Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution
Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution
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DOI：
10.1002/jez.b.00040
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发表时间：
2003-10-15
影响因子：
2.2
通讯作者：
Gibson-Brown, JJ
中科院分区：
文献类型：
--
作者：
Horton, AC;Mahadevan, NR;Gibson-Brown, JJ
在早期脊椎动物进化过程中发生了两次全基因组复制（2 R假说），这一被广泛接受的观点源于脊椎动物通常拥有对应于一个无脊椎动物同源物的几个基因。然而，人类基因组计划预测的基因数量不到果蝇或秀丽隐杆线虫基因组的两倍。这一比例可以通过两轮基因组复制随后的广泛基因丢失、通过单次基因组复制、通过连续局部复制或通过上述任何组合来解释。用于区分这些可能性的传统方法是重建脊椎动物基因与其无脊椎动物直系同源物的系统发育关系;然后使用无脊椎动物与脊椎动物对应物的比率来推断基因重复事件的数量。文昌鱼是脊椎动物中最接近的无脊椎动物，与原口动物如苍蝇或线虫不同，文昌鱼是理解所有脊椎动物最后共同祖先基因组组成的最合适的外类群。我们分析了所有可用的文昌鱼基因的脊椎动物同源物的关系。在大多数情况下，一至三个脊椎动物基因轮胎正交每个文昌鱼基因（中位数=2）。显然，这个结果，以及以前使用这种方法的研究结果，不能区分脊索动物基因组扩增的替代方案。我们的结论是，单靠系统发育分析永远不足以确定早期脊索动物进化过程中是否发生了基因组复制，并认为，如果要重建早期脊索动物基因组进化的模式和过程，就需要一种“同源基因组”方法，该方法比较了来自完整文昌鱼和人类基因组序列的连锁基因的旁系同源簇。(C)2003 Wiley-Liss，Inc.
The widely accepted notion that two whole-genome duplications occurred during early vertebrate evolution (the 2R hypothesis) stems from the fact that vertebrates often possess several genes corresponding to a single invertebrate homolog. However the number of genes predicted by the Human Genome Project is less than twice as many as in the Drosophila melanogaster or Caenorhabditis elegans genomes. This ratio could be explained by two rounds of genome duplication followed by extensive gene loss, by a single genome duplication, by sequential local duplications, or by a combination of any of the above. The traditional method used to distinguish between these possibilities is to reconstruct the phylogenetic relationships of vertebrate genes to their invertebrate orthologs; ratios of invertebrate-to-vertebrate counterparts are then used to infer the number of gene duplication events. The lancelet, amphioxus, is the closest living invertebrate relative of the vertebrates, and unlike protostomes such as flies or nematodes, is therefore the most appropriate outgroup for understanding the genomic composition of the last common ancestor of all vertebrates. We analyzed the relationships of all available amphioxus genes to their vertebrate homologs. In most cases, one to three vertebrate genes tire orthologous to each amphioxus gene (median number=2). Clearly this result, and those of previous studies using this approach, cannot distinguish between alternative scenarios of chordate genome expansion. We conclude that phylogenetic analyses alone will never be sufficient to determine whether genome duplication(s) occurred during early chordate evolution, and argue that a "phylogenomic" approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed. (C) 2003 Wiley-Liss, Inc.