Evolution of the spinach sex-linked region within a rarely recombining pericentro-meric region

Hongbing Shen, Zhiyuan Liu, Shufen Li, Zhaosheng Xu, Helong Zhang, Feng Cheng, Jian Wu, Xiaowu Wang, Chuanliang Deng, Deborah Charlesworth, Wujun Gao, Wei Qian

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a “Y duplication region” or “YDR” whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
Original languageEnglish
Number of pages18
JournalPlant physiology
Early online date5 Jul 2023
Publication statusE-pub ahead of print - 5 Jul 2023

Keywords / Materials (for Non-textual outputs)

  • inversion
  • recombination
  • sex linked region
  • gene duplication
  • pericentromeric region
  • sex chromosome turnover


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