BACKGROUND Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. RESULTS Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. CONCLUSIONS We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

中文翻译：

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脊椎动物嗅觉受体的统一命名法。

背景技术嗅觉受体（OR）是G蛋白偶联受体，在气味检测中起关键作用。一个典型的哺乳动物基因组具有〜1000个OR基因和假基因。但是，每个物种都发生了不同的基因复制/删除事件，从而导致复杂的正交关系。尽管人类OR命名法已被广泛接受，并且基于系统发育分类分为18个科目，再进一步细分为亚科，但对于其他哺乳动物，当前正在使用不同和多个命名法系统，因此隐藏了重要的进化和功能见解。结果在这里，我们描述了互最大相似度（MMS）算法，这是一种基于物种间等级成对相似度为任何OR基因分配以人为中心的命名法的系统分类器。MMS已应用于七个哺乳动物和斑马鱼的OR类别。我们总共将符号分配给10,249个OR。系统发育分析和同义分析都支持该命名法。统一命名的可用性为各种研究提供了框架，其中文本符号比较允许立即识别潜在的直系同源基团以及特定于物种的扩展/缺失；例如，Or52e5和Or52e5b代表大鼠特定的OR52E5复制。另一个例子是在灵长类OR符号中完全不存在OR子家族OR6Z。在其他哺乳动物中，OR6Z成员位于一个基因组簇中，这表明大猿猴谱系中存在大量缺失。灵长类动物基因组中缺少另外的14个哺乳动物OR亚科。在黑猩猩中，有87％的符号与人类符号相同，在狗和牛中，这一数字下降到约50％，在啮齿动物中下降到约30％，反映了OR基因超家族在不同生态位中的适应性变化。拟议的命名法在斑马鱼上的应用表明与哺乳动物OR的相似性，这从当前的斑马鱼嗅觉受体基因命名法中无法发现。结论我们为脊椎动物或超家族整合了统一的标准命名系统。脊椎动物基因命名委员会将把新的命名系统应用于牛，马，狗和黑猩猩，其他有关物种的特定命名委员会目前正在考虑实施。拟议的命名法在斑马鱼上的应用表明与哺乳动物OR的相似性，这从当前的斑马鱼嗅觉受体基因命名法中无法发现。结论我们为脊椎动物或超家族整合了统一的标准命名系统。脊椎动物基因命名委员会将把新的命名系统应用于牛，马，狗和黑猩猩，其他有关物种的特定命名委员会目前正在考虑实施。拟议的命名法在斑马鱼上的应用表明与哺乳动物OR的相似性，这从当前的斑马鱼嗅觉受体基因命名法中无法发现。结论我们为脊椎动物或超家族整合了统一的标准命名系统。脊椎动物基因命名委员会将把新的命名系统应用于牛，马，狗和黑猩猩，其他有关物种的特定命名委员会目前正在考虑实施。