Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

Chenxi Xu, Chen Jiao (), Honghe Sun, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Yi Zheng, Wenli Liu, Xuepeng Sun, Yimin Xu, Jie Deng, Zhonghua Zhang, Sanwen Huang, Shaojun Dai, Beiquan Mou, Quanxi Wang, Zhangjun Fei () and Quanhua Wang ()
Additional contact information
Chenxi Xu: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Chen Jiao: Boyce Thompson Institute, Cornell University
Honghe Sun: Boyce Thompson Institute, Cornell University
Xiaofeng Cai: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Xiaoli Wang: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Chenhui Ge: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Yi Zheng: Boyce Thompson Institute, Cornell University
Wenli Liu: Boyce Thompson Institute, Cornell University
Xuepeng Sun: Boyce Thompson Institute, Cornell University
Yimin Xu: Boyce Thompson Institute, Cornell University
Jie Deng: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Zhonghua Zhang: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Sanwen Huang: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences
Shaojun Dai: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Beiquan Mou: USDA-Agricultural Research Service, Crop Improvement and Protection Research Unit
Quanxi Wang: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Zhangjun Fei: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
Quanhua Wang: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: 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.

Date: 2017
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DOI: 10.1038/ncomms15275

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