End Sequencing and chromosomal in silico mapping of BAC clones derived from an indica rice cultivar, Kasalath
End Sequencing and chromosomal in silico mapping of BAC clones derived from an indica rice cultivar, Kasalath
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DOI：
10.1270/jsbbs.54.273
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发表时间：
2004-09-01
期刊：
影响因子：
2.4
通讯作者：
Sasaki, T
中科院分区：
文献类型：
--
作者：
Katagiri, S;Wu, JZ;Sasaki, T
为了研究水稻表型多样性和进化关系的分子基础，我们对来自籼稻品种‘Kasalath’的水稻BAC（细菌人工染色体）克隆进行了大规模的末端测序和染色体计算机作图（序列同源性作图）。从47，194个BAC克隆中总共获得了78，427个高质量BAC末端序列（BES），其显示出482 bp的平均读取长度，具有总共37.8 Mb的基因组序列。在去除那些含有重复序列的BES之后，使用粳稻栽培品种“日本晴”的高质量基因组序列作为参考标准，通过计算机将12，170个具有成对BES的克隆定位到12条染色体上。这些克隆由450个重叠群组成，总物理长度为308.5 Mb，表明水稻基因组的覆盖率约为80%。使用特异性DNA标记对Kasalath BAC克隆在1号染色体上定位的染色体位置进行确认，结果显示该图谱的准确性极高：至少94.8%。总的来说，这两个亚种的所有染色体的基因组组成和结构是高度保守的。然而，我们仍然发现证据表明，在两个亚种的基因组中存在不同的成分，特别是在染色体11和12上。对日本晴和Kasalath的基因组序列的广泛分析显示，单核苷酸多态性（SNP）的频率为0.71%，插入缺失（1-16 bp长度）的频率为1.23个位点/酶。基于BAC的Kasalath图谱可能成为一种宝贵的资源，不仅用于分离基因，而且用于对基因组序列进行广泛分析，以进行物种内或物种间的比较基因组研究。
To investigate the molecular basis for the phenotypic diversity and evolutionary relationships within Oryza sativa, we performed large-scale end sequencing and chromosomal in silico mapping (mapping by sequence homology) of rice BAC (bacterial artificial chromosome) clones derived from an indica rice cultivar, 'Kasalath'. In total, 78,427 high-quality BAC-end sequences (BESs) showing an average read-length of 482 bp with a total of 37.8 Mb of genomic sequences were obtained from 47,194 BAC clones. After removal of those BESs containing repetitive sequences and use of the high-quality genomic sequence of the japonica rice cultivar 'Nipponbare' as a reference standard, 12,170 clones with paired BESs were mapped in silico to the 12 chromosomes. These clones consisted of 450 contigs and showed a total physical length of 308.5 Mb, indicating a coverage of the rice genome of about 80%. Confirmation of the chromosomal positions of the Kasalath BAC clones mapped on chromosome 1 using specific DNA markers revealed that the map accuracy was extremely high: at least 94.8%. In general, the genomic composition and structure of all the chromosomes were highly conserved between the two subspecies. However, we still found evidence suggesting the existence of different components in the genome of the two subspecies within large chromosomal fragments, especially on chromosomes 11 and 12. Extensive analysis of the genomic sequences of Nipponbare and Kasalath revealed a frequency of 0.71% for single nucleotide polymorphisms (SNPs) and 1.23 sites per kilobase for indels (1-16 bp length), respectively. The BAC-based Kasalath map could become an invaluable resource, not only for the isolation of genes, but also for conducting extensive analyses of genomic sequences for comparative genomic studies within or between species.