Tutaj Monika, Smith Jennifer R, Bolton Elizabeth R
Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
Methods Mol Biol. 2019;2018:43-70. doi: 10.1007/978-1-4939-9581-3_2.
The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.
大鼠参考基因组序列的首个也是唯一已发表版本是RGSC3.1，由大鼠基因组测序计划联盟完成。在此，我们介绍了在完善过程中修正序列错误和填补缺失间隙并为研究人员提供高质量大鼠参考序列的社区努力历程。基因组组装的改进、随着时间推移添加不同的证据资源（如RNA-Seq数据）以及软件开发方法对基因模型注释产生了积极影响。多年来，我们观察到基因、蛋白质编码序列、预测转录本和转录本特征的数量大幅增加。在大鼠基因组测序成为可能之前，首先是生化标记，随后是RAPD、AFLP、RFLP和SSLP等基因组标记，在涉及不同大鼠品系杂交的研究、寻找多态性水平、连锁图谱构建和系统发育研究中起着基础性作用。连锁图谱提供有关重组率的信息，深入了解种内和种间基因重排，并有助于识别孟德尔位点和数量性状位点（QTL）。在20世纪90年代，发表了许多关于大鼠连锁图谱构建的报告，这些图谱纳入了越来越多的标记并促进了疾病位点的定位。当前的遗传监测和连锁图谱构建依赖于单核苷酸多态性（SNP）。大鼠基因组数据库收集了来自全球大鼠研究人员群体的遗传变异信息，并提供搜索和检索这些数据的工具。截至目前，我们在变异可视化工具中展示了来自许多研究的近6.05亿个变异的详细信息。
