Diverse small circular single-stranded DNA viruses identifie

Details of Research

TitleDiverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica)AbstractAntarctica has some of the harshest environmental conditions for existence of life on Earth. In this pilot study we recovered eight diverse circular single-stranded DNA (ssDNA) viral genome sequences (1904-3120. nts) from benthic mats dominated by filamentous cyanobacteria in a freshwater pond on the McMurdo Ice Shelf sampled in 1988. All genomes contain two to three major open reading frames (ORFs) that are uni- or bi-directionally transcribed and all have an ORF encoding a replication-associated protein (Rep). In one genome, the second ORF has similarity to a capsid protein (CP) of Nepavirus which is most closely related to geminiviruses. Additionally, all genomes have two intergenic regions that contain putative stem loop structures, six genomes have NANTATTAC as the nonanucleotide motif, while one has CCTTATTAC, and another has a non-canonical stem loop. In the large intergenic region, we identified iterative sequences flanking the putative stem-loop elements which are a hallmark of most circular ssDNA viruses encoding rolling circle replication (RCR) initiators of the HUH endonuclease superfamily. The Reps encoded by ssDNA viral genomes recovered in this study shared <38% pairwise identity to all other Reps of known ssDNA viruses. A previous study on Lake Limnopolar (Livingston Island, South Shetland Islands), using next-generation sequencing identified circular ssDNA viruses and their putative Reps share <35% pairwise identity to those from the viral genomes removed in this study. It is evident from our pilot study that the global diversity of ssDNA viruses is grossly underestimated and there is limited knowledge on ssDNA viruses in Antarctica. â"' 2014 Elsevier B.V.AcknowledgementsThe molecular work in this study was supported by personal funds of AV. SK is supported by a School of Biological Sciences (University of Canterbury, New Zealand) scholarship. PAB thanks Antarctica New Zealand for logistic support in the summer of 1987-88.

Details

1st AuthorZawar-Reza, P. AuthorZawar-Reza, P.Arguello-Astorga, G.Kraberger, S.Julian, L.Stainton, D.Broady, P.Varsani, A.Year2014JournalInfection, Genetics and EvolutionVolume26Pages132-138DOI10.1016/j.meegid.2014.05.018URLhttps://www.scopus.com/inward/recor.....9a6412657dc322688fa4e4eccKeywordsadeninecapsid proteincircular DNAcytosineendonucleasehelicasenucleotidesingle stranded DNAthyminevirus DNAcircular DNAsingle stranded DNAvirus DNA, Antarcticaarticlebenthoscontrolled studycyanobacteriumDNA determinationDNA flanking regionDNA sequenceDNA transcriptionDNA virusfreshwater environmentGeminivirusgene sequencegene structuregenetic variabilitygenome analysisisland (geological)Nepavirusnonhumannucleotide sequenceopen reading framepilot studypondpriority journalprotein familyprotein motifsequence homologyunindexed sequencevirus genomeamino acid sequencebiodiversityclassificationmicrobiologymolecular cloningmolecular geneticsphylogenyphysiologyvirologyvirus genomevirus replication, Amino Acid MotifsAmino Acid SequenceAntarctic RegionsBiodiversityCloning, MolecularConserved SequenceDNA, CircularDNA, Single-StrandedDNA, ViralGenome, ViralMolecular Sequence DataPhylogenyPondsSequence Analysis, DNAVirus ReplicationWater Microbiology, rank5Author KeywordsAntarcticaReplication-associated proteinSsDNA virusesViral metagenomics

Other

TypeArticleCitationZawar-Reza, P., Arguello-Astorga, G., Kraberger, S., Julian, L., Stainton, D., Broady, P. and Varsani, A. (2014). Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infection, Genetics and Evolution, 26: 132-138