Recent segmental and gene duplications in the mouse genome.
Recent segmental and gene duplications in the mouse genome.
复制标题
小鼠基因组中最近的分段和基因重复。
DOI：
10.1186/gb-2003-4-8-r47
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发表时间：
2003
期刊：
影响因子：
12.3
通讯作者：
Scherer, Stephen W
中科院分区：
文献类型：
--
作者：
Cheung, Joseph;Wilson, Michael D;Zhang, Junjun;Khaja, Razi;MacDonald, Jeffrey R;Heng, Henry H Q;Koop, Ben F;Scherer, Stephen W
使用基于BLAST的计算遗传学来鉴定小鼠基因组序列中的大的和最近的片段重复。这里提供了一个最近复制的小鼠基因组区域的数据库。高质量的小鼠基因组草图序列及其相关注释是非常宝贵的生物资源。确定最近在小鼠基因组中的重复，特别是在含有基因的区域，可能会突出最近的小鼠进化中的重要事件。此外，检测最近的序列重复可以揭示基因组组装的潜在问题区域。我们使用基于BLAST的计算化学来鉴定小鼠基因组序列中的大的（≥ 5 kb）和最近的（≥ 90%序列同一性）片段重复。在这里，我们提出了一个数据库，最近重复的小鼠基因组中发现的小鼠基因组测序联盟（MGSC）2002年2月和2003年2月的大会区域。我们确定，2003年2月小鼠基因组序列组装的2，695 Mb序列中的33.6 Mb（1.2%）参与了最近的片段重复，这低于在人类基因组中观察到的（约3.5-5%）。从这个数据集，8.9 Mb（26%）的重复内容组成的“未映射”的染色体序列。此外，我们怀疑，一个额外的18.5 Mb的序列是涉及在这个基因组组装的序列错配错误所产生的重复文物。通过寻找位于这些区域内的基因，我们确定了675个基因，这些基因映射到小鼠基因组的重复区域。其中16个基因似乎在人类基因组中独立复制。从我们的数据集，我们进一步表征了一个42 kb的最近的节段性重复的Mater，母效应基因在小鼠胚胎发生所必需的。我们的研究结果提供了一个初步的分析最近重复的序列和基因内容的小鼠基因组。许多这些重复的基因座，以及被鉴定为涉及潜在的序列错配错误的区域，将需要进一步的定位和测序以实现准确性。建立了一个基因组浏览器数据库，以显示在这项工作中提出的识别的重复内容。这些数据也将与越来越多的使用基因组序列草图进行实验设计和分析的研究人员有关。
BLAST-based computational heuristics were used to identify large and recent segmental duplications in the mouse genome sequence. Here a database of recently duplicated regions of the mouse genome is presented. The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (≥ 5 kb) and recent (≥ 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of 'unmapped' chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. Our results provide an initial analysis of the recently duplicated sequence and gene content of the mouse genome. Many of these duplicated loci, as well as regions identified to be involved in potential sequence misassignment errors, will require further mapping and sequencing to achieve accuracy. A Genome Browser database was set up to display the identified duplication content presented in this work. This data will also be relevant to the growing number of investigators who use the draft genome sequence for experimental design and analysis.