Hoegg Simone, Meyer Axel
Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
BMC Evol Biol. 2007 Aug 15;7:139. doi: 10.1186/1471-2148-7-139.
Gene clusters are of interest for the understanding of genome evolution since they provide insight in large-scale duplications events as well as patterns of individual gene losses. Vertebrates tend to have multiple copies of gene clusters that typically are only single clusters or are not present at all in genomes of invertebrates. We investigated the genomic architecture and conserved non-coding sequences of vertebrate KCNA gene clusters. KCNA genes encode shaker-related voltage-gated potassium channels and are arranged in two three-gene clusters in tetrapods. Teleost fish are found to possess four clusters. The two tetrapod KNCA clusters are of approximately the same age as the Hox gene clusters that arose through duplications early in vertebrate evolution. For some genes, their conserved retention and arrangement in clusters are thought to be related to regulatory elements in the intergenic regions, which might prevent rearrangements and gene loss. Interestingly, this hypothesis does not appear to apply to the KCNA clusters, as too few conserved putative regulatory elements are retained.
We obtained KCNA coding sequences from basal ray-finned fishes (sturgeon, gar, bowfin) and confirmed that the duplication of these genes is specific to teleosts and therefore consistent with the fish-specific genome duplication (FSGD). Phylogenetic analyses of the genes suggest a basal position of the only intron containing KCNA gene in vertebrates (KCNA7). Sistergroup relationships of KCNA1/2 and KCNA3/6 support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of KCNA clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. The orthologous teleost clusters, however, show sequence conservation in these regions.
The lack of overall conserved sequences in intergenic regions suggests that there are either other processes than regulatory evolution leading to cluster conservation or that the ancestral regulatory relationships among genes in KCNA clusters have been changed together with their regulatory sites.
基因簇对于理解基因组进化具有重要意义，因为它们能为大规模复制事件以及单个基因丢失模式提供见解。脊椎动物往往拥有多个基因簇拷贝，而这些基因簇在无脊椎动物基因组中通常只是单个簇或根本不存在。我们研究了脊椎动物KCNA基因簇的基因组结构和保守非编码序列。KCNA基因编码与震颤相关的电压门控钾通道，在四足动物中以两个三基因簇的形式排列。硬骨鱼被发现拥有四个簇。四足动物的两个KNCA簇与在脊椎动物进化早期通过复制产生的Hox基因簇年龄大致相同。对于一些基因，它们在簇中的保守保留和排列被认为与基因间区域的调控元件有关，这些调控元件可能会防止重排和基因丢失。有趣的是，这一假设似乎不适用于KCNA簇，因为保留的保守推定调控元件太少。
我们从基部辐鳍鱼（鲟鱼、雀鳝、弓鳍鱼）中获得了KCNA编码序列，并证实这些基因的复制是硬骨鱼特有的，因此与鱼类特有的基因组复制（FSGD）一致。对这些基因的系统发育分析表明，脊椎动物中唯一含有内含子的KCNA基因（KCNA7）处于基部位置。KCNA1/2和KCNA3/6的姐妹群关系支持了一次大规模复制产生了四足动物基因组中发现的两个簇。我们分析了脊椎动物KCNA簇的基因间区域，发现四足动物和硬骨鱼之间或旁系同源簇之间仅共享少数保守序列。然而，直系同源的硬骨鱼簇在这些区域显示出序列保守性。
基因间区域缺乏整体保守序列表明，要么存在除调控进化之外导致簇保守的其他过程，要么KCNA簇中基因之间的祖先调控关系与其调控位点一起发生了变化。
