Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.
Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.
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DOI：
10.1186/s12864-017-3744-0
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发表时间：
2017-05-04
期刊：
影响因子：
4.4
通讯作者：
Thomas MA
中科院分区：
文献类型：
--
作者：
Chung CH;Walter MH;Yang L;Chen SG;Winston V;Thomas MA
大多数尾状噬菌体（phages）具有线性dsDNA基因组。表征新的噬菌体需要了解完整的基因组序列，包括基因组物理末端的定义。我们对48株蜡样芽孢杆菌噬菌体进行了测序，并分析了下一代测序（NGS）数据，以确定这些新型噬菌体的基因组结构。大多数组装的contigs都具有映射到两个contigs并形成环状contigs的特征。31个几乎相同的i48样芽孢杆菌噬菌体分离物的独立组装使我们观察到组装程序倾向于在环状结构上产生随机切割。然而，目前可用的组装器无法从序列数据中报告潜在的噬菌体基因组结构。为了识别噬菌体的基因组结构，利用读取比对文件中的“邻近覆盖比”和“读取边缘频率”建立了一种末端预测方法。引物行走证实了末端，并通过DNA末端酶蛋白大序列的系统发育推断得到了支持。利用噬菌体NGS数据和连续圆度的Terminus包可以有效地识别噬菌体基因组末端的近端位置。完整的噬菌体基因组序列允许提出潜在包装机制的表征和更精确的基因组注释。本文的在线版本（doi:10.1186/s12864-017-3744-0）包含补充材料，可供授权用户使用。
Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends. We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of ‘neighboring coverage ratios’ and ‘read edge frequencies’ from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences. The Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation. The online version of this article (doi:10.1186/s12864-017-3744-0) contains supplementary material, which is available to authorized users.