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.

Molecular basis and genetic improvement of economically important traits in aquaculture animals

“…Especially in infectious virus diseases, a lot of pathogenic viruses were identified from freshwater and marine culture animals [103], and the complete genomes of several viruses, such as grass carp hemorrhage virus (GCHV) [104], shrimp white spot syndrome virus (WSSV) [105], mandarin fish infectious spleen and kidney necrosis iridovirus (ISKNV) [106], and flounder lymphocystis disease virus isolated in China (LCDV-C) [107], were sequenced in China. Moreover, their structure proteins were characterized [108][109][110][111], and some of them were functionally analyzed [112,113].…”

Genomic and Proteomic Analysis of Invertebrate Iridovirus Type 9

“…Vertebrate IV genomes range from 105 kbp for tiger frog virus (17) to 186 kbp for lymphocystis disease virus, China strain (LCDV-C) (46). The Ranavirus and Megalocytivirus species have GϩC contents of approximately 50%, while the Lymphocystivirus species have GϩC contents of less than 30%.…”

Sequencing and analysis of the complete genome of Rana grylio virus (RGV)

“…These include lymphocystis disease virus 1 (LCDV-1) and lymphocystis disease virus-China (LCDV-C), belonging to the genus Lymphocystivirus, and infectious spleen and kidney necrosis virus (ISKNV), rock bream iridovirus (RBIV), turbot reddish body iridovirus (TRBIV), and other viruses, belonging to the genus Megalocytivirus that can infect fish species. Iridoviruses of the genus Ranavirus, including frog virus 3 (FV3), soft-shelled turtle iridovirus (STIV), epizootic hematopoietic necrosis virus (EHNV), and other viruses can infect amphibians, fish and reptiles [5][6][7][8][9][10][11][12].…”