Dating the early evolution of plants: detection and molecular clock analyses of orthologs
Dating the early evolution of plants: detection and molecular clock analyses of orthologs
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DOI：
10.1007/s00438-007-0257-6
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发表时间：
2007-10-01
影响因子：
3.1
通讯作者：
Rensing, Stefan A.
中科院分区：
文献类型：
--
作者：
Zimmer, Andreas;Lang, Daniel;Rensing, Stefan A.
直系同源基因通常承受着防止功能丧失的选择压力，而同源基因通常会积累突变，最终在功能或调节方面死亡或偏离。大多数直系同源数据检测方法都会用大量的平行同源数据来污染结果数据集。因此，我们的目标是实现一种简单的方法，允许从完全测序的基因组中检测到同源基因簇，同时减少同源基因的数量。所描述的互反最佳BLAST命中方法的跨物种扩展是用于同源基因检测的时效性方法，其导致68%的真正同源基因簇，并且该程序特别丰富了单拷贝同源基因。真同源基因的检测可以为更好地理解进化过程提供一个系统发育工具包。在一项对六种光合作用真核生物的研究中，推测线粒体起源的核基因在单拷贝同源基因中被证明是过度表达的。这些同源基因涉及基本的生物过程，如氨基酸代谢或翻译。基于这一数据集的分子时钟分析得到了红藻/绿藻(1,142 MYA)、绿藻/陆地植物(725 MYA)、苔藓/种子植物(496 MYA)、裸子植物/被子植物(385 MYA)和单子叶植物/核心双子叶植物(301 MYA)分歧时间的估计。
Orthologs generally are under selective pressure against loss of function, while paralogs usually accumulate mutations and finally die or deviate in terms of function or regulation. Most ortholog detection methods contaminate the resulting datasets with a substantial amount of paralogs. Therefore we aimed to implement a straightforward method that allows the detection of ortholog clusters with a reduced amount of paralogs from completely sequenced genomes. The described cross-species expansion of the reciprocal best BLAST hit method is a time-effective method for ortholog detection, which results in 68% truly orthologous clusters and the procedure specifically enriches single-copy orthologs. The detection of true orthologs can provide a phylogenetic toolkit to better understand evolutionary processes. In a study across six photosynthetic eukaryotes, nuclear genes of putative mitochondrial origin were shown to be over-represented among single copy orthologs. These orthologs are involved in fundamental biological processes like amino acid metabolism or translation. Molecular clock analyses based on this dataset yielded divergence time estimates for the red/green algae (1,142 MYA), green algae/land plant (725 MYA), mosses/seed plant (496 MYA), gymno-/angiosperm (385 MYA) and monocotyledons/core eudicotyledons (301 MYA) divergence times.