Table_2_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.

局限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广泛存在。近年来，随着跨生命之树的多项研究将TRGs的表达与新奇表型建立关联，TRGs逐渐被认为与演化新奇性的产生密切相关。然而，那些支撑古老支系特异性性状的TRGs，在关于TRGs普遍重要性的讨论中基本被忽略。
本文主张，若将所有TRGs纳入考量范畴，则可明确TRGs是生物学与演化的核心基础，且可能与已被充分认知的工具箱基因（toolkit genes）发挥诸多互补作用。例如，支撑光合作用与骨骼系统的基因，便是常见的基础性TRGs。
本质而言，尽管基础细胞生物学在整个生命之树中具有高度保守的遗传基础，但绝大多数主要演化支也拥有与其生物学功能核心相关的支系特异性性状，而这些性状往往以TRGs为遗传基础。简言之，工具箱基因支撑了不同生物类群间的保守共性，而TRGs则在诸多情况下定义了生物的独特性。
对TRGs重要性的认知，将推动我们对演化过程的理解，促使学界开展TRGs占据核心地位的被忽视课题的研究。