●Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine-rich repeat receptor-like kinases (LRR-RLKs) are signal receptors critical in development and defense. LRR-RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well-resolved LRR-RLK gene tree has remained elusive. ●To resolve the LRR-RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR-RLK subclades and reconstructed the deepest nodes of the full gene family. ●We discovered that the LRR-RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR-RLK variants as members of other gene families. Our work corrects this misclassification. ●Our results reveal ongoing structural evolution generating novel LRR-RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family.

中文翻译：

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结构进化推动了大型LRR-RLK基因家族的多样化。

●电池不断暴露于化学信号中，必须对其进行区分并做出适当响应。在胚胎植物中，富含亮氨酸的重复受体样激酶（LRR-RLK）是在发育和防御中至关重要的信号受体。LRR-RLK已在许多植物基因组中多样化为数百个基因。尽管进行了深入研究，但良好解析的LRR-RLK基因树仍然难以捉摸。●为解决LRR-RLK基因树，我们基于迭代隐马尔可夫模型搜索和系统发育推断，开发了一种改进的基因发现方法。我们使用此方法为LRR-RLK子片段中的每个子片段推断出完整的基因树，并重建了完整基因家族的最深节点。●我们发现LRR-RLK基因家族比以前认为的还要大，并且蛋白质域的得失普遍存在。这些结构修饰，其中一些可能早于胚胎植物多样化，导致某些LRR-RLK变异体误分类为其他基因家族的成员。我们的工作纠正了这种错误分类。●我们的结果揭示了正在进行的结构进化，产生了新的LRR-RLK基因。这些新基因是发展和防御中信号转导多样化的原材料。我们的方法还可以在任何大型基因家族中进行系统发育重建。