A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing
A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing
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DOI：
10.1016/j.mod.2004.03.024
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发表时间：
2004-07-01
影响因子：
2.6
通讯作者：
Himmelbauer, H
中科院分区：
文献类型：
--
作者：
Khorasani, MZ;Hennig, S;Himmelbauer, H
为了充分发挥青竹作为发育生物学和遗传学模式系统的潜力，需要建立特征化的基因组资源，最终确定青竹基因组的序列。为了促进基于图谱的诱导突变基因的克隆，并为基于克隆的基因组测序提供模板，我们在细菌人工染色体(BAC)克隆中创建了青竹基因组的第一代物理图谱。特别是，我们利用了与河豚紧密相关的基因组的同源性，通过标记含量作图。作为第一步，我们对103,144个公共青竹EST序列进行了聚类，以获得一组21.121个非冗余序列实体。避免了对基因密集区的过度采样，11,254个EST簇与河豚基因组草稿序列成功匹配，2363个基因被选入BAC图谱项目。我们从选定的基因中设计了35个寡核苷酸探针，并将它们与菌株Cab和HD-RR的64,500个BAC克隆杂交，代表了青竹基因组覆盖率的14倍。我们的数据集进一步补充了437个结果，这些结果是通过PCR扩增插入青竹cdna克隆和BAC末端片段标记而产生的。我们目前编辑的第一代青竹BAC图谱由902个图谱片段组成，覆盖了青竹基因组的约74%。该地图包含2721个标记。其中，2534个来自表达序列，相当于2328个座位的非冗余集合。这934个标记(724个不同)被锚定在青竹遗传图谱上。因此，遗传图谱的分配提供了对潜在克隆和重叠群的即时访问，简化了对候选基因区域及其特征的分子访问。(C)2004爱思唯尔爱尔兰有限公司。保留所有权利。
In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21.121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization. (C) 2004 Elsevier Ireland Ltd. All rights reserved.