School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721.
Plant Physiol. 2013 Sep;163(1):354-62. doi: 10.1104/pp.113.219444. Epub 2013 Jul 29.
In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.
在动植物中，基于保守的同源基因组块的染色体断裂和融合事件导致了同一科物种之间的染色体组进化的保守模式。然而，染色体组信息在基因组比较研究中尚未得到充分利用。我们提出了 CrusView，这是一个基于 Java 的生物信息学应用程序，利用标准小部件工具包/Swing 图形库和 SQLite 数据库来对十字花科（芸苔属）植物的比较基因组学数据进行可视化分析。与类似的软件和数据库相比，CrusView 的一个独特功能是在比较两个基因组时整合了染色体组信息。此功能允许用户使用芸苔属基因组的预设染色体组模式进行基于染色体组的基因组组装和染色体组辅助的基因组同线性分析。此外，CrusView 是一个本地程序，在分析未公布的基因组时为其用户提供了高度的灵活性，并允许用户上传自定义的基因组信息，以便他们可以直观地研究基因组结构变异与遗传元件之间的关联，包括染色体重排、基因组大协同进化、基因家族、高频重组位点以及相关物种之间的串联和片段重复。该工具将极大地促进使用可视化比较基因组学方法研究十字花科物种的染色体组、染色体和基因组进化。CrusView 可在 http://www.cmbb.arizona.edu/CrusView/ 免费获得。
