Zhou Shiguo, Deng Wen, Anantharaman Thomas S, Lim Alex, Dimalanta Eileen T, Wang Jun, Wu Tian, Chunhong Tao, Creighton Robert, Kile Andrew, Kvikstad Erika, Bechner Michael, Yen Galex, Garic-Stankovic Ana, Severin Jessica, Forrest Dan, Runnheim Rod, Churas Chris, Lamers Casey, Perna Nicole T, Burland Valerie, Blattner Frederick R, Mishra Bhubaneswar, Schwartz David C
Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, 53706, USA.
Appl Environ Microbiol. 2002 Dec;68(12):6321-31. doi: 10.1128/AEM.68.12.6321-6331.2002.
Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.
鼠疫耶尔森菌是腺鼠疫、败血性鼠疫和肺鼠疫（也称为黑死病）的病原体，在历史上曾多次引发毁灭性的大流行。为了进一步了解这种致病细菌并加速正在进行的测序项目，利用鸟枪法光学图谱构建了鼠疫耶尔森菌KIM菌株的两个全基因组限制性图谱（XhoI和PvuII）。这种方法从直接从细胞中提取的随机剪切的单个DNA分子构建有序的限制性图谱。这两个图谱有不同的用途；XhoI图谱通过提供高分辨率比对的支架促进序列组装，而PvuII图谱验证基因组序列组装。我们的结果表明，这些图谱有助于封闭序列缺口，最重要的是，提供了一种完全独立的序列验证方法。鉴于光学图谱系统最近的进展，分辨率和通量的提高使得这些图谱能够在微生物测序项目的非常早期阶段指导序列组装。
