Haplotype-resolved genome assembly of seed hemp (Cannabis sativa) revealed molecular divergence of Y chromosome evolution

  1. Huawei Wei
  2. Zhuqing Yang
  3. Lingling Zhuang
  4. Xueqing Pan
  5. Haifeng Jia
  6. Shaolian Jiang
  7. Qin Li
  8. Jiantang Xu
  9. Aifen Tao
  10. Pingping Fang
  11. Jianmin Qi
  12. Ray Ming
  13. Liwu Zhang
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Abstract

Seed hemp (Cannabis sativa L.) is an important economic dioecious plant with an XY sex chromosome system, yet its Y chromosome and sex-determining regions (SDR) have not been characterized. Here, we assembled a high-quality haplotype-resolved genome (female: 770.8 Mb; male: 804.7 Mb), and identified an 84 Mb SDR, covering 71% of the Y chromosome, via comparative genomics. X/Y divergence occurred ~37.7 Mya (Ks analysis). Resequencing 35 cannabis accessions revealed higher genetic diversity on the X chromosome. This study provides the first Y chromosome and SDR assembly in seed hemp, offering insights into sex differentiation in dioecious plants.

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