Development of the Mitsucal computer system to identify causal mutation with a high-throughput sequencer
Development of the Mitsucal computer system to identify causal mutation with a high-throughput sequencer
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DOI：
10.1007/s00497-018-0331-8
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发表时间：
2018-03-01
影响因子：
3.4
通讯作者：
Higashiyama, Tetsuya
中科院分区：
文献类型：
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作者：
Suzuki, Takamasa;Kawai, Tsutae;Higashiyama, Tetsuya
DNA 测序技术的最新进展促进了突变体和变体的全基因组测序。然而，使用计算机分析大型序列数据集仍然比操作测序仪更困难。即使在有性生殖中，正向遗传方法也能有效识别关键基因。因此，我们开发了 Mitsucal 计算机系统，利用全基因组序列数据来识别突变体的致病基因。 Mitsucal 包括一个用户友好的 Web 界面，用于配置分析变量，例如背景和交叉菌株。除了配置之外，用户只需要上传简短的读数。所有结果都通过网络界面呈现，用户可以轻松获得候选突变的简短列表。在本研究中，我们提出了有性生殖缺陷的拟南芥突变体的三个例子，其中 Mitsucal 用于识别因果突变。从带有报告基因的转基因品系的种子中筛选出一种突变体，以阐明参与种子油储存调节的机制。已鉴定的蛋白质基因编码可能参与 mRNA 剪接。另外两个突变体的花粉表面壁（称为外壁）有缺陷。两个致病基因都被鉴定出来，并且发现突变体是已知突变体的等位基因。这些结果表明 Mitsucal 可以促进因果基因的识别。
Recent advances in DNA sequencing technology have facilitated whole-genome sequencing of mutants and variants. However, the analyses of large sequence datasets using a computer remain more difficult than operating a sequencer. Forward genetic approach is powerful even in sexual reproduction to identify key genes. Therefore, we developed the Mitsucal computer system for identifying causal genes of mutants, using whole-genome sequence data. Mitsucal includes a user-friendly web interface to configure analysis variables, such as background and crossed strains. Other than configuration, users are only required to upload short reads. All results are presented through a web interface where users can easily obtain a short list of candidate mutations. In the present study, we present three examples of Arabidopsis mutants defective in sexual reproduction in which Mitsucal is used to identify causal mutation. One mutant was screened from seeds of a transgenic line with a reporter gene to elucidate the mechanisms involved in the regulation of seed oil storage. The identified gene codes for a protein may be involved in mRNA splicing. Other two mutants had defects in the surface walls on pollen termed exine. Both causal genes were identified, and mutants were found to be allele of known mutants. These results show that Mitsucal could facilitate identification of causal genes.