Abstract
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.
Highlights
Spinach is an important leafy vegetable enriched with multiple necessary nutrients
Illumina paired-end libraries with insert sizes of 150 bp, 200 bp, 300 bp, 500 bp and 1 kb, and mate-pair libraries with insert sizes of 3 kb, 10 kb and 15 kb were constructed and sequenced, which generated a total of 169 Gb high-quality cleaned sequences (Supplementary Table 1), representing approximately 168-fold coverage of the spinach genome that has an estimated size of 1,009 Mb based on k-mer analysis of the Illumina sequences (Supplementary Fig. 1) and 989 Mb based on flow cytometry[13]
De novo assembly of these molecules resulted in a total of 898 genome consensus maps with a total length of 1,087.6 Mb and individual map lengths ranging from 49.8 kb to 8.9 Mb
Summary
Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n 1⁄4 12), which contains 25,495 protein-coding genes. Spinach (Spinacia oleracea L., 2n 1⁄4 2 Â 1⁄4 12) is an important and nutritious green leafy vegetable and a rich source of carotenoids, folate, vitamin C, calcium and iron. We report a high-quality genome assembly of a Chinese spinach cultivar, Sp75, in addition to transcriptome sequences of 120 cultivated and wild spinach accessions. These sequences provide insights into the structure and evolution of the spinach genome, the phylogeny and genetic diversity of spinach populations, genomic signatures underlying spinach domestication, and the underlying molecular basis of specific agronomically important traits. The spinach genome sequence represents a solid foundation for comparative genomic studies in Caryophyllales and eudicots, and together with the transcriptome variation data, provide valuable resources for facilitating spinach research and improvement
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