Yu Wei-Ping, Rajasegaran Vikneswari, Yew Kenneth, Loh Wai-Lin, Tay Boon-Hui, Amemiya Chris T, Brenner Sydney, Venkatesh Byrappa
Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore.
Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3819-24. doi: 10.1073/pnas.0800398105. Epub 2008 Mar 4.
Cartilaginous fishes are the oldest living phylogenetic group of jawed vertebrates. Here, we demonstrate the value of cartilaginous fish sequences in reconstructing the evolutionary history of vertebrate genomes by sequencing the protocadherin cluster in the relatively small genome (910 Mb) of the elephant shark (Callorhinchus milii). Human and coelacanth contain a single protocadherin cluster with 53 and 49 genes, respectively, that are organized in three subclusters, Pcdhalpha, Pcdhbeta, and Pcdhgamma, whereas the duplicated protocadherin clusters in fugu and zebrafish contain >77 and 107 genes, respectively, that are organized in Pcdhalpha and Pcdhgamma subclusters. By contrast, the elephant shark contains a single protocadherin cluster with 47 genes organized in four subclusters (Pcdhdelta, Pcdhepsilon, Pcdhmu, and Pcdhnu). By comparison with elephant shark sequences, we discovered a Pcdhdelta subcluster in teleost fishes, coelacanth, Xenopus, and chicken. Our results suggest that the protocadherin cluster in the ancestral jawed vertebrate contained more subclusters than modern vertebrates, and the evolution of the protocadherin cluster is characterized by lineage-specific differential loss of entire subclusters of genes. In contrast to teleost fish and mammalian protocadherin genes that have undergone gene conversion events, elephant shark protocadherin genes have experienced very little gene conversion. The syntenic block of genes in the elephant shark protocadherin locus is well conserved in human but disrupted in fugu. Thus, the elephant shark genome appears to be less prone to rearrangements compared with teleost fish genomes. The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes.
软骨鱼类是现存最古老的有颌脊椎动物系统发育群体。在此，我们通过对姥鲨（Callorhinchus milii）相对较小的基因组（910 Mb）中的原钙黏蛋白基因簇进行测序，证明了软骨鱼类序列在重建脊椎动物基因组进化历史中的价值。人类和腔棘鱼分别含有一个原钙黏蛋白基因簇，其中有53个和49个基因，这些基因被组织成三个亚簇，即Pcdhalpha、Pcdhbeta和Pcdhgamma，而河豚和斑马鱼中重复的原钙黏蛋白基因簇分别包含超过77个和107个基因，它们被组织成Pcdhalpha和Pcdhgamma亚簇。相比之下，姥鲨含有一个单一的原钙黏蛋白基因簇，其中有47个基因，被组织成四个亚簇（Pcdhdelta、Pcdhepsilon、Pcdhmu和Pcdhnu）。通过与姥鲨序列进行比较，我们在硬骨鱼类、腔棘鱼、非洲爪蟾和鸡中发现了一个Pcdhdelta亚簇。我们的结果表明，原始有颌脊椎动物中的原钙黏蛋白基因簇包含的亚簇比现代脊椎动物更多，并且原钙黏蛋白基因簇的进化特征是特定谱系中整个基因亚簇的差异性丢失。与经历了基因转换事件的硬骨鱼类和哺乳动物原钙黏蛋白基因不同，姥鲨原钙黏蛋白基因经历的基因转换很少。姥鲨原钙黏蛋白基因座中的基因共线性区域在人类中保存良好，但在河豚中被破坏。因此，与硬骨鱼类基因组相比，姥鲨基因组似乎更不容易发生重排。姥鲨的小而“稳定”的基因组是理解脊椎动物基因组进化的宝贵参考。
