Gershgorin Roman A, Gorbunov Konstantin Yu, Zverkov Oleg A, Rubanov Lev I, Seliverstov Alexandr V, Lyubetsky Vassily A
Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia.
Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskiye Gory 1, Main Building, Moscow 119991, Russia.
Life (Basel). 2017 Feb 27;7(1):9. doi: 10.3390/life7010009.
Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome.
最近的系统发育分析纳入了超保守元件（UCEs）和高度保守元件（HCEs）。基因组结构和HCEs的进化模型最初面临着相当大的算法挑战，这对这些模型产生了（通常是不自然的）限制，即使对于诸如计算两个结构之间的距离或识别UCEs这样概念上简单的任务也是如此。在我们最近的工作中，这些限制已经通过快速有效的解决方案得到解决，且对基础模型没有限制。这些方法让我们得到了一个意想不到的结果：对于一些细胞器和分类群，基因组结构和HCE集尽管本身包含的信息相对较少，但仍然足以解析物种的进化。我们还利用HCE识别来寻找表征基因组功能进化的启动子和调控元件。
