Reconstructing genome trees of prokaryotes using overlapping genes.
Reconstructing genome trees of prokaryotes using overlapping genes.
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DOI：
10.1186/1471-2105-11-102
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发表时间：
2010-02-24
影响因子：
3
通讯作者：
Lu CL
中科院分区：
文献类型：
--
作者：
Cheng CH;Yang CH;Chiu HT;Lu CL
重叠基因（OG）被定义为编码序列部分或完全重叠的相邻基因。事实上，它们在微生物基因组中无处不在，并且在物种之间比非重叠基因更加保守。基于这个特性，我们之前实现了一个名为 OGtree 的网络服务器，它允许用户根据一些原核生物的成对 OG 距离重建基因组树。通过类比基因内容和基因顺序的分析，我们定义的两个基因组之间的 OG 距离是基于整个基因组中 OG 内容（即共享直系同源 OG 对的归一化数量）和 OG 顺序（即归一化 OG 断点距离）的组合的度量。使用断点概念定义OG距离的缺点是无法分析多染色体基因组的OG距离。此外，一些远缘相关的原核生物基因组之间重叠编码序列的数量可能是有限的，因此很难找到足够的OG来正确评估它们成对的OG距离。因此，在这项研究中，我们定义了一个新的 OG 顺序距离，该距离基于更生物学上准确的重排（例如逆转、转座和易位）而不是断点，并且适用于单染色体和多染色体基因组。此外，我们将术语“基因”扩展为包括其编码序列和调控区，因此编码序列或调控区彼此重叠的两个相邻基因被视为一对重叠基因。这是因为不同基因的调控区域的重叠表明这些基因的表达调控应该或多或少地相互关联。基于这些修改，我们重新实现了 OGtree 作为一个新的 Web 服务器，命名为 OGtree2，并且还在由 21 个变形菌基因组组成的测试数据集上评估了其基因组树重建的准确性。我们的实验结果最终表明，我们当前的 OGtree2 在基因组树重建质量方面确实优于其先前版本的 OGtree 以及另一个类似的服务器 BPhyOG，因为 OGtree2 获得的系统发育树与参考树非常一致，而参考树与生物学家对这些变形菌所接受的分类法一致。在这项研究中，我们在http://bioalgorithm.life.nctu.edu.tw/OGtree2.0/引入了一个新的网络服务器OGtree2，它可以作为根据重叠基因重建更精确和稳健的原核生物基因组树的有用工具。
Overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, they are ubiquitous in microbial genomes and more conserved between species than non-overlapping genes. Based on this property, we have previously implemented a web server, named OGtree, that allows the user to reconstruct genome trees of some prokaryotes according to their pairwise OG distances. By analogy to the analyses of gene content and gene order, the OG distance between two genomes we defined was based on a measure of combining OG content (i.e., the normalized number of shared orthologous OG pairs) and OG order (i.e., the normalized OG breakpoint distance) in their whole genomes. A shortcoming of using the concept of breakpoints to define the OG distance is its inability to analyze the OG distance of multi-chromosomal genomes. In addition, the amount of overlapping coding sequences between some distantly related prokaryotic genomes may be limited so that it is hard to find enough OGs to properly evaluate their pairwise OG distances. In this study, we therefore define a new OG order distance that is based on more biologically accurate rearrangements (e.g., reversals, transpositions and translocations) rather than breakpoints and that is applicable to both uni-chromosomal and multi-chromosomal genomes. In addition, we expand the term "gene" to include both its coding sequence and regulatory regions so that two adjacent genes whose coding sequences or regulatory regions overlap with each other are considered as a pair of overlapping genes. This is because overlapping of regulatory regions of distinct genes suggests that the regulation of expression for these genes should be more or less interrelated. Based on these modifications, we have reimplemented our OGtree as a new web server, named OGtree2, and have also evaluated its accuracy of genome tree reconstruction on a testing dataset consisting of 21 Proteobacteria genomes. Our experimental results have finally shown that our current OGtree2 indeed outperforms its previous version OGtree, as well as another similar server, called BPhyOG, significantly in the quality of genome tree reconstruction, because the phylogenetic tree obtained by OGtree2 is greatly congruent with the reference tree that coincides with the taxonomy accepted by biologists for these Proteobacteria. In this study, we have introduced a new web server OGtree2 at http://bioalgorithm.life.nctu.edu.tw/OGtree2.0/ that can serve as a useful tool for reconstructing more precise and robust genome trees of prokaryotes according to their overlapping genes.
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影响因子：
14.9
作者：
Jiang LW;Lin KL;Lu CL
通讯作者：
Lu CL
DOI：
10.1111/j.1096-0031.1996.tb00196.x
发表时间：
1994-09-01
期刊：
CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY
影响因子：
--
作者：
FARRIS, JS;KALLERSJO, M;BULT, C
通讯作者：
BULT, C
影响因子：
3.3
作者：
Krakauer, DC
通讯作者：
Krakauer, DC
影响因子：
2.6
作者：
Janga, Sarath Chandra;Collado-Vides, J.
通讯作者：
Collado-Vides, J.
影响因子：
14.9
作者：
Fukuda, Y;Washio, T;Tomita, M
通讯作者：
Tomita, M