DNA-dependent RNA polymerase detects hidden giant viruses in published databanks

Abstract

Environmentalmetagenomic studies show that there is a "darkmatter, " composed of sequences not linked to any knownorganism, as determinedmainly using ribosomal DNA (rDNA) sequences, which therefore ignore giant viruses. DNA-dependent RNA polymerase (RNAP) genes are universal in microbes and conserved in giant viruses andmay replace rDNA for identifying microbes.Wefound while reconstructing RNAPsubunit 2(RNAP2) phylogeny that a giant virus sequenced together with the genome of a large eukaryote, Hydra magnipapillata, has been overlooked. To explore the dark matter, we used viral RNAP2 and reconstructed putative ancestral RNAP2, which were significantly superior in detecting distant clades than current sequences, and we revealed two additional unknown mimiviruses, misclassified as an euryarchaeote and an oomycete plant pathogen, and detected unknown putative viral clades.We suggest using RNAP systematically to decipher the black matter and identify giant viruses. © The Author(s) 2014.