Scrutinizing virus genome termini by high-throughput sequencing

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA, Viral*
  • Genome, Viral*
  • High-Throughput Nucleotide Sequencing*
  • Virus Assembly / genetics
  • Virus Replication


  • DNA, Viral

Associated data

  • RefSeq/NC_003298

Grant support

This research was supported by grants from the National Natural Science Foundation of China (NO.30872223), the National Hi-Tech Research and Development (863) Program of China (No. 2012AA022-003), and the China Mega-Project on Infectious Disease Prevention (No. 2013ZX10004-605). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.