Li Shasha, Fan Hang, An Xiaoping, Fan Huahao, Jiang Huanhuan, Chen Yubao, Tong Yigang
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
Beijing Computing Center, Beijing, China.
PLoS One. 2014 Jan 20;9(1):e85806. doi: 10.1371/journal.pone.0085806. eCollection 2014.
Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS) have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs) found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.
基因组末端序列分析一直是病毒DNA复制和包装机制研究中的重要一步。然而，由于传统的研究基因组末端的方法耗时且效率低下，关键细节容易丢失，因此具有挑战性。新一代测序技术（NGS）的最新进展使其成为研究基因组末端的有力工具。在本研究中，我们使用NGS对一个虹彩病毒基因组和二十个噬菌体基因组进行了测序，并首次证实了在NGS读数中发现的高频序列（HFSs）确实是病毒基因组的末端序列。此外，我们建立了一个标准来区分末端类型和病毒包装模式。我们还获得了额外的末端细节，如末端重复序列、多个末端、不对称末端。通过这种方法，我们能够同时检测基因组末端的细节，并获得噬菌体基因组的完整序列。从理论上讲，这种应用可以进一步扩展到分析更大、更复杂的植物和动物病毒基因组。本研究提出了一种新颖且高效的方法，用于研究病毒复制、包装、末端酶活性、转录调控以及宿主细胞的代谢。
