OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs.
OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs.
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DOI：
10.1186/1471-2105-11-114
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发表时间：
2010-03-02
影响因子：
3
通讯作者：
Hao W
中科院分区：
文献类型：
--
作者：
Hao W
线粒体和叶绿体的祖先可以追溯到曾经自由生活的细菌的分离内共生体。因此，这两种细胞器的高度简化的基因组包含非常遥远的同源物，这些同源物直到最近才被证明在线粒体基因组内重组。由于缺乏合适的计算机程序，以前不可能检测线粒体和叶绿体同源物之间的基因转换。最近，我开发了一种新的方法，并首次发现了叶绿体线粒体基因之间的重复基因转换。该方法将进一步加深我们对植物细胞器基因组进化的理解，并有助于识别和删除在植物系统学中广泛使用的几个基因的不一致的系统发育信号的基因区域。在这里，我实现了这样一个方法，可以在用户友好的Web界面中使用。OrgConv（Organellar Conversion）是一个用于检测线粒体和叶绿体同源基因之间的基因转换的计算机软件包。OrgConv有两种形式;源代码可以在Linux平台上安装和运行，Web界面可以在多个操作系统上使用。特征程序的输入文件是来自不同细胞器区室的FASTA格式的两个多序列比对。该程序将每个检查的序列与每个序列比对的共有序列进行比较，而不是彻底检查每个可能的组合。利用共有序列显著减少了比较的数量，因此减少了总体计算时间，这允许分析非常大的数据集。最重要的是，随着比较次数的显著减少，面对多重检验的校正，统计功效仍然很高。OrgConv的源代码和Web界面都可以从OrgConv网站http://www.indiana.edu/~orgconv免费获得。虽然OrgConv的开发主要集中在检测线粒体和叶绿体基因之间的基因转换，但它也可用于检测任何两组不同同源序列之间的基因转换。
The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface. OrgConv (Organellar Conversion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. OrgConv is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests. Both the source code and the web interface of OrgConv are available for free from the OrgConv website http://www.indiana.edu/~orgconv. Although OrgConv has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.
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