Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
Highlights
Viral metagenomics, or shotgun sequencing of total nucleic acids from purified virus particles, enables examination of viral communities without prior knowledge of the viruses present, resulting in an unprecedented view of viral diversity (Breitbart et al, 2002; Edwards and Rohwer, 2005; Angly et al, 2006)
Metagenomic studies have revealed a prodigious amount of diversity in eukaryotic CRESS-DNA viruses in the marine environment (Rosario et al, 2009a; Rosario and Breitbart, 2011; Labonte and Suttle, 2013; McDaniel et al, 2014)
Building upon recent studies suggesting that CRESS-DNA viruses are associated with marine invertebrates (Dunlap et al, 2013; Hewson et al, 2013a,b; Ng et al, 2013; Pham et al, 2014; Soffer et al, 2014; Dayaram et al, 2015a), this study investigated a variety of marine invertebrates, including under sampled taxa, for the presence of these viruses
Summary
Shotgun sequencing of total nucleic acids from purified virus particles, enables examination of viral communities without prior knowledge of the viruses present, resulting in an unprecedented view of viral diversity (Breitbart et al, 2002; Edwards and Rohwer, 2005; Angly et al, 2006). This technique has uncovered many novel viral types and extended the environmental distribution of known viral groups (Delwart, 2007; Rosario and Breitbart, 2011). CRESS-DNA viruses similar to circoviruses, which were previously thought to only infect vertebrates, have been identified in a myriad of invertebrates, including insects (Ng et al, 2011; Rosario et al, 2011, 2012b; Dayaram et al, 2013; Padilla-Rodriguez et al, 2013; Pham et al, 2013a,b; Garigliany et al, 2015), crustaceans (Dunlap et al, 2013; Hewson et al, 2013a,b; Ng et al, 2013; Pham et al, 2014), cnidarians (Soffer et al, 2014), and gastropods (Dayaram et al, 2015a), suggesting that CRESS-DNA viruses may be prevalent amongst unexplored taxa
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