Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome
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DOI：
10.1101/gr.2336604
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发表时间：
2004-04-01
期刊：
影响因子：
7
通讯作者：
Schein, J
中科院分区：
文献类型：
--
作者：
Krzywinski, M;Wallis, J;Schein, J
作为褐家鼠基因组测序工作的一部分，我们利用CHORI-230细菌人工染色体文库中的细菌人工染色体（BAC）克隆指纹图谱构建了褐家鼠物理图谱。这些BAC克隆提供了-13倍的基因组冗余覆盖率，并已组装成376个指纹组。利用酵母人工染色体（YAC）图谱和P1人工染色体克隆（PACs）指纹图谱，构建酵母人工染色体（YAC）图谱，并与酵母人工染色体（BAC）图谱进行比对。我们使用bac端序列和计算机作图方法，对95%的指纹图谱克隆在3.1版大鼠基因组序列汇编上的坐标进行了标记。这些坐标允许将376个指纹图谱组合中的358个锚定到序列集合上。其中，324个contigs锚定在定位于染色体的大鼠基因组序列上，34个contigs锚定在大鼠序列组装的非定位部分上。剩下的18个contigs，包含54个克隆，仍然需要放置。指纹图谱是一种高分辨率的综合数据资源，它提供了BAC、YAC和PAC克隆之间的基因组顺序关联以及大鼠基因组的组装序列。
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide -13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.