Genome analysis of a novel Group I alphabaculovirus obtained from Oxyplax ochracea

PLoS One. 2018 Feb 1;13(2):e0192279. doi: 10.1371/journal.pone.0192279. eCollection 2018.

Abstract

Oxyplax ochracea (Moore) is a pest that causes severe damage to a wide range of crops, forests and fruit trees. The complete genome sequence of Oxyplax ochracea nucleopolyhedrovirus (OxocNPV) was determined using a Roche 454 pyrosequencing system. OxocNPV has a double-stranded DNA (dsDNA) genome of 113,971 bp with a G+C content of 31.1%. One hundred and twenty-four putative open reading frames (ORFs) encoding proteins of >50 amino acids in length and with minimal overlapping were predicted, which covered 92% of the whole genome. Six baculoviral typical homologous regions (hrs) were identified. Phylogenetic analysis and gene parity plot analysis showed that OxocNPV belongs to clade "a" of Group I alphabaculoviruses, and it seems to be close to the most recent common ancestor of Group I alphabaculoviruses. Three unique ORFs (with no homologs in the National Center for Biotechnology Information database) were identified. Interestingly, OxocNPV lacks three auxiliary genes (lef7, ie-2 and pcna) related to viral DNA replication and RNA transcription. In addition, OxocNPV has significantly different sequences for several genes (including ie1 and odv-e66) in comparison with those of other baculoviruses. However, three dimensional structure prediction showed that OxocNPV ODV-E66 contain the conserved catalytic residues, implying that it might possess polysaccharide lyase activity as AcMNPV ODV-E66. All these unique features suggest that OxocNPV represents a novel species of the Group I alphabaculovirus lineage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Baculoviridae / genetics*
  • Baculoviridae / isolation & purification
  • Base Sequence
  • DNA Replication
  • Genome, Viral*
  • Lepidoptera / virology*
  • Open Reading Frames
  • RNA, Viral / genetics
  • Sequence Homology, Nucleic Acid
  • Transcription, Genetic

Substances

  • RNA, Viral

Grants and funding

This work was supported by the grants from the National Key R&D Program of China (Grants No. 2017YFD0200400 to FD and 2016YFE0113500 to ZH); the National Natural Science Foundation of China (Grant No. 31621061) to ZH; the Key Research Program of Frontier Sciences of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SMC021) to ZH, the Virology Key Frontier Science Program of State Key Laboratory of Virology (Grant No. klv-2016-03) to ZH and HW, and the National Natural Science Foundation of China (Grant No. 31400140) to SS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.