Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 R E S E A R C H A R T I C L E Open Access Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus Yu-Shin Nai1†, Chih-Yu Wu2†, Tai-Chuan Wang2†, Yun-Ru Chen1†, Wei-Hong Lau4, Chu-Fang Lo2*, Meng-Feng Tsai3*, Chung-Hsiung Wang2* Abstract Background: Outbreaks of the casuarina moth, Lymantria xylina Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of host plants to include more than 65 species of broadleaf trees. LyxyMNPV (L. xylina multiple nucleopolyhedrovirus) is highly virulent to the casuarina moth and has been investigated as a possible biopesticide for controlling this moth. LdMNPV-like virus has also been isolated from Lymantria xylina larvae but LyxyMNPV was more virulent than LdMNPV-like virus both in NTU-LY and IPLB-LD-652Y cell lines. To better understand LyxyMNPV, the nucleotide sequence of the LyxyMNPV DNA genome was determined and analysed. Results: The genome of LyxyMNPV consists of 156,344 bases, has a G+C content of 53.4% and contains 157 putative open reading frames (ORFs). The gene content and gene order of LyxyMNPV were similar to those of LdMNPV, with 151 ORFs identified as homologous to those reported in the LdMNPV genome. Two genes (Lyxy49 and Lyxy123) were homologous to other baculoviruses, and four unique LyxyMNPV ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified in the LyxyMNPV genome, including a gag-like gene that was not reported in baculoviruses. LdMNPV contains 23 ORFs that are absent in LyxyMNPV. Readily identifiable homologues of the gene host range factor-1 (hrf-1), which appears to be involved in the susceptibility of L. dispar to NPV infection, were not present in LyxyMNPV. Additionally, two putative odv-e27 homologues were identified in LyxyMNPV. The LyxyMNPV genome encoded 14 bro genes compared with 16 in LdMNPV, which occupied more than 8% of the LyxyMNPV genome. Thirteen homologous regions (hrs) were identified containing 48 repeated sequences composed of 30-bp imperfect palindromes. However, they differed in the relative positions, number of repeats and orientation in the genome compared to LdMNPV. Conclusion: The gene parity plot analysis, percent identity of the gene homologues and a phylogenetic analysis suggested that LyxyMNPV is a Group II NPV that is most closely related to LdMNPV but with a highly distinct genomic organisation. Background Baculoviruses (family Baculoviridae) consist of rod- shaped, arthropod-specific viruses with double-stranded, circular DNA genomes ranging from 80 to 180 kb and enveloped nucleocapsids [1]. The occluded form of the virus is embedded in proteinaceous occlusion bodies (OBs) [1]. Baculoviridae is subdivided into four genera, * Correspondence: gracelow@ntu.edu.tw; tsaimf@mail.dyu.edu.tw; wangch@ntu.edu.tw † Contributed equally 2Department of Zoology, National Taiwan University, Taipei, Taiwan 3Department of Molecular Biotechnology, Dayeh University, No 112, Shanjiao Rd, Dacun, Changhua, Taiwan Alphabaculovirus (lepidopteran-specific nucleopolyhe- drovirus, NPV), Betabaculovirus (lepidopteran-specific granulovirus), Gammabaculovirus (hymenopteran-speci- fic NPV) and Deltabaculovirus (dipteran-specific NPV) [2]. The lepidopteran-specific NPVs are further classed into two groups, I and II, based on the phylogenetic analysis of their polyhedrin (polh) genes [3,4]. Most of the NPVs with sequenced genomes are lepidopteran specific. However, the genomes of Culex nigripalpus NPV, which infects dipteran, and three Neodiprion NPVs which have been isolated from hymenopteran insect species, have also been sequenced [5-8]. To date, more than fifty baculovirus isolates have been sequenced © 2010 Nai et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.