Exploring the Diversity of Plant DNA Viruses and Their Satellites Using Vector-Enabled Metagenomics on Whiteflies

Current knowledge of plant virus diversity is biased towards agents of visible and economically important diseases. Less is known about viruses that have not caused major diseases in crops, or viruses from native vegetation, which are a reservoir of biodiversity that can contribute to viral emergence. Discovery of these plant viruses is hindered by the traditional approach of sampling individual symptomatic plants. Since many damaging plant viruses are transmitted by insect vectors, we have developed “vector-enabled metagenomics” (VEM) to investigate the diversity of plant viruses. VEM involves sampling of insect vectors (in this case, whiteflies) from plants, followed by purification of viral particles and metagenomic sequencing. The VEM approach exploits the natural ability of highly mobile adult whiteflies to integrate viruses from many plants over time and space, and leverages the capability of metagenomics for discovering novel viruses. This study utilized VEM to describe the DNA viral community from whiteflies (Bemisia tabaci) collected from two important agricultural regions in Florida, USA. VEM successfully characterized the active and abundant viruses that produce disease symptoms in crops, as well as the less abundant viruses infecting adjacent native vegetation. PCR assays designed from the metagenomic sequences enabled the complete sequencing of four novel begomovirus genome components, as well as the first discovery of plant virus satellites in North America. One of the novel begomoviruses was subsequently identified in symptomatic Chenopodium ambrosiodes from the same field site, validating VEM as an effective method for proactive monitoring of plant viruses without a priori knowledge of the pathogens. This study demonstrates the power of VEM for describing the circulating viral community in a given region, which will enhance our understanding of plant viral diversity, and facilitate emerging plant virus surveillance and management of viral diseases

How Does Lagenaria siceraria (Bottle Gourd) Metabolome Compare to Cucumis sativus (Cucumber) F. Cucurbitaceae? A Multiplex Approach of HR-UPLC/MS/MS and GC/MS Using Molecular Networking and Chemometrics

Cucurbitaceae comprises 800 species, the majority of which are known for their nutritive, economic, and health-promoting effects. This study aims at the metabolome profiling of cucumber (Cucumis sativus) and bottle gourd (Lagenaria siceraria) fruits in a comparative manner for the first time, considering that both species are reported to exhibit several in-common phytochemical classes and bioactivities. Nevertheless, bottle gourd is far less known and/or consumed than cucumber, which is famous worldwide. A multiplex approach, including HR-UPLC/MS/MS, GNPS networking, SPME, and GC/MS, was employed to profile primary and secondary metabolites in both species that could mediate for new health and nutritive aspects, in addition to their aroma profiling, which affects the consumers’ preferences. Spectroscopic datasets were analyzed using multivariate data analyses (PCA and OPLS) for assigning biomarkers that distinguish each fruit. Herein, 107 metabolites were annotated in cucumber and bottle gourd fruits via HR-UPLC/MS/MS analysis in both modes, aided by GNPS networking. Metabolites belong to amino acids, organic acids, cinnamates, alkaloids, flavonoids, pterocarpans, alkyl glycosides, sesquiterpenes, saponins, lignans, fatty acids/amides, and lysophospholipids, including several first-time reported metabolites and classes in Cucurbitaceae. Aroma profiling detected 93 volatiles presented at comparable levels in both species, from which it can be inferred that bottle gourds possess a consumer-pleasant aroma, although data analyses detected further enrichment of bottle gourd with ketones and esters versus aldehydes in cucumber. GC/MS analysis of silylated compounds detected 49 peaks in both species, including alcohols, amino acids, fatty acids/esters, nitrogenous compounds, organic acids, phenolic acids, steroids, and sugars, from which data analyses recognized that the bottle gourd was further enriched with fatty acids in contrast to higher sugar levels in cucumber. This study provides new possible attributes for both species in nutrition and health-care fields based on the newly detected metabolites, and further highlights the potential of the less famous fruit “bottle gourd”, recommending its propagation

Seasonal and taxa impact on edible sea cucumber's metabolome and in relation to its cytotoxicity as analyzed via UHPLC/HR‐MS/MS‐based molecular networking and chemometrics

Abstract Sea cucumbers, belonging to class Holothuroidea, are marine invertebrates with substantial bioactive compounds. This study provides the first comparative metabolome profiling of Holothuria atra and Actinopyga crassa sea cucumbers in relation to their season of collection to dissect between winter and summer samples, providing several first‐time reported metabolites as well as the effect of metabolome variation on their cytotoxic activity against colon and prostate cancer cell lines. Ultrahigh‐performance liquid chromatography coupled with high‐resolution mass spectrometry and global natural products social molecular networking followed by multivariate data analysis were employed for metabolite profiling and seasonal biomarker assignment for each species. The cytotoxic activity was evaluated using in vitro assays against prostate and colon cancer cell lines. A total of 113 metabolites were annotated in both species, including 4 organic acids, 21 sulfoquinovosyl glycerol (sulfolipids), 5 alkyl sulfates, 13 sulfated/saponins, 8 sulfated/triterpene mono/di‐glycosides, 10 triterpenes, 13 sulfated/sterols, 32 phospholipids, 4 sphingolipids, and 3 glycerolipids, several of which are new or first‐time reported. Multivariate data analyses revealed lipid accumulation in summer samples versus triterpene and saponin enrichment in winter‐collected samples, particularly in H. atra, rationalizing its potent cytotoxic activity (IC50 6–12 µg/mL) as revealed using a regression model. However, winter‐collected samples of A. crassa are relatively the least abundant in antinutrient saponins, thus considered to have higher food value