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.

FIG. 1.

Genomic organization of the LCDV-C. Arrows, locations of 176 potentially putative genes with respect of their sizes, positions, and orientations. The scale is in kilobase pairs. Black arrows, ORFs that are homologous to the potentially putative genes of LCDV-1; white arrows, potentially novel genes that were not found in LCDV-1 and other iridoviruses.

FIG. 2.

Repeated sequences of bp 1 to 530 in the LCDV-C genome. There are eight direct repeated sequences with 66 bp, and each repeat sequence includes three short AAAGAA repeated sequences (boxes). The individual changed nucleotides and different nucleotides beyond the repeats are in boldface.

FIG. 3.

Phylogenetic tree based on the multiple alignments of the amino aced sequences of the MCPs of iridoviruses. The GenBank accession numbers for the virus nucleotide sequences are as follows: LCDV-1, AAC24486; CIV, AAK82135; ISKNV, AAL98730; RSIV, BAC66968; FV3, Q67473; TFV, AF389451; EHNV, AA032315; BIV, AY187046.