Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.
Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.
复制标题
叶绿体基因组的基因重排分析和祖先的序列推断具有倒重复。
DOI：
10.1186/1471-2164-9-s1-s25
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发表时间：
2008
期刊：
影响因子：
4.4
通讯作者：
Tang, Jijun
中科院分区：
文献类型：
--
作者：
Yue, Feng;Cui, Liying;Depamphilis, Claude W.;Moret, Bernard M. E.;Tang, Jijun
基因组进化不仅受到核苷酸替换的影响，还受到包括基因和基因组复制、插入、缺失和基因顺序重排在内的结构变化的影响。从基因组重排中重建系统发育最常用的方法包括GRAPPA和MGR。然而，这些方法仅限于基因含量相等或很少缺失的情况下可以假设。由于许多叶绿体基因组都存在保守的重复区域，因此在叶绿体系统发育分析和祖先基因组重建中需要反向重复序列的推断。我们扩展了GRAPPA，并开发了GRAPPA- ir处理叶绿体基因组的新方法。利用陆地植物和绿藻的不同叶绿体基因组进行的GRAPPA-IR测试恢复了与先前研究一致的系统发育，而不考虑IR结构的分析未能获得公认的拓扑结构。我们大量的模拟研究也证实了GRAPPA比现有方法具有更好的精度。在生物和模拟数据集上的测试表明，GRAPPA-IR可以准确地恢复基因组系统发育以及祖先基因顺序。对祖先基因组结构的密切分析表明，基因组在叶绿体中的重排可能受到具有保守核心区域的反向重复的限制。此外，反向重复序列的边界是基因重复或缺失的热点。新的GRAPPA-IR可从。
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction. We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR using divergent chloroplast genomes from land plants and green algae recovers the phylogeny congruent with prior studies, while analysis that do not consider IR structure fail to obtain the accepted topology. Our extensive simulation study also confirms that GRAPPA has better accuracy then the existing methods. Tests on a biological and simulated dataset show GRAPPA-IR can accurately recover the genome phylogeny as well as ancestral gene orders. Close analysis of the ancestral genome structure suggests that genome rearrangement in chloroplasts is probably limited by inverted repeats with a conserved core region. In addition, the boundaries of inverted repeats are hot spots for gene duplications or deletions. The new GRAPPA-IR is available from .