Data from: Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function

CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12–13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies.CLV3/ESR（CLE）蛋白是植物中一类重要的信号肽。由12~13个氨基酸组成的短CLE肽从更大的前原肽中切割产生，并作为胞外配体发挥功能。CLE家族规模庞大，且难以实现统一分类，这是由于CLE结构域过短，无法开展可靠的系统发育分析，同时前原肽序列变异度极高。 本研究采用基于模型的检索方法，对57个植物基因组中的CLE结构域进行检索，并利用完整的前原肽序列开展全面的聚类分析。 研究团队共在陆生植物中鉴定得到1628个CLE基因，未在绿藻中发现任何可识别的同源序列。这些CLE蛋白可划分为12个类群，类群内的CLE结构域高度保守，且前原肽序列可进行多序列比对。多数聚类簇包含单子叶植物、双子叶植物以及无油樟（Amborella trichopoda）的序列，挪威云杉（Picea abies）、卷柏（Selaginella moellendorffii）与小立碗藓（Physcomitrella patens）的序列则分散分布于部分聚类簇中。 研究团队可轻松识别出此前已报道的、参与维管分化与结瘤过程的聚类簇。此外，本研究还发现了多个功能尚未得到充分表征的独立类群。 现有数据表明，同一聚类簇内的CLE蛋白大概率具有相似的功能，而不同聚类簇的CLE蛋白则至少存在部分功能差异。 本研究的分析结果为后续的进化与功能研究奠定了坚实基础。