The receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others have found to be involved in defence responses. However, functional data is to date, only available for a small subset of RLPs, leaving the remaining ones classified as RLPs of unknown function. Using publicly available datasets, we annotated those RLPs of unknown functions as either likely defence-related or likely fulfilling a more basal function in plants. Using these categories, we can identify important characteristics that differ between the RLP sub classes. We find the two classes differ in abundance on both transcriptome and proteome level, physical clustering in the genome and putative interaction partners. However, the classes do not differ in the genetic diversity of their individual members in accessible pan-genome data. Our work has several implications for work related to functional studies on RLPs as well as for the understanding of RLP gene family evolution. Using our annotations, we can make suggestions of which RLPs can be identified as potential immune receptors using genetics tools, which can be useful for disease studies. The lack of differences in nucleotide diversity between the two RLP subclasses further suggests that non-synonymous diversity of gene sequences alone cannot distinguish defence from developmental genes. By contrast, differences in transcript and protein abundance or clustering at genomic loci might also allow for functional annotations and characterisation in other plant species.

中文翻译：

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多组学方法突显了拟南芥中功能性RLP类之间的差异

受体样蛋白（RLP）家族是一个复杂的基因家族，在拟南芥中有57个成员。众所周知，RLP家族的一些成员参与了基础发育过程，而其他成员则参与了防御反应。但是，到目前为止，功能数据仅可用于一小部分RLP，而其余数据则归类为功能未知的RLP。使用公开可用的数据集，我们将未知功能的RLP注释为可能与防御相关或可能在植物中履行了更基础的功能。使用这些类别，我们可以确定RLP子类之间不同的重要特征。我们发现这两个类别在转录组和蛋白质组水平，基因组中的物理簇和推定的相互作用伙伴方面都存在差异。然而，在可访问的全基因组数据中，这些类别的个体成员的遗传多样性没有差异。我们的工作对与RLP的功能研究相关的工作以及对RLP基因家族进化的理解都有一些启示。使用我们的注释，我们可以建议使用遗传学工具将哪些RLP识别为潜在的免疫受体，这对于疾病研究很有用。两个RLP亚类之间核苷酸多样性的差异的缺乏进一步表明，仅基因序列的非同义多样性不能将防御与发育基因区分开。相比之下，基因组位点的转录本和蛋白质丰度或簇的差异也可能允许其他植物物种进行功能注释和表征。