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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]

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]