynamics, geometric restrictions provided by peristaltic pump operation, as well as viscoelastic tube material properties and tube material fatigue effects. A variety of validation experiments were conducted within this work. The experiments point to the high degree of quantitative accuracy of the novel software and qualify it as the basis for elaborating an a priori drive correction

A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ε

Casein kinase 1 (CK1) plays central roles in various signal transduction pathways and performs many cellular activities. For many years CK1 was thought to act independently of modulatory subunits and in a constitutive manner. Recently, DEAD box RNA helicases, in particular DEAD box RNA helicase 3 X-linked (DDX3X), were found to stimulate CK1 activity in vitro In order to observe CK1 activity in living cells and to study its interaction with DDX3X, we developed a CK1-specific FRET biosensor. This tool revealed that DDX3X is indeed required for full CK1 activity in living cells. Two counteracting mechanisms control the activity of these enzymes. Phosphorylation by CK1 impairs the ATPase activity of DDX3X and RNA destabilizes the DDX3X-CK1 complex. We identified possible sites of interaction between DDX3X and CK1. While mutations identified in the DDX3X genes of human medulloblastoma patients can enhance CK1 activity in living cells, the mechanism of CK1 activation by DDX3X points to a possible therapeutic approach in CK1-related diseases such as those caused by tumors driven by aberrant Wnt/beta-catenin and Sonic hedgehog (SHH) activation. Indeed, CK1 peptides can reduce CK1 activity

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of sci- entific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To over- come this problem, we sequenced its genome using diverse technologies with sufficient cover- age and assembled it via a novel multiple hybrid assembly workflow that combines next- generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano IrysVR system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the as- sembly of other allotetraploid genomes

Stable regular critical points of the Mumford–Shah functional are local minimizers

Abstract. In this paper it is shown that any regular critical point of the Mumford-Shah func-tional, with positive definite second variation, is an isolated local minimizer with respect to competitors which are sufficiently close in the L1-topology. A global minimality result in small tubular neighborhoods of the discontinuity set is also established. 1