Wotton Karl R, Shimeld Sebastian M
Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK.
BMC Genomics. 2006 Oct 24;7:271. doi: 10.1186/1471-2164-7-271.
Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown.
To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region.
Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.
脊椎动物基因组包含众多重复基因，其中许多基因被组织成旁系同源区域，这表明基因连锁群发生了重复。比较不同谱系中的基因组组织通常可以追溯这些区域的进化历史。一个典型的例子是Hox基因，文昌鱼中单个连续的Hox簇以及四个脊椎动物簇的存在使得该区域的基因组进化得以确立。C、F、L1和Q1类的Fox转录因子在文昌鱼和人类中也成簇组织。然而，与Hox基因不同的是，迄今为止在人类基因组中仅鉴定出两个旁系同源Fox基因簇，其他脊椎动物中的组织情况尚不清楚。
为了揭示Fox基因簇的进化历史，我们报告了这些基因座的比较基因组学。我们在人类基因组中发现了另外两个旁系同源区域，并在哺乳动物、鸡、青蛙和硬骨鱼基因组中鉴定出直系同源区域，确定这些重复发生在辐鳍鱼和肉鳍鱼谱系分离之前。还发现另外一个Fox类，即FoxS，也存在于这个重复的基因组区域中。
对基因座的比较确定了多个谱系中基因重复、丢失和簇断裂的模式，并表明FoxS1可能是Fox基因簇重复的残余物。
