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Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding. Spinach is a nutritious leafy vegetable growing worldwide. Here, the authors report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 accessions, and provide insights into spinach domestication and the genetic basis of agronomic traits. [ABSTRACT FROM AUTHOR]

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]

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In the original version of this Article, Taiwan was coloured differently from mainland China in the map presented in Figure 3a. The map has now been updated according to authors' request in both PDF and HTML version of the Article. The original article can be found online at https://doi.org/10.1038/s41467-021-27432-z. [Extracted from the article]

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]