Abstract
BackgroundThe White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps. Mass mortalities caused by WSSV have pronounced commercial impact on shrimp aquaculture. Until now WSSV is the only known member of the virus family Nimaviridae, a group with obscure phylogenetic affinities. Its isolated position makes WSSV studies challenging due to large number of genes without homology in other viruses or cellular organisms.ResultsHere we report the discovery of an unusually large amount of sequences with high similarity to WSSV in a genomic library from the Jamaican bromeliad crab Metopaulias depressus. De novo assembly of these sequences allowed for the partial reconstruction of the genome of this endogenized virus with total length of 200 kbp encompassed in three scaffolds. The genome includes at least 68 putative open reading frames with homology in WSSV, most of which are intact. Among these, twelve orthologs of WSSV genes coding for non-structural proteins and nine genes known to code for the major components of the WSSV virion were discovered. Together with reanalysis of two similar cases of WSSV-like sequences in penaeid shrimp genomic libraries, our data allowed comparison of gene composition and gene order between different lineages related to WSSV. Furthermore, screening of published sequence databases revealed sequences with highest similarity to WSSV and the newly described virus in genomic libraries of at least three further decapod species. Analysis of the viral sequences detected in decapods suggests that they are less a result of contemporary WSSV infection, but rather originate from ancestral infection events. Phylogenetic analyses suggest that genes were acquired repeatedly by divergent viruses or viral strains of the Nimaviridae.ConclusionsOur results shed new light on the evolution of the Nimaviridae and point to a long association of this viral group with decapod crustaceans.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0380-7) contains supplementary material, which is available to authorized users.
Highlights
The White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps
Our results suggest that these viral sequences, together with fragments detected in systematic screenings of previously published decapod genomic libraries [17, 18], stem from several related viral species divergent from WSSV and provide valuable information on the evolutionary history of Nimaviridae
We postulate that this virus is not independent, but endogenized in the genome of its host, because: 1) despite the high sequencing coverage we were not able to reconstruct a single circular molecule as known for WSSV, and no connection between the three reconstructed scaffolds could be detected with PCR, 2) some fragments of WSSV-like genes are clearly not functional, 3) several transposon-derived sequences are found in association with the WSSV-like sequences, 4) there is considerable intra-individual variation in the specimen chosen for sequencing, and 5) analogous variation is obtained in a test fragment sequenced for several other crab specimens from Jamaica
Summary
The White Spot Syndrome Virus (WSSV) is an important pathogen that infects a variety of decapod species and causes a highly contagious disease in penaeid shrimps. The White Spot Syndrome Virus (WSSV) is a widespread pathogen of several commercially important penaeid shrimp species which causes mass mortalities in aquaculture with high economic impact [1]. All WSSV strains known to date belong to the same viral species, formally classified in the genus Whispovirus and a monotypic family – Nimaviridae [1, 10, 11] This fact is Rozenberg et al BMC Evolutionary Biology (2015) 15:142 especially noteworthy in the light of the isolated position of this group among DNA viruses as revealed by phylogenetic reconstructions based on DNA polymerase and protein kinase amino acid sequences [12, 13]. About one third of the gene products have been functionally characterized in direct experiments or homology-based bioinformatic approaches: proteins involved in cellular functions (e.g. DNA polymerase, helicase, protein kinases etc.), virion proteins, gene products with proposed roles in latency and early phase of infection and others [1, 8, 9, 14]
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