Winters Noah P, Wafula Eric K, Timilsena Prakash R, Ralph Paula E, Maximova Siela N, dePamphilis Claude W, Guiltinan Mark J, Marden James H
IGDP Ecology, The Pennsylvania State University, University Park, PA 16802, USA.
Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
G3 (Bethesda). 2025 Sep 3;15(9). doi: 10.1093/g3journal/jkaf147.
Nucleotide-binding leucine-rich repeat receptors (NLR) are an essential component of plant immunity. NLR evolution is complex and dynamic, with rapid expansions, contractions, and polymorphism. Hundreds of high-quality plant genomes generated over the last 2 decades provide substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity in long-lived perennial species. In this study, we investigated the evolution of NLR genes across 11 high-quality genomes of the chocolate tree, Theobroma cacao L. We found 3-fold variation in NLR copy number across genotypes, a pattern driven primarily by expansion of NLR clusters via tandem and proximal duplication. Our results indicate local duplications can radically reshape gene families over short evolutionary time scales, creating extensive intraspecific variation and a source of NLR diversity that could be utilized to enrich our understanding of both plant-pathogen interactions and resistance breeding.
核苷酸结合富含亮氨酸重复序列受体（NLR）是植物免疫的重要组成部分。NLR的进化复杂且动态，具有快速的扩增、收缩和多态性。在过去20年中产生的数百个高质量植物基因组为深入了解NLR基因的进化动态提供了大量信息。尽管测序成本不断下降，但高质量基因组的测序、组装和注释难度导致关于长寿多年生物种种内NLR多样性的全基因组信息相对较少。在本研究中，我们调查了可可树（Theobroma cacao L.）11个高质量基因组中NLR基因的进化。我们发现不同基因型的NLR拷贝数存在3倍差异，这种模式主要由NLR簇通过串联和近端重复的扩增驱动。我们的结果表明，局部重复可以在短时间进化尺度上从根本上重塑基因家族，产生广泛的种内变异以及NLR多样性来源，可用于丰富我们对植物 - 病原体相互作用和抗性育种的理解。
