Martin Kyle J, Holland Peter W H
Department of Zoology, University of Oxford, Oxford, United Kingdom.
Department of Zoology, University of Oxford, Oxford, United Kingdom
Mol Biol Evol. 2014 Oct;31(10):2592-611. doi: 10.1093/molbev/msu202. Epub 2014 Jun 27.
Numerous ancient whole-genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. Although two vertebrate WGD events (1R/2R) occurred over 525 Ma, we have focused on the more recent 3R or TGD (teleost genome duplication) event which occurred approximately 350 Ma in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and bacterial artificial chromosome clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC, and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional "a" and "b" post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favor a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that although the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term "tetralogy" to describe the homology relationship which exists between duplicated sequences which originate through a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
在真核生物进化过程中发生了许多古老的全基因组复制（WGD）事件。在脊椎动物中，复制的发育基因及其功能分歧对形态进化产生了重要影响。尽管两次脊椎动物WGD事件（1R/2R）发生在5.25亿年前，但我们关注的是更近的3R或硬骨鱼基因组复制（TGD）事件，该事件大约发生在3.5亿年前，发生在超过26000种硬骨鱼的共同祖先中。通过全基因组和细菌人工染色体克隆测序相结合的方法，我们对骨舌鱼目早期分支亚纲成员潘氏非洲肺鱼（Pantodon buchholzi）的所有Hox基因簇进行了表征。我们发现45个Hox基因仅组织成五个簇，这表明潘氏非洲肺鱼比其他已知物种遭受了更多的Hox簇丢失。尽管有充分证据表明潘氏非洲肺鱼的五个簇与四个典型的TGD前脊椎动物簇（一个HoxA、两个HoxB、一个HoxC和一个HoxD）具有同源性，但我们无法确定地解析潘氏非洲肺鱼的四个簇与其他硬骨鱼的八个TGD后簇之间的1:1直系同源关系。系统发育分析表明，许多潘氏非洲肺鱼基因在传统的TGD后“a”和“b”直系同源组之外分离，单个簇上物理连锁的基因之间存在广泛的拓扑不一致，并且信号分歧导致在串联Hox簇分析中指定1:1直系同源关系时存在矛盾。在对这一现象的几种可能解释中，我们倾向于一种模型，该模型与硬骨鱼辐射前单一TGD的普遍观点一致，但也考虑了复制后二倍体化的时间，相对于物种形成事件。我们认为，尽管复制的hoxa簇在骨舌鱼目分歧之前就已经二倍体化，但复制的hoxb、hoxc和hoxd簇在骨舌鱼目和其他硬骨鱼中独立完成了二倍体化。我们使用“四倍体同源性”一词来描述通过共享WGD产生的复制序列之间存在的同源关系，这些序列在物种形成后在两个谱系中从共同的等位基因库中独立二倍体化为不同的旁系同源物。
