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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #330266

Research Project: Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species

Location: Crop Improvement and Protection Research

Title: Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

Author
item Xu, Chenxi - Shanghai Normal University
item Jiao, Chen - Cornell University - New York
item Sun, Honghe - Cornell University - New York
item Cai, Xiaofeng - Shanghai Normal University
item Wang, Xiaoli - Shanghai Normal University
item Ge, Chenhui - Shanghai Normal University
item Zheng, Yi - Cornell University - New York
item Liu, Wenli - Cornell University - New York
item Sun, Xuepeng - Cornell University - New York
item Xu, Yimin - Cornell University - New York
item Deng, Jie - Chinese Academy Of Agricultural Sciences
item Zhang, Zhonghua - Chinese Academy Of Agricultural Sciences
item Huang, Sanwen - Chinese Academy Of Agricultural Sciences
item Dai, Shaojun - Shanghai Normal University
item Mou, Beiquan
item Wang, Quanxi - Shanghai Normal University
item Fei, Zhangjun - Cornell University - New York
item Wang, Quanhua - Shanghai Normal University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/7/2017
Publication Date: 5/24/2017
Citation: Xu, C., Jiao, C., Sun, H., Cai, X., Wang, X., Ge, C., Zheng, Y., Liu, W., Sun, X., Xu, Y., Deng, J., Zhang, Z., Huang, S., Dai, S., Mou, B., Wang, Q., Fei, Z., Wang, Q. 2017. Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nature Communications. 8:15275. doi: 10.1038/ncomms15275.

Interpretive Summary: Spinach is an important leafy green vegetable and a rich source of carotenoids (vitamin A and lutein), folate, vitamin C, calcium and iron. Here we report the draft genome sequence of cultivated spinach (Spinacia oleracea), which contains 25,495 genes. The spinach genome is highly repetitive with 74.4% of its content in the form of “jumping genes.” We identified genes encoding several enzymes involved in the carotenoid and folate syntheses. We also sequenced 120 cultivated and wild spinach accessions and identified more than 420K variants. Our data suggest that the wild species S. turkestanica is likely the direct progenitor of cultivated spinach. We identified 517 genes involved in spinach domestication. The spinach genome sequence and variants provide valuable resources for genetic studies and spinach research and breeding.

Technical Abstract: Spinach is an important leafy vegetable enriched with multiple and necessary nutrients. It belongs to the order of Caryophyllales, which constitutes the basal clade in core eudicots. Here we report the draft genome sequence of cultivated 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 were observed in spinach, though genes encoding several rate-limiting enzymes in the carotenoid and folate pathways have undergone expansions. Transcriptome sequencing of 120 cultivated and wild spinach accessions identified more than 420K variants. Our data suggest that S. turkestanica is likely the direct progenitor of cultivated spinach and spinach domestication has a weak bottleneck. We identified 307 domestication sweeps involving 517 genes. The spinach genome sequence and transcriptome variants provide valuable resources for comparative genomic studies and spinach research and breeding.