Table_1_Taxonomically Restricted Genes Are Fundamental to Biology and Evolution.XLSX

Genes limited to particular clades, taxonomically restricted genes (TRGs), are common in all sequenced genomes. TRGs have recently become associated with the evolution of novelty, as numerous studies across the tree of life have now linked expression of TRGs with novel phenotypes. However, TRGs that underlie ancient lineage specific traits have been largely omitted from discussions of the general importance of TRGs. Here it is argued that when all TRGs are considered, it is apparent that TRGs are fundamental to biology and evolution and likely play many complementary roles to the better understood toolkit genes. Genes underlying photosynthesis and skeletons, for example, are examples of commonplace fundamental TRGs. Essentially, although basic cell biology has a highly conserved genetic basis across the tree of life, most major clades also have lineage specific traits central to their biology and these traits are often based on TRGs. In short, toolkit genes underlie what is conserved across organisms, while TRGs define in many cases what is unique. An appreciation of the importance of TRGs will improve our understanding of evolution by triggering the study of neglected topics in which TRGs are of paramount importance.

仅存在于特定演化支的基因，即分类限制基因（taxonomically restricted genes，TRGs），在所有已测序基因组中均广泛分布。近年来，TRGs与新颖性状演化的关联逐渐受到学界关注，目前已有诸多横跨生命之树的研究表明，TRGs的表达与新表型存在直接关联。然而，支撑古老演化支特异性性状的TRGs，在当前关于TRGs总体重要性的学术讨论中却被大幅忽略。本文主张，若将所有TRGs纳入考量范畴，则不难发现TRGs是生物学与演化研究的核心基础，且相较于已被广泛研究的核心工具箱基因，TRGs很可能承担诸多互补性功能。例如，介导光合作用与生物骨架形成的基因，便是普遍存在的核心TRGs的典型案例。本质而言，尽管基础细胞生物学的遗传基础在整个生命之树中高度保守，但绝大多数主要演化支均具备与其核心生物学功能息息相关的支系特异性性状，而这些性状往往以TRGs为分子基础。简言之，核心工具箱基因构成了生物界保守性状的遗传基础，而TRGs则在诸多情况下界定了各演化支的独特性。重视TRGs的重要性，将推动学界开展此前被忽视的TRGs核心研究主题，从而深化我们对演化过程的认知。