Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes

Abstract

Background: Members of the family Iridoviridae can cause severe diseases resulting in significant economic and environmental losses. Very little is known about how iridoviruses cause disease in their host. In the present study, we describe the re-analysis of the Iridoviridae family of complex DNA viruses using a variety of comparative genomic tools to yield a greater consensus among the annotated sequences of its members.

Results: A series of genomic sequence comparisons were made among, and between the Ranavirus and Megalocytivirus genera in order to identify novel conserved ORFs. Of these two genera, the Megalocytivirus genomes required the greatest number of altered annotations. Prior to our re-analysis, the Megalocytivirus species orange-spotted grouper iridovirus and rock bream iridovirus shared 99% sequence identity, but only 82 out of 118 potential ORFs were annotated; in contrast, we predict that these species share an identical complement of genes. These annotation changes allowed the redefinition of the group of core genes shared by all iridoviruses. Seven new core genes were identified, bringing the total number to 26.

Conclusion: Our re-analysis of genomes within the Iridoviridae family provides a unifying framework to understand the biology of these viruses. Further re-defining the core set of iridovirus genes will continue to lead us to a better understanding of the phylogenetic relationships between individual iridoviruses as well as giving us a much deeper understanding of iridovirus replication. In addition, this analysis will provide a better framework for characterizing and annotating currently unclassified iridoviruses.

Figure 1

Conserved Iridovirus Genes. Every Iridoviridae gene that has an ortholog in at least 2 Iridoviridae genera are shown. Orthologs share the same row on the table. The genes within each genus are color-coded for easier identification. As long as at least one member of the genus contains an ortholog, the entire genus is highlighted. Where multiple ORFs are listed for a particular gene name, the ORFs represent multiple orthologs of the gene in that viral species. The remainder of the figure showing just the genes conserved between the Iridovirus and Chloriridovirus genera are included in Additional File 3.

Figure 2

Phylogenetic relationships between the five iridovirus genera based on gene content. Individual viral species were compared within a genus to identify the number of orthologous genes. Orthologous genes between viral genera were then determined. The numbers on each line identify the number of orthologous genes shared between viral species or genera including the 26 core genes. The Iridovirus and Chloriridovirus genera have a high degree of gene conservation and a combined genera box (Iridovirus/Chloriridovirus) was used to compare orthologous genes between genera. In addition, two subgroups of the Ranavirus genus are shown. Each subgroup contains a virtually identical complement of genes. However, a comparison between the FV3/TFV/ATV subgroup with the SGIV/GIV subgroup revealed 72 orthologous genes.

Figure 3

Co-linearity found within the Ranavirus genus. (A) FV3 and ATV, both members of the Ranavirus genus possess almost complete co-linearity of orthologous genes as visualized by a dotplot. However, 2 inversions have occurred. The FV3 genes 10–52 and 77–88 have switched genomic locations as shown, potentially through two recombination events. The inversion has also resulted in the loss of the ortholog of FV3 9L in ATV. (B) There is a limited amount of co-linearity found between FV3/TFV/ATV and SGIV/GIV. The co-linearity has been visualized using a dotplot analysis between FV3 (horizontal sequence) and GIV (vertical sequence). Genes are colored either red or blue representing right- or left-ward transcription respectively. (C) The co-linearity between FV3 and GIV is generally composed of stretches of 2 or 3 co-linear orthologous genes. Orthologous genes, in a co-linear arrangement are schematically shown as blocks of the same color on either FV3 or GIV genomic sequence.