Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, MD, USA.
Sci Rep. 2011;1:169. doi: 10.1038/srep00169. Epub 2011 Nov 24.
We performed whole-genome amplification followed by hybridization of custom-designed resequencing arrays to resequence 303 kb of genomic sequence from a worldwide panel of 39 Bacillus anthracis strains. We used an efficient algorithm contained within a custom software program, UniqueMER, to identify and mask repetitive sequences on the resequencing array to reduce false-positive identification of genetic variation, which can arise from cross-hybridization. We discovered a total of 240 single nucleotide variants (SNVs) and showed that B. anthracis strains have an average of 2.25 differences per 10,000 bases in the region we resequenced. Common SNVs in this region are found to be in complete linkage disequilibrium. These patterns of variation suggest there has been little if any historical recombination among B. anthracis strains since the origin of the pathogen. This pattern of common genetic variation suggests a framework for recognizing new or genetically engineered strains.
我们进行了全基因组扩增，然后对定制的重测序阵列进行杂交，以对来自全球 39 株炭疽杆菌菌株的 303 kb 基因组序列进行重测序。我们使用了一种包含在自定义软件程序 UniqueMER 中的高效算法，来识别和屏蔽重测序阵列上的重复序列，以减少由于交叉杂交而导致的遗传变异的假阳性识别。我们总共发现了 240 个单核苷酸变异（SNVs），并表明我们重测序的区域中，炭疽杆菌菌株平均每 10000 个碱基有 2.25 个差异。该区域中的常见 SNVs 被发现处于完全连锁不平衡状态。这些变异模式表明，自病原体起源以来，炭疽杆菌菌株之间的历史重组很少（如果有的话）。这种常见遗传变异的模式为识别新的或经过基因工程改造的菌株提供了一个框架。
