光学图谱作为细菌基因组序列完成的常规工具。
Optical mapping as a routine tool for bacterial genome sequence finishing.
作者信息
Latreille Phil, Norton Stacie, Goldman Barry S, Henkhaus John, Miller Nancy, Barbazuk Brad, Bode Helge B, Darby Creg, Du Zijin, Forst Steve, Gaudriault Sophie, Goodner Brad, Goodrich-Blair Heidi, Slater Steven
机构信息
Monsanto Company, 800 North Lindbergh Boulevard St. Louis, MO 63167, USA.
出版信息
BMC Genomics. 2007 Sep 14;8:321. doi: 10.1186/1471-2164-8-321.
BACKGROUND
In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila.
RESULTS
Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.
CONCLUSION
Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.
背景
在对两种致病杆菌属物种的基因组进行测序时，我们遇到了大量的序列重复和组装异常情况，这阻碍了完成测序的工作。其中包括一段约12千碱基对的区域，嗜线虫致病杆菌的质粒和染色体之间该区域的序列相似度超过99.9%。
结果
通过光学图谱技术绘制了已测序菌株的全基因组限制酶切图谱。这些图谱能够快速解决序列组装问题，实现基因组的封闭，并校正了我们原本认为已完成的一个基因组组装中的一个大的倒位。
结论
我们的经验表明，在细菌基因组序列完成过程中常规使用光学图谱是有必要的。当与通过454测序产生的数据相结合时，光学图谱能够快速且低成本地生成一组有序且定向的重叠群，以产生近乎完整的基因组序列组装。
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