PDF(Pubmed)
Abstract：
The polymorphism of SINE-containing loci reflects the evolutionary processes that occurred both during the period before the divergence of the taxa and after it. Orthologous loci containing SINE in two or more genomes indicate the relatedness of the taxa, while different copies may have a specific set of mutations and degree of difference. Polymorphic insertion can be interpreted with a high degree of confidence as a shared derived character in the phylogenetic reconstruction of the history of the taxon. The computational comparison of the entire set of SINE-containing loci between genomes is a challenging task, and we propose to consider it in detail using the genomes of representatives of squamate reptiles (lizards) as an example. Our approach allows us to extract copies of SINE from the genomes, find pairwise orthologous loci by using flanking genomic sequences, and analyze the resulting sets of loci for the presence or absence of SINE, the degree of similarity of the flanks, and the similarity of the SINE themselves. The workflow we propose allows us to efficiently extract and analyze orthologous SINE loci for the downstream analysis, as shown in our comparison of species- and genus-level taxa in lacertid lizards.
摘要：
含SINE基因座的多态性反映了在分类单元分歧之前和之后的进化过程。在两个或多个基因组中含有SINE的直系同源基因座表明分类单元的相关性，而不同的拷贝可能有一组特定的突变和程度的差异。多态性插入可以高度自信地解释为分类单元历史的系统发育重建中的共同衍生特征。基因组之间的整套含SINE基因座的计算比较是一项具有挑战性的任务，我们建议以鳞类爬行动物（蜥蜴）代表的基因组为例进行详细考虑。我们的方法允许我们从基因组中提取SINE的拷贝，通过使用侧翼基因组序列找到成对直系同源基因座，并分析所得到的基因座集是否存在正弦，侧翼的相似程度，以及正弦本身的相似性。我们提出的工作流程使我们能够有效地提取和分析直系同源SINE基因座，用于下游分析，如我们对lacertid蜥蜴的物种和属级分类群的比较所示。
