Kaufmann Stefanie, Frishman Dmitrij
Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Bavaria, Germany.
Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Bavaria, Germany; Institute of Bioinformatics and Systems Biology, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany; Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia.
PLoS One. 2014 Nov 6;9(11):e112341. doi: 10.1371/journal.pone.0112341. eCollection 2014.
High-quality mapping of genomic regions and genes between two organisms is an indispensable prerequisite for evolutionary analyses and comparative genomics. Existing approaches to this problem focus on either delineating orthologs or finding extended sequence regions of common evolutionary origin (syntenic blocks). We propose SyntenyMapper, a novel tool for refining predefined syntenic regions. SyntenyMapper creates a set of blocks with conserved gene order between two genomes and finds all minor rearrangements that occurred since the evolutionary split of the two species considered. We also present TrackMapper, a SyntenyMapper-based tool that allows users to directly compare genome features, such as histone modifications, between two organisms, and identify genes with highly conserved features. We demonstrate SyntenyMapper's advantages by conducting a large-scale analysis of micro-rearrangements within syntenic regions of 25 eukaryotic species. Unsurprisingly, the number and length of syntenic regions is correlated with evolutionary distance, while the number of micro-rearrangements depends only on the size of the harboring region. On the other hand, the size of rearranged regions remains relatively constant regardless of the evolutionary distance between the organisms, implying a length constraint in the rearrangement process. SyntenyMapper is a useful software tool for both large-scale and gene-centric genome comparisons.
对两个生物体之间的基因组区域和基因进行高质量的图谱绘制，是进化分析和比较基因组学不可或缺的前提条件。解决这个问题的现有方法要么侧重于划定直系同源基因，要么侧重于寻找具有共同进化起源的扩展序列区域（共线性区域）。我们提出了SyntenyMapper，这是一种用于优化预定义共线性区域的新型工具。SyntenyMapper创建了一组在两个基因组之间具有保守基因顺序的区域，并找出了自所考虑的两个物种进化分化以来发生的所有微小重排。我们还展示了TrackMapper，这是一种基于SyntenyMapper的工具，它允许用户直接比较两个生物体之间的基因组特征，如组蛋白修饰，并识别具有高度保守特征的基因。我们通过对25个真核生物物种共线性区域内的微重排进行大规模分析，展示了SyntenyMapper的优势。不出所料，共线性区域的数量和长度与进化距离相关，而微重排的数量仅取决于所包含区域的大小。另一方面，重排区域的大小无论生物体之间的进化距离如何，都保持相对恒定，这意味着重排过程中存在长度限制。SyntenyMapper是一个对大规模和以基因为中心的基因组比较都有用的软件工具。
