Zhang Qi-Ya, Xiao Feng, Xie Jian, Li Zheng-Qiu, Gui Jian-Fang
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.
J Virol. 2004 Jul;78(13):6982-94. doi: 10.1128/JVI.78.13.6982-6994.2004.
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.
世界各地鱼类的淋巴囊肿病已被广泛描述。在此,我们报道了在中国分离出的淋巴囊肿病病毒(LCDV-C)的全基因组序列,这是一种从中国患有淋巴囊肿病的养殖牙鲆(Paralichthys olivaceus)中分离出的LCDV。LCDV-C基因组为186,250 bp,碱基组成中G+C含量为27.25%。计算机辅助分析显示有240个潜在的开放阅读框(ORF)和176个不重叠的推定病毒基因,这些基因编码的多肽长度从40到1193个氨基酸不等。编码密度为67%,每个ORF的平均长度为702 bp。使用这176个单独的推定基因搜索GenBank数据库,发现与LCDV-1相应ORF有103个同源物,以及在LCDV-1和其他虹彩病毒中未发现的73个潜在基因。在这73个基因中,有8个基因包含细胞基因的保守结构域,65个新基因与公共数据库中的序列没有任何显著同源性。尽管LCDV-C推定基因产物与LCDV-1相应蛋白之间显示出一定程度的相似性,但在比较它们的ORF排列和编码策略时未检测到共线性,这表明它们之间发生了高度的基因重排。并且在LCDV-C基因组中观察到大量串联和重叠的重复序列。主要衣壳蛋白(MCP)的推导氨基酸序列在LCDV-C基因产物中与LCDV-1和其他虹彩病毒的氨基酸序列具有最高的同一性。此外,基于九个MCP氨基酸序列的多重比对构建了系统发育树。有趣的是,LCDV-C和LCDV-1聚在一起,但它们的氨基酸同一性远低于其他聚类中的情况。它们基因组在大小、基因组织和基因产物同一性方面出人意料的差异水平表明,LCDV-C和LCDV-1不应属于同一物种,LCDV-C应被视为与LCDV-1不同的一个物种。