Abstract
Nucleo-cytoplasmic large DNA viruses are doubled stranded DNA viruses capable of infecting eukaryotic cells. Since the discovery of Mimivirus and Pandoravirus, there has been no doubt about their extraordinary features compared to “classic” viruses. Recently, we reported the expansion of the proposed family Pithoviridae, with the description of Cedratvirus and Orpheovirus, two new viruses related to Pithoviruses. Studying the major capsid protein of Orpheovirus, we detected a homologous sequence in a mine drainage metagenome. The in-depth exploration of this metagenome, using the MG-Digger program, enabled us to retrieve up to 10 contigs with clear evidence of viral sequences. Moreover, phylogenetic analyses further extended our screening with the discovery in another marine metagenome of a second virus closely related to Orpheovirus IHUMI-LCC2. This virus is a misidentified virus confused with and annotated as a Rickettsiales bacterium. It presents a partial genome size of about 170 kbp.
Highlights
Metagenomic analysis is a powerful method to detect micro-organisms in their ecosystems
A wide part of these metagenomic results are still unknown in database, and is referred to as “dark matter” [6]
PSI-BLAST against metagenomes database of the Orpheovirus’s Major capsid protein (MCP) detected an homology with the same protein detected by HHblits (47% coverage, 24%identity) with the sequence EQD26795.1 and with 2 additional proteins issued from different marine metagenomes [15, 16]
Summary
Metagenomic analysis is a powerful method to detect micro-organisms in their ecosystems. We detected and revealed 10 contigs from the series AUZX and AUZY as showing best hit informing the viral presence (samples B1A and B1B) (Table 1, Additional file 2) with no doubt that their origins are viral They presented a score higher than 60 for all queries with an average coverage of 79,2% (ranging from 53 to 99%), e-value inferior at 10− 7 and identity with an average of about 38% (ranging from 27% to 48%). Six viral contigs retrieved as best hit proteins from the members of the proposed family Pithoviridae (Pithoviruses and Cedratviruses) and Orpheovirus Detailed annotation of these 6 proteins encoded by these contigs revealed 1 DNA polymerase B family, 1 DNA topoisomerase IIA, 1 mRNA capping enzyme, 1, ribonucleoside-diphosphate reductase, 1 Very Early Transcription Factor (VETF) and the previously found MCP. We retrieved homologous sequences by Blast protein strategy with Orpheovirus, Cedratviruses, Pithoviruses and some of the 9 contigs and with a
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