An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion
An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion
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被子植物 NLR 图谱揭示 NLR 基因减少与生态特化和信号转导成分缺失相关。
DOI：
10.1016/j.molp.2021.08.001
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发表时间：
2021-12-06
期刊：
影响因子：
27.5
通讯作者：
Shao, Zhu-Qing
中科院分区：
文献类型：
--
作者：
Liu, Yang;Zeng, Zhen;Shao, Zhu-Qing
核苷酸结合富含亮氨酸重复序列(NLR)基因构成最大的植物抗病基因家族。被子植物 NLR 基因在系统发育上分为 TNL、CNL 和 RNL 亚类。被子植物基因组中 NLR 拷贝数和亚类组成差异巨大。然而，由于基因组可用性有限，基因组 NLR 含量与生态适应之间或 NLR 含量与信号转导成分之间的进化关联性很难表征。在本研究中，我们建立了被子植物 NLR 图谱（ANNA，https://biobigdata.nju.edu.cn/ ANNA/），其中包括来自 300 多个被子植物基因组的 NLR 基因。使用 ANNA，我们发现由于基因快速丢失和获得，密切相关的物种之间的 NLR 拷贝数差异高达 66 倍。有趣的是，NLR 收缩与对水生、寄生和肉食生活方式的适应有关。水生植物中 NLR 的趋同性减少类似于绿藻在陆地殖民之前的长期进化过程中 NLR 缺乏扩展。还发现了 NLR 亚类和植物免疫途径成分之间的共同进化模式，表明免疫途径缺陷可能导致 TNL 损失。最后，我们确定了一个保守的 TNL 谱系，它可以独立于 EDS1-SAG101-NRG1 模块发挥作用。总的来说，这些发现为生态适应和基因组内容变异背景下 NLR 基因的进化提供了新的见解。
Nucleotide-binding leucine-rich-repeat (NLR) genes comprise the largest family of plant disease -resistance genes. Angiosperm NLR genes are phylogenetically divided into the TNL, CNL, and RNL subclasses. NLR copy numbers and subclass composition vary tremendously across angiosperm genomes. However, the evolutionary associations between genomic NLR content and ecological adaptation, or between NLR content and signal transduction components, are poorly characterized because of limited genome availability. In this study, we established an angiosperm NLR atlas (ANNA, https://biobigdata.nju.edu.cn/ ANNA/) that includes NLR genes from over 300 angiosperm genomes. Using ANNA, we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and gain. Interestingly, NLR contraction was associated with adaptations to aquatic, parasitic, and carnivorous lifestyles. The convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land. A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified, suggesting that immune pathway deficiencies may drive TNL loss. Finally, we identified a conserved TNL lineage that may function independently of the EDS1-SAG101-NRG1 module. Collectively, these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation.