The spinach YY genome reveals sex chromosome evolution, domestication, and introgression history of the species

• DOI: 10.1186/s13059-022-02633-x
• Publication Date: 2022-03-07T15:02:46Z
• Authors: Xiaokai Ma; Li’ang Yu; Mahpara Fatima; William H. Wadlin...; Amanda M. Hulse-Kemp; Xingtan Zhang; Shengcheng Zhang; Xindan Xu; Jingjing Wang; Huaxing Huang; Jing Lin; Ban Deng; Zhenyang Liao; Zhenhui Yang; Yanhong Ma; Haibao Tang; Allen Van Deynze; Ray Ming
• Keywords: Spinacia; Introgression

Abstract Background Spinach ( Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y has not been fully characterized. Our knowledge about the history of domestication and improvement remains limited. Results A high-quality YY genome spinach assembled into 952 Mb in six pseudo-chromosomes. By combination genetic mapping, Genome-Wide Association Studies, genomic analysis, we characterize 17.42-Mb determination region (SDR) on 1. The chromosomes evolved when insertion containing genes occurred, followed by large inversion 1.98 Mya. subsequent burst SDR-specific repeats (0.1–0.15 Mya) explains size this SDR. We identify Y-specific gene, NRT1/PTR 6.4 which resides insertion, as strong candidate for or differentiation factor. Resequencing 112 genomes reveals severe bottleneck approximately 10.87 Kya, dates 7000 years earlier than archeological record. demonstrate that selection signal associated internode elongation leaf area expansion edibility traits spinach. find several introgressions from wild turkestanica tetrandra harbor desirable alleles related to downy mildew resistance, frost morphology, flowering-time shift, likely contribute improvement. Conclusions Analysis uncovers evolutionary forces shaping nascent evolution findings provide novel insights