端粒对端粒梨 (Pyrus pyrifolia) 参考基因组揭示了细分和全基因组重复驱动基因组进化
Manyi Sun1,2, Chenjie Yao1,2, Qun Shu3
1College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
Horticulture research
|November 29, 2023
概括
使用端粒到端粒测序组装了一个完整的,没有空隙的红皮梨基因组 (Pyrus pyrifolia). 这种高完整性基因组揭示了对细分重复,抗病性和氨酸生物合成的洞察力,有助于梨的进化研究.
科学领域:
- 基因组学就是基因组学.
- 植物生物学 植物生物学
- 进化生物学 进化生物学
背景情况:
- 以前的梨基因组 (Pyrus pyrifolia) 存在许多缺口和未定区域,限制了全面的遗传分析.
- 红皮梨"云红号"的红皮梨 1' (YH1) 是来自中国主要梨原产区的重要品种.
研究的目的:
- 为了生成一个端粒到端粒 (T2T),无间隙的基因组组合的红皮梨"Yunhong No. 1' (YH1) 的情况.
- 调查细分重复 (SDs) 在梨子进化,抗病和农学特征中的作用.
- 探索红色皮肤颜色的遗传基础,专注于安东素生物合成调节剂.
主要方法:
- 端粒到端粒 (T2T) 测序和YH1基因组的组装.
- 分段重复 (SDs) 和重复基因的识别和特征.
- 分析中心和端粒区域,包括像吉普赛LTRs这样的重复元素.
- 调查MYB10和MYB114的基因重复事件,这些基因都参与了氨酸生物合成.
主要成果:
- 实现了501.20 Mb T2T无缺口的YH1基因组组合,具有34个特征的端粒和17个中心粒.
- 确定了1531个SD驱动的重复基因,富含压力反应途径,与与抗病基因扩张相关的染色体内SDs.
- 重复的基因显示剂量效应或子/新功能化影响特征,如糖含量和水果皮肤.
- 发现了MYB10和MYB114的多个副本,显示了剂量影响对于皮肤红色发育至关重要.
结论:
- 没有T2T缺口的YH1基因组为Pyrus pyrifolia提供了高完整性的资源,大大改善了之前的组装.
- 分段重复在梨的适应性进化中发挥着关键作用,特别是在扩大抗病能力和影响农学特征方面.
- 基因重复和MYB转录因子的剂量效应是梨的红色皮肤颜色的关键机制,为功能基因组学和育种提供了宝贵的见解.
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