The Bioinformatic Applications of Hi-C and Linked Reads.

Long-range sequencing grants insight into additional genetic information beyond that which can be accessed by both short reads and modern long-read technology. Several new sequencing technologies are available for long-range datasets such as "Hi-C" and "Linked Reads" with high-throughput and high-resolution genome analysis, and are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this article, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-C), 10x Genomics Linked Reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single tube long fragment read (stLFR). We detailed the mechanisms and data products of the five platforms, introduced several of the most important applications, evaluated the quality of sequencing data from different platforms, and discussed the currently available bioinformatics tools. We hope this work will benefit the selection of appropriate long-range technology for specific biological studies.

Effects of Volatile Flavour Compound Variations on the Varying Aroma of Mangoes 'Tainong' and 'Hongyu' during Storage.

The aroma, taste, and flavour profiles of mango cultivars vary, directly influencing their marketability and consumer acceptance. In this study, we explored the effects of volatile organic compounds (VOCs) on the distinct aromas of two mango cultivars during storage using GC-IMS and HS-SPME-GC-MS combined with OPLS-DA analysis. Our findings revealed that the terpene and aldehyde contents were higher in the 'Tainong' mango cultivar, compared to the 'Hongyu' mango, while the ester content was lower. The aroma was attributed to the presence of terpinolene, 2-nonenal, delta-carene, and alpha-phellandrene in the early stages of storage, and later-between 5 and 11 days-to ethyl acetate, ethyl butyrate, and ethyl propanoate. Further analysis of characteristic VOCs using OPLS-DA demonstrated and explained the strong grassy aroma of the 'Tainong' mango, and the strong fruity and sweet aromas of the 'Hongyu' mango. Additionally, esters mainly accumulated during the later periods of storage, especially propyl butyrate, which was produced and accumulated when fruit quality deteriorated in the later storage period. Our study provides a theoretical basis for detecting mango VOCs during storage to determine the appropriate marketing time for the two mango cultivars and enables informed consumer choice.

Facile preparation of a metal-phenolic network-based lymph node targeting nanovaccine for antitumor immunotherapy.

Cancer vaccines are being explored for enhanced cancer immunotherapy and prophylaxis. Some of their prevailing weaknesses, however, such as complicated preparation, poor biocompatibility, and failure to elicit strong cellular immune responses, have limited their further clinical applications. Here, we reported a multifunctional nanovaccine that was prepared in a quick and simple way. During the self-assembly of metal-phenolic networks (MPNs), the antigen ovalbumin (OVA) and immunoreactive chlorogenic acid (CHA) were simultaneously loaded. Owing to its dual pH and reduction sensitivities, the nanovaccine could deliver antigens into the cytoplasm of dendritic cells (DCs) and facilitate the cross-presentation of antigens. Moreover, the results of in vivo immunization assays demonstrated that the nanovaccine significantly excited the antigen presentation of DCs and provoked a robust cellular immune response with the restrained activation of regulatory T cells (Tregs), by targeting lymph nodes and executing the function of CHA. In vivo antitumor assays indicated that the nanovaccine with good biocompatibility afforded conspicuous cancer treatment and prevention effects. Overall, the nanovaccine presented in this study shows a promise for potentiating cancer immunotherapy by the lymph node-targeted delivery. STATEMENT OF SIGNIFICANCE: Cancer nanovaccines can be used for cancer immunotherapy. However, some existing shortcomings, such as cumbersome preparation, poor biocompatibility, and failure to elicit strong immune responses, limit the clinical application of cancer nanovaccines. This study developed a multifunctional nanovaccine that was readily prepared through the self-assembly of metal-phenolic networks. The nanovaccine with dual pH and reduction sensitivities could efficiently promote the antigen lysosome escape and cross-presentation. In vivo, it efficiently delivered antigen into lymph nodes and provoked strong cellular immune responses, and thus it showed significant cancer immunotherapy and prevention effect.

Physiological and Transcriptome Analyses of CaCl2 Treatment to Alleviate Chilling Injury in Pineapple.

The post-harvest ripening of pineapples can be effectively postponed by refrigerated storage. Nevertheless, internal browning (IB) frequently appears in pineapples after refrigerated storage during the course of the shelf life at room temperature, which is known as chilling injury (CI). In this study, the chilling injury of pineapple fruit was induced by a low temperature (6 °C) and transferred to normal-temperature storage; the best concentration of 50 µmol/L of CaCl2 was selected by the IB appearance and electrical conductivity. Fruit quality, reactive oxygen species (ROS), antioxidants, and transcription factors were investigated. The physiological data results indicated that pineapples treated with 50 µmol/L of CaCl2 maintained fruit quality, decreased reactive oxygen species (ROS), and enhanced the antioxidant activity of fruits, alleviating internal browning (IB) symptoms in pineapple fruit. The expressions of related genes were also consistent with the physiological changes by the transcriptome data analysis. In addition, we focused on some related metabolic pathways, including phenylpropanoid biosynthesis, MAPK pathway, plant hormone, plant-pathogen interaction, tricarboxylic acid cycle (TAC), and fatty acid biosynthesis. We performed integrative analyses of transcriptome data combined with a series of physiology and experimental analyses on the internal browning of pineapples, which will be of great significance to extending the shelf life of pineapples through molecular biology in the future.

SlBEL11 affects tomato carotenoid accumulation by regulating SlLCY-b2.

Extensive data have demonstrated that carotenoid accumulation in tomato fruit is influenced by environmental cues and hormonal signals. However, there is insufficient information on the mechanism of its transcriptional regulation, as many molecular roles of carotenoid biosynthetic pathways remain unknown. In this work, we found that the silence of the BEL1-like family transcription factor (TF) BEL1-LIKE HOMEODOMAIN 11 (SlBEL11) enhanced carotenoid accumulation in virus induced gene silencing (VIGS) analysis. In its RNA interference (RNAi) transgenic lines, a significant increase in the transcription level for the lycopene beta cyclase 2 (SlLCY-b2) gene was detected, which encoded a key enzyme located at the downstream branch of the carotenoid biosynthetic pathway. In Electrophoretic mobility shift assay (EMSA), SlBEL11 protein was confirmed to bind to the promoter of SlLCY-b2 gene. In addition, the dual-luciferase reporter assay showed its intrinsic transcriptional repression activity. Collectively, our findings added a new member to the carotenoid transcriptional regulatory network and expanded the functions of the SlBEL11 transcription factor.

Proteomic profiling of 24-epibrassinolide-induced chilling tolerance in harvested banana fruit.

The mechanism of 24-epibrassinolide (EBR)-induced chilling tolerance in harvested banana fruit was investigated. Results showed that EBR pretreatment remarkably suppressed the development of chilling injury (CI) in harvested banana fruit during 12 days of cold storage at 8 °C, as indicated by lower CI index in treated fruit. Physiological measurements exhibited that EBR treatment reduced the relative electrolyte leakage and malondialdehyde (MDA) content while increased the chlorophyll fluorescence (Fv/Fm), total soluble solids (TSS) and ratio of TSS and titratable acidity. Furthermore, the differentially accumulated proteins of banana fruit in response to EBR and cold treatment were investigated by employing gel-based proteomic in combination with MALDI-TOF-TOF MS and LC-ESI-MS/MS analyses. There were fifty five protein spots to be successfully identified. Notably, most of up-regulated proteins by EBR treatment were related to energy biosynthesis, stress response and cell wall modification. In contrast, proteins involved in protein degradation and energy consumption were down-regulated by EBR treatment. These results suggest that EBR treatment could enhance the defense ability, promote the synthesis and utilization of energy, as well as maintain the protein function via enhancing protein biosynthesis and inhibiting protein degradation, consequently contributing to improvement of cold tolerance in harvested banana fruit. SIGNIFICANCE: To extend our understanding of chilling injury (CI) of harvested banana fruit, we reported the effect of 24-epibrassinolide (EBR) on CI of banana fruit when stored at 8 °C. It was the first report on the comprehensive proteomic analysis of banana fruit in response to EBR treatment at low temperature. EBR pretreatment significantly reduced CI in harvested banana fruit. Fifty five protein spots were successfully identified. Notably, the most of up-regulated proteins by EBR treatment were related to energy biosynthesis, stress response and cell wall modification. In contrast, proteins involved in protein degradation and energy consumption were down-regulated. These results suggest that exogenous EBR treatment could enhance the defense ability and maintain high energy status. Meanwhile, EBR treatment maintained protein function via enhancing protein biosynthesis and inhibiting protein degradation. These results may help us to understand the molecular mechanism of the chilling tolerance induced by EBR treatment and broaden the current knowledge of the mechanism of CI of harvested banana fruit.

Effect of postharvest spray of apple polyphenols on the quality of fresh-cut red pitaya fruit during shelf life.

Fresh-cut (FC) red pitaya fruit were treated with 5ga.i.l-1 apple polyphenols (APP) and then stored at 20°C for up to 4days to evaluate the effects on attributes. Results showed that FC pitaya fruit with APP treatment showed greater colour retention, delayed softening, reduced loss of soluble solids content, titratable acidity, betacyanin and total phenolics compared with untreated FC fruit. APP treatment also maintained antioxidant activity, as indicated by higher DPPH radical-scavenging activity and reducing power compared with untreated FC pitaya fruit. APP treatment strongly suppressed microbial growth, contributing to improvement of product safety. Because APP is a natural product, we propose that application of APP could be a convenient, safe and low-cost approach to maintain the quality and extend the shelf life of FC red pitaya fruit.

Antifungal activity of 1-methylcyclopropene (1-MCP) against anthracnose (Colletotrichum gloeosporioides) in postharvest mango fruit and its possible mechanisms of action.

Anthracnose caused by Colletotrichum gloeosporioides is one of the most important postharvest diseases in mango fruit, often causing huge economic losses. In this study, the effect of 1-methylcyclopropene (1-MCP) against anthracnose in postharvest mango fruit and the mechanisms involved were investigated. 1-MCP induced reactive oxygen species (ROS) generation, damaged the mitochondria and destroyed the integrity of plasma membrane of spores of C. gloeosporioides, significantly suppressing spore germination and mycelial growth of C. gloeosporioides. 1-MCP also decreased the decay incidence and lesion expansion of mango fruit caused by C. gloeosporioides. For the first time this study demonstrated that 1-MCP suppressed anthracnose of postharvest mango fruit by directly inhibiting spore germination and mycelial growth of C. gloeosporioides, thus providing a promising strategy for disease control.

High-throughput sequencing and degradome analysis identify miRNAs and their targets involved in fruit senescence of Fragaria ananassa.

In non-climacteric fruits, the respiratory increase is absent and no phytohormone is appearing to be critical for their ripening process. They must remain on the parent plant to enable full ripening and be picked at or near the fully ripe stage to obtain the best eating quality. However, huge losses often occur for their quick post-harvest senescence. To understanding the complex mechanism of non-climacteric fruits post-harvest senescence, we constructed two small RNA libraries and one degradome from strawberry fruit stored at 20°C for 0 and 24 h. A total of 88 known and 1224 new candidate miRNAs, and 103 targets cleaved by 19 known miRNAs families and 55 new candidatemiRNAs were obtained. These targets were associated with development, metabolism, defense response, signaling transduction and transcriptional regulation. Among them, 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence. The present study provided valuable information for understanding the quick senescence of strawberry fruit, and offered a foundation for studying the miRNA-mediated senescence of non-climacteric fruits.

Antifungal Activity and Possible Mode of Action of Borate Against Colletotrichum gloeosporioides on Mango.

The effect of potassium tetraborate on germination of conidia of Colletotrichum gloeosporioides, and postharvest rot of mango were studied. An application of K2B4O7 to mango trees at flowering increased fruit set and decreased the incidence of anthracnose on harvested fruit. The effects of borate on the germination, nuclear division, endocytosis, and ultrastructure of conidia of C. gloeosporioides were studied using light, confocal, and transmission electron microscopy. The results showed that borate inhibited germination and germ tube elongation, delayed nuclear division, and impaired endocytosis of C. gloeosporioides conidia. Ultrastructural abnormalities also occurred in conidia treated with borate, and these included an increase in numbers of vacuoles, cytoplasmic disintegration, mitochondria degradation, and plasmolysis. These results suggest that borate can serve as a potential alternative to synthetic fungicides for the control of the postharvest disease of mango fruit caused by C. gloeosporioides.