Berkemer Sarah J, Hoffmann Anne, Murray Cameron R A, Stadler Peter F
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
Life (Basel). 2017 Oct 31;7(4):42. doi: 10.3390/life7040042.
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available.
几个多拷贝基因家族，如转运核糖核酸（tRNA）和核糖体RNA（rRNA），会经历协同进化，这种效应使得旁系同源基因的序列实际上保持相同。在这种情况下，仅根据序列相似性无法区分直系同源基因和旁系同源基因。然而，基因组位置的相对保存情况，即共线性，在此种情形下对于厘清进化关系仍具有参考价值。在本论文中，我们描述了一种自动流程，用于此类情况的进化分析，该流程以全基因组比对为起点，来确定由共线性决定的直系同源关系。灵长类动物中tRNA的进化以及脊椎动物和线虫中Y RNA家族的历史被用来展示该方法。此流程可免费获取。
