Virologica Sinica

, Volume 28, Issue 5, pp 280–290

Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China

  • Xingyi Ge
  • Yongquan Wu
  • Meiniang Wang
  • Jun Wang
  • Lijun Wu
  • Xinglou Yang
  • Yuji Zhang
  • Zhengli Shi
Research Article

DOI: 10.1007/s12250-013-3365-y

Cite this article as:
Ge, X., Wu, Y., Wang, M. et al. Virol. Sin. (2013) 28: 280. doi:10.1007/s12250-013-3365-y

Abstract

East Lake (Lake Donghu), located in Wuhan, China, is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years. Marine and fresh water are considered to contain a large number of viruses. However, little is known about their genetic diversity because of the limited techniques for culturing viruses. In this study, we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring, Summer, Autumn, and Winter. The libraries from four samples each generated 234,669, 71,837, 12,820, and 34,236 contigs (> 90 bp each), respectively. The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families, with the majority of contigs homologous to DNA viruses, including members of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and Microviridae, which infect bacteria or algae, and members of Circoviridae, which infect invertebrates and vertebrates. The highest viral genetic diversity occurred in samples collected in August, then December and June, and the least diversity in March. Most contigs have low-sequence identities with known viruses. PCR detection targeting the conserved sequences of genes (g20, psbA, psbD, and DNApol) of cyanophages further confirmed that there are novel cyanophages in the East Lake. Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future.

Keywords

Viral metagenomics East Lake Solexa high-throughput sequencing High-throughput sequencing (HTS) Cyanophage 

Copyright information

© Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Xingyi Ge
    • 1
  • Yongquan Wu
    • 1
  • Meiniang Wang
    • 1
  • Jun Wang
    • 1
  • Lijun Wu
    • 1
  • Xinglou Yang
    • 1
  • Yuji Zhang
    • 1
  • Zhengli Shi
    • 1
  1. 1.Center for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of VirologyChinese Academy of SciencesWuhanChina