title: Complete genome sequence of lymphocystis disease virus isolated from China.
abstract: Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Wuhan Center for Developmental Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China. zhangqy@ihb.ac.cn
authors.forename: Qi-Ya
authors.initials: QY
authors.lastname: Zhang
authors.forename: Feng
authors.initials: F
authors.lastname: Xiao
authors.forename: Jian
authors.initials: J
authors.lastname: Xie
authors.forename: Zheng-Qiu
authors.initials: ZQ
authors.lastname: Li
authors.forename: Jian-Fang
authors.initials: JF
authors.lastname: Gui
mesh_terms: D000818:Animals; D001483:Base Sequence; D002681:China; D004266:DNA Virus Infections / Q000662:veterinary* / Q000821:virology; D005393:Fish Diseases / Q000821:virology*; D005432:Flounder / Q000821:virology*; D016679:Genome, Viral; D007497:Iridoviridae / Q000235:genetics / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins