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Gene expression divergence following gene and genome duplicatio

Gene expression divergence following gene and genome duplicatio EAcademic
2025-10-18
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摘要

Abstract

Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of coexpression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or subfunctionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles, and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.


AI解读

【要点】

  • 基因和基因组的重复增加了遗传多样性,并促进了功能创新。
  • 段落或全基因组复制产生的副本在多个组织中显示出相似且部分冗余的表达谱,而其他复制方式则导致了更高的分化,进而带来功能上的新奇变化。
  • 研究探索了五种植物(拟南芥、大豆、蝴蝶兰、玉米及大麦)中不同复制机制后基因表达的变化情况。
  • 大规模复制事件(包括全基因组复制)产生的同源基因表现出冗余或重叠的表达模式,提示功能冗余或亚功能化;小规模复制事件通常导致不对称分化,支持新功能化理论。
  • 剂量敏感型基因倾向于保持高度一致的表达模式,而参与更专门过程的基因则更快地发生分化。

【方法】

  • 采用高分辨率空间转录组学技术分析来自拟南芥、大豆、蝴蝶兰、玉米以及大麦的数据。
  • 比较不同类型复制事件(如段落复制与全基因组复制)后产生的同源基因之间的表达特征差异。
  • 评估保留顺式调控区域的不同复制机制如何影响同源基因的表达模式。

【实验】

  • 收集并处理上述五种植物的空间转录组数据。
  • 根据基因起源(即通过何种类型的复制事件产生),将基因分类,并分析它们在特定细胞类型中的表达水平、表达广度、空间变异性和共表达伙伴数量。
  • 随着时间推移,观察并记录由不同复制机制引起的表达模式差异是如何演变的。

【声明】内容源于网络
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