Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions.
Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions.
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DOI：
10.4137/ebo.s33491
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Lin K
中科院分区：
文献类型：
--
作者：
Zhang YC;Lin K
重叠基因（overlappinggenes，OG）是细菌基因组中广泛存在的一种基因组特征，已被用作细菌亲缘关系密切的物种的遗传学推断中的稀有基因组标记。然而，对于太近或太远相关基因组的重复基因组分析，推断可能会经历性能下降。OG作为系统发育标记的另一个缺点是它们通常很少考虑基因组重排对相似性估计的影响，例如染色体/基因组内易位、水平基因转移和基因丢失。为了探索这种影响的准确性的系统发育重建，我们结合联合收割机系统发育信号的OG共线基因组区域，这里称为局部共线块（LCB）。通过把这些放在一起，我们改进了我们以前的两个密切相关的细菌基因组之间的成对相似性度量。作为一个案例研究，我们使用这种新的方法来重建的88个肠杆菌基因组的γ-变形菌类。我们的研究结果表明，当同时考虑OG和LCB时，推断的系统发育的拓扑准确性得到提高，这表明将这两个系统发育标记相结合可能会在一定程度上减少基因丢失对系统发育推断的影响。我们相信，这样的细菌基因组研究将帮助我们探索一种更有效的方法来增加密切相关的细菌生物体的同源性重建的鲁棒性。
Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms.
影响因子：
3
作者：
Cheng CH;Yang CH;Chiu HT;Lu CL
通讯作者：
Lu CL
BPhyOG：基于重叠基因的细菌系统发育全基因组推断的交互式服务器
影响因子：
3
作者：
Luo Y;Fu C;Zhang DY;Lin K
通讯作者：
Lin K