Background
The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time.

Results
We present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits.

Conclusions
The introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.



中文翻译：

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使用彩色 de Bruijn 图进行无比对和无参考的系统发育组学

背景
可用基因组序列数据的不断增加使得大规模的比较研究成为可能。一个常见的任务是系统发育的推断——如果没有紧密的参考序列、基因组序列组装不完整、或者大量的基因组妨碍了在合理时间内进行多重序列比对，那么这是一项具有挑战性的任务。

结果
我们提出了一种新的基于全基因组的方法来推断系统发育，该方法无需比对和参考。与其他方法相比，它不依赖于成对比较来确定推断树中边缘的距离。相反，构建了彩色 de Bruijn 图，并提取有关公共子序列的信息以推断系统发育分裂。

结论
所引入的大规模系统基因组学新方法显示出巨大的潜力。对不同数据集的应用证实了该方法的稳健性。与其他最先进的基于全基因组的方法相比，表明具有可比或更高的准确性和效率。