High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features

Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.

植物依赖核苷酸结合富亮氨酸重复受体（Nucleotide-binding, Leucine-rich repeat Receptors, NLRs）进行病原体识别。高变异NLRs（hvNLRs）展现出显著的种内多样性，而其低变异旁系同源基因（non-hvNLRs）则在不同生态型间保持保守。在种群层面，hvNLRs可赋予新的病原体识别特异性，但等位基因多样性与基因组、表观基因组特征之间的关联尚未明确。本研究对拟南芥Col-0品系中的NLRs展开分析后发现，相较于non-hvNLRs，hvNLRs的表达水平更高、基因体胞嘧啶甲基化程度更低，且更靠近转座因子。hvNLRs具有更高的同义及非同义核苷酸多样性，且处于与突变概率升高相关的染色质状态中。歧化选择维持了hvNLRs部分密码子的变异，而净化选择则保持了non-hvNLRs的序列保守性。阐明这些特征的形成与维持机制，以及它们是否有助于hvNLRs已观测到的多样性，是理解植物先天免疫受体演化的关键。