title: Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica).
abstract: Antarctica 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.
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Geography, University of Canterbury, Christchurch, New Zealand.
authors.forename: Peyman
authors.initials: P
authors.lastname: Zawar-Reza
authors.affiliation: División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, S.L.P., Mexico.
authors.forename: Gerardo R
authors.initials: GR
authors.lastname: Argüello-Astorga
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Simona
authors.initials: S
authors.lastname: Kraberger
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Laurel
authors.initials: L
authors.lastname: Julian
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Daisy
authors.initials: D
authors.lastname: Stainton
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Broady
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand. Electronic address: arvind.varsani@canterbury.ac.nz.
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000864:Antarctic Regions; D044822:Biodiversity; D003001:Cloning, Molecular; D017124:Conserved Sequence; D004270:DNA, Circular; D004277:DNA, Single-Stranded / Q000145:classification* / Q000502:physiology*; D004279:DNA, Viral; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D061005:Ponds / Q000821:virology*; D017422:Sequence Analysis, DNA; D014779:Virus Replication; D014871:Water Microbiology
chemical_list: D004270:DNA, Circular; D004277:DNA, Single-Stranded; D004279:DNA, Viral
keywords: Antarctica; Replication-associated protein; Viral metagenomics; ssDNA viruses