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Spinach (Spinacia oleracea L.) accumulates high amounts of carotenoids, vitamin C, nitrate and oxalate. Breeding to reduce nitrate and oxalate levels and increase vitamin C and carotenoid levels is a major target in spinach nutritional quality improvement. Here we investigate natural variations in the levels of nitrate, oxalate, vitamin C, and total carotenoid in 98 spinach accessions, and correlations among these four nutritional components and 12 important morphological traits. Our results showed that the concentrations of nitrate, oxalate, vitamin C, and total carotenoid ranged from 0.21-3.83, 2.38-34.72, 0.51-1.30, and 0.18-0.58 mg g−1 fresh weight (FW), respectively. Moderate positive correlations were observed between the levels of oxalate and vitamin C, and between vitamin C and total carotenoid, whereas the levels of nitrate were correlated weakly and negatively with those of vitamin C and total carotenoid. The nitrate contents of crinkle-leaf accessions were significant higher than those of smooth-leaf accessions, and the smooth-leaf accessions had significantly higher concentrations of oxalate and vitamin C than crinkle-leaf accessions. Furthermore, hierarchical clustering analysis identified eight spinach accessions that could be served as starting materials for breeding new spinach cultivars with increased levels of vitamin C and carotenoids and simultaneously decreased accumulation of nitrate and oxalate. [ABSTRACT FROM AUTHOR]

Spinach is one of the most nutritious green-leaf vegetables. In the spinach production, diseases cause a significant loss in both yield and quality. Improving disease resistance is one of the major challenges in spinach breeding. Arabidopsis nucleoporin CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 (CPR5) functions as a negative regulator of plant cell death and immunity as cpr5 mutant exhibits spontaneous cell death and heightened immunity. In addition, CPR5 play a role in trichome development as the majority of cpr5 mutant trichomes are branchless whereas wild type trichomes are often three-branched. In the spinach genome, we identified a homolog of Arabidopsis CPR5, referred to as Spinacia oleracea CPR5 (SoCPR5). To investigate the function of SoCPR5, we introduced SoCPR5 into Arabidopsis cpr5 mutant. Our data showed that both spontaneous cell death and heightened immunity were suppressed in the SoCPR5-transgenic cpr5 mutants, verifying that SoCPR5 functions as its Arabidopsis counterpart in plant cell death and immunity. SoCPR5 also fully restored wild type trichome phenotype of the cpr5 mutant. Our study therefore indicates that the function of SoCPR5 is conserved between plant species and SoCPR5 can be applied for genetic manipulation of plant immunity in spinach. [ABSTRACT FROM AUTHOR]

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The phenomenon of granular flows appears frequently in industrial and daily life. The particle–particle interaction plays an important role in granular flows, which makes the flows have some strong nonlinear characteristics and so different from the normal materials, either solids or liquids. Discrete element method (DEM) is a powerful tool to catch this interaction in meso-scopic scale. A brief review of DEM is presented, including some of our new works in this area. DEM can also be coupled with other CFD methods for simulations of solid–liquid suspension flow. An example of such coupling is presented in this article as well. [ABSTRACT FROM AUTHOR]

Spinach (Spinacia oleracea L.) is a nutritious vegetable enriched with many essential minerals and vitamins. A reference spinach genome has been recently released, and additional spinach genomic resources are being rapidly developed. Therefore, there is an urgent need of a central database to store, query, analyze and integrate various resources of spinach genomic data. To this end, we developed SpinachBase (http://spinachbase.org), which provides centralized public accesses to genomic data as well as analytical tools to assist research and breeding in spinach. The database currently stores the spinach reference genome sequence, and sequences and comprehensive functional annotations of protein-coding genes predicted from the genome. The database also contains gene expression profiles derived from RNA-Seq experiments as well as highly co-expressed genes and genetic variants called from transcriptome sequences of 120 cultivated and wild Spinacia accessions. Biochemical pathways have been predicted from spinach protein-coding genes and are available through a pathway database (SpinachCyc) within SpinachBase. SpinachBase provides a suite of analysis and visualization tools including a genome browser, sequence similarity searches with BLAST, functional enrichment and functional classification analyses and functions to query and retrieve gene sequences and annotations. [ABSTRACT FROM AUTHOR]

Spinach (Spinacia oleracea L.) is one of most important leafy vegetables because of its high nutritional value and high oxalate content, which can be toxic with negative effects on human nutrition. Ammonium and nitrate can effectively regulate oxalate accumulation, although the mechanisms underlying the oxalate biosynthesis and regulation are still undetermined in plants. In the present study, we identified 25 putative genes that are involved in the oxalate biosynthetic and degradation pathway, before analyzing the oxalate content and the expression levels of the corresponding proteins under normal growth conditions, with or without ammonium and nitrate treatments, using high and low oxalate-accumulated spinach genotypes. The two cultivars exhibited different profiles of total oxalate and soluble oxalate accumulation. The high oxalate concentrations in spinach were as a result of the high transcription levels of the genes that are involved in oxalate biosynthesis under normal growth conditions, such as SoGLO2, SoGLO3, three SoOXACs, SoMLS, SoMDH1, SoMDH2, and SoMDH4. The results revealed that the ammonium and nitrate were able to control the oxalate content in leaves, possibly because of the different transcription levels of the genes. The oxalate content is regulated by complex regulatory mechanisms and is varied in the different varieties of spinach. The results from this research may be used to assist the investigation of the mechanism of oxalate regulation and breeding for reduced oxalate content in spinach. [ABSTRACT FROM AUTHOR]

Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 protein-coding genes. The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome duplication events are observed in spinach. Genome syntenic analysis between spinach and sugar beet suggests substantial inter- and intra-chromosome rearrangements during the Caryophyllales genome evolution. Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. Our data suggests that S. turkestanica is likely the direct progenitor of cultivated spinach and spinach domestication has a weak bottleneck. We identify 93 domestication sweeps in the spinach genome, some of which are associated with important agronomic traits including bolting, flowering and leaf numbers. This study offers insights into spinach evolution and domestication and provides resources for spinach research and improvement. [ABSTRACT FROM AUTHOR]

Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases. IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases., (Copyright © 2017 American Society for Microbiology.)