Institutdes Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.
CIRAD, UMR ASTRE, Montpellier, France.
Genome Biol Evol. 2023 Nov 1;15(11). doi: 10.1093/gbe/evad197.
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.
嗅觉受体 (OR) 基因是哺乳动物基因组中最大的多基因家族，其编码的蛋白质可以与环境中的气味分子结合。OR 基因在物种间具有极大的变异性，并且经历了许多基因的重复和丢失，这些重复和丢失与哺乳动物的生态适应有关。尽管已经在广泛的分类学尺度上（即胎盘类）对它们进行了研究，但很少有更精细的采样来更好地捕捉驱动 OR 基因库进化的机制。在胎盘哺乳动物中，啮齿动物非常适合这项任务，因为它们表现出多样化的生活史特征，并且大多数主要家族和多样化的生活方式都有基因组数据。在这项研究中，从 53 种啮齿动物的已发表基因组中挖掘它们的 OR 亚基因组。我们检索到了超过 85000 个功能和假基因 OR 序列，随后将其分类为系统发育簇。啮齿动物之间的拷贝数变异与其他哺乳动物相似。使用我们的 OR 计数以及比较系统发育方法，我们证明了生态位，如饮食、活动期和穴居生活方式，强烈影响了 OR 假基因的比例。在 OR 亚基因组中，系统发育惯性是解释 13 个 OR 基因家族相对变化的主要因素。然而，一个引人注目的例外是，在属于 Bathyergidae 和 Spalacidae 科的地下鼹鼠谱系中，OR 家族 14 发生了惊人的 10 倍扩张，尽管这些谱系在系统发育上存在分歧。这项研究说明了 OR 基因库的多样性在啮齿动物中是如何进化的，这既受到物种生活史特征的选择压力的影响，也受到沿啮齿动物系统发育的中性进化的影响。
