State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
BMC Evol Biol. 2011 Jan 26;11:25. doi: 10.1186/1471-2148-11-25.
Hox genes are known to play a key role in shaping the body plan of metazoans. Evolutionary dynamics of these genes is therefore essential in explaining patterns of evolutionary diversity. Among extant sarcopterygians comprising both lobe-finned fishes and tetrapods, our knowledge of the Hox genes and clusters has largely been restricted in several model organisms such as frogs, birds and mammals. Some evolutionary gaps still exist, especially for those groups with derived body morphology or occupying key positions on the tree of life, hindering our understanding of how Hox gene inventory varied along the sarcopterygian lineage.
We determined the Hox gene inventory for six sarcopterygian groups: lungfishes, caecilians, salamanders, snakes, turtles and crocodiles by comprehensive PCR survey and genome walking. Variable Hox genes in each of the six sarcopterygian group representatives, compared to the human Hox gene inventory, were further validated for their presence/absence by PCR survey in a number of related species representing a broad evolutionary coverage of the group. Turtles, crocodiles, birds and placental mammals possess the same 39 Hox genes. HoxD12 is absent in snakes, amphibians and probably lungfishes. HoxB13 is lost in frogs and caecilians. Lobe-finned fishes, amphibians and squamate reptiles possess HoxC3. HoxC1 is only present in caecilians and lobe-finned fishes. Similar to coelacanths, lungfishes also possess HoxA14, which is only found in lobe-finned fishes to date. Our Hox gene variation data favor the lungfish-tetrapod, turtle-archosaur and frog-salamander relationships and imply that the loss of HoxD12 is not directly related to digit reduction.
Our newly determined Hox inventory data provide a more complete scenario for evolutionary dynamics of Hox genes along the sarcopterygian lineage. Limbless, worm-like caecilians and snakes possess similar Hox gene inventories to animals with less derived body morphology, suggesting changes to their body morphology are likely due to other modifications rather than changes to Hox gene numbers. Furthermore, our results provide basis for future sequencing of the entire Hox clusters of these animals.
众所周知，Hox 基因在塑造后生动物体模式方面发挥着关键作用。因此，这些基因的进化动态对于解释进化多样性的模式至关重要。在现存的肉鳍鱼类（包括肺鱼和四足动物）中，我们对 Hox 基因和基因簇的了解主要局限于几种模式生物，如青蛙、鸟类和哺乳动物。仍然存在一些进化上的差距，特别是对于那些具有衍生体型或占据生命之树关键位置的群体，这阻碍了我们理解 Hox 基因库如何沿着肉鳍鱼谱系发生变化。
我们通过全面的 PCR 调查和基因组步行确定了六个肉鳍鱼类群体的 Hox 基因库：肺鱼、蚓螈、蝾螈、蛇、海龟和鳄鱼。与人类 Hox 基因库相比，六个肉鳍鱼类群体代表物种中的可变 Hox 基因进一步通过 PCR 调查在许多代表该群体广泛进化覆盖范围的相关物种中得到了验证。海龟、鳄鱼、鸟类和胎盘哺乳动物拥有相同的 39 个 Hox 基因。蛇、两栖动物和可能的肺鱼中没有 HoxD12。青蛙和蚓螈丢失了 HoxB13。肉鳍鱼类、两栖动物和有鳞目爬行动物拥有 HoxC3。HoxC1 仅存在于蚓螈和肉鳍鱼类中。与腔棘鱼类似，肺鱼也拥有迄今为止仅在肉鳍鱼类中发现的 HoxA14。我们的 Hox 基因变异数据支持肺鱼-四足动物、海龟-主龙类和青蛙-蝾螈的关系，并暗示 HoxD12 的缺失与指（趾）的减少没有直接关系。
我们新确定的 Hox 基因库数据为沿肉鳍鱼谱系的 Hox 基因进化动态提供了一个更完整的情景。无肢、蠕虫状的蚓螈和蛇与具有较少衍生体型的动物具有相似的 Hox 基因库，这表明它们体型的变化可能是由于其他改变而不是 Hox 基因数量的改变。此外，我们的结果为未来对这些动物的整个 Hox 基因簇进行测序提供了基础。
