School of Information Technology, Center for Computational Biology and Bioinformatics, Jawaharlal Nehru University, New Delhi, India.
PLoS One. 2010 Nov 30;5(11):e14159. doi: 10.1371/journal.pone.0014159.
Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species.
可以使用一系列分子进化工具来研究一组生物体的表型行为，这些工具有助于确定进化关系。传统上，使用一个基因或一组基因序列来生成系统发育树。在少数选定的基因中，不完整的进化信息会导致系统发育树构建出现问题。现在，我们的任务是确定合适的参数，从整个基因组序列中提取真正代表进化信息的隐藏信息。在这项研究中，我们探索了一种基于随机锚（100 个核苷酸的一段）的方法（ABWGP）来寻找任意两个基因组之间的距离，并使用距离估计值来计算进化树。我们使用了许多分枝杆菌的菌株和物种进行了这项研究。以成对的方式计算了锚定衍生参数，如累积归一化得分、锚定顺序和插入/缺失，并使用这些得分来计算距离/系统发育树。分支的强度通过自举分析来确定。使用这里描述的距离估计值可以清楚地区分末端分支。一般来说，不同的度量标准给出了相似的树，除了基于插入/缺失的树。总的来说，树拓扑反映了生物体的已知生物学。这对不同的大肠杆菌菌株也是如此。这里描述了一种新的基于全基因组的方法，用于研究细菌菌株和物种之间的进化关系。
