Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.Zheng, Y.; Wu, S.; Bai, Y.; Sun, H.; Jiao, C.; Guo, S.; Zhao, K.... (2018). Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):D1128-D1136. https://doi.org/10.1093/nar/gky944SD1128D113647D

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits

Attentive SOLO for Sonar Target Segmentation

Imaging sonar systems play an important role in underwater target detection and location. Due to the influence of reverberation noise on imaging sonar systems, the task of sonar target segmentation is a challenging problem. In order to segment different types of targets in sonar images accurately, we proposed the gated fusion-pyramid segmentation attention (GF-PSA) module. Specifically, inspired by gated full fusion, we improved the pyramid segmentation attention (PSA) module by using gated fusion to reduce the noise interference during feature fusion and improve segmentation accuracy. Then, we improved the SOLOv2 (Segmenting Objects by Locations v2) algorithm with the proposed GF-PSA and named the improved algorithm Attentive SOLO. In addition, we constructed a sonar target segmentation dataset, named STSD, which contains 4000 real sonar images, covering eight object categories with a total of 7077 target annotations. The experimental results show that the segmentation accuracy of Attentive SOLO on STSD is as high as 74.1%, which is 3.7% higher than that of SOLOv2

IRSDD-YOLOv5: Focusing on the Infrared Detection of Small Drones

With the rapid growth of the global drone market, a variety of small drones have posed a certain threat to public safety. Therefore, we need to detect small drones in a timely manner so as to take effective countermeasures. At present, the method based on deep learning has made a great breakthrough in the field of target detection, but it is not good at detecting small drones. In order to solve the above problems, we proposed the IRSDD-YOLOv5 model, which is based on the current advanced detector YOLOv5. Firstly, in the feature extraction stage, we designed an infrared small target detection module (IRSTDM) suitable for the infrared recognition of small drones, which extracted and retained the target details to allow IRSDD-YOLOv5 to effectively detect small targets. Secondly, in the target prediction stage, we used the small target prediction head (PH) to complete the prediction of the prior information output via the infrared small target detection module (IRSTDM). We optimized the loss function by calculating the distance between the true box and the predicted box to improve the detection performance of the algorithm. In addition, we constructed a single-frame infrared drone detection dataset (SIDD), annotated at pixel level, and published an SIDD dataset publicly. According to some real scenes of drone invasion, we divided four scenes in the dataset: the city, sky, mountain and sea. We used mainstream instance segmentation algorithms (Blendmask, BoxInst, etc.) to train and evaluate the performances of the four parts of the dataset, respectively. The experimental results show that the proposed algorithm demonstrates good performance. The AP50 measurements of IRSDD-YOLOv5 in the mountain scene and ocean scene reached peak values of 79.8% and 93.4%, respectively, which are increases of 3.8% and 4% compared with YOLOv5. We also made a theoretical analysis of the detection accuracy of different scenarios in the dataset

Pristimerin Exacerbates Cellular Injury in Conditionally Reprogrammed Patient-Derived Lung Adenocarcinoma Cells by Aggravating Mitochondrial Impairment and Endoplasmic Reticulum Stress through EphB4/CDC42/N-WASP Signaling

Lung cancer is the most common and lethal malignant disease for which the development of efficacious chemotherapeutic agents remains an urgent need. Pristimerin (PRIS), a natural bioactive component isolated from various plant species in the Celastraceae and Hippocrateaceae families, has been reported to exhibit outstanding antitumor effects in several types of cells. However, the underlying mechanisms involved remain poorly understood. Here, we reported the novel finding that PRIS significantly suppressed lung cancer growth in conditionally reprogrammed patient-derived lung adenocarcinoma cells (CRLCs). We demonstrated that PRIS inhibited the cell viabilities, migrative and invaded abilities, and capillary structure formation of CRLCs. Furthermore, our results clarified that PRIS induced mitochondrial dysfunction through reactive oxygen species (ROS) generation, activation of caspase-9, caspase-3, and caspase-4, and expression of endoplasmic reticulum (ER) stress-associated proteins. Inhibition of ER stress by 4-PBA (4-phenylbutyric acid, a specific ER stress inhibitor) or CHOP siRNA transfection ameliorated PRIS-induced loss of mitochondrial membrane potential and intrinsic apoptosis. The present study also provides mechanistic evidence that PRIS suppressed the EphB4/CDC42/N-WASP signaling pathway, which is required for mitochondrial-mediated intrinsic apoptosis, activation of ER stress, and stimulation of caspase-4 induced by PRIS, and consequently resulting in suppressed cell viability, migration, and angiogenesis in CRLCs. Taken together, by providing a mechanistic insight into the modulation of ER stress-induced cell death in CRLCs by PRIS, we suggest that PRIS has a strong potential of being a new antitumor therapeutic agent with applications in the fields of human lung adenocarcinoma

A monofluoride ether-based electrolyte solution for fast-charging and low-temperature non-aqueous lithium metal batteries

Abstract The electrochemical stability window of the electrolyte solution limits the energy content of non-aqueous lithium metal batteries. In particular, although electrolytes comprising fluorinated solvents show good oxidation stability against high-voltage positive electrode active materials such as LiNi0.8Co0.1Mn0.1O2 (NCM811), the ionic conductivity is adversely affected and, thus, the battery cycling performance at high current rates and low temperatures. To address these issues, here we report the design and synthesis of a monofluoride ether as an electrolyte solvent with Li-F and Li-O tridentate coordination chemistries. The monofluoro substituent (-CH2F) in the solvent molecule, differently from the difluoro (-CHF2) and trifluoro (-CF3) counterparts, improves the electrolyte ionic conductivity without narrowing the oxidation stability. Indeed, the electrolyte solution with the monofluoride ether solvent demonstrates good compatibility with positive and negative electrodes in a wide range of temperatures (i.e., from −60 °C to +60 °C) and at high charge/discharge rates (e.g., at 17.5 mA cm−2). Using this electrolyte solution, we assemble and test a 320 mAh Li||NCM811 multi-layer pouch cell, which delivers a specific energy of 426 Wh kg−1 (based on the weight of the entire cell) and capacity retention of 80% after 200 cycles at 0.8/8 mA cm−2 charge/discharge rate and 30 °C

Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber

Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter selected against during domestication. QTL mapping and analysis of transgenic plants reveal a novel role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either, and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding