RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)
Citation
Lopez-Bueno A, Rastrojo A, Peiro R, Arenas M, Alcami A, Sweetlove M (2019). RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica). SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/9ya44h accessed via GBIF.org on 2024-08-17.Description
RNA shotgun sequencing (454 pyrosequencing) metagenome dataset of viruses in lake Limnopolar (Livingston Island, Antarctica), over a three-year period.Sampling Description
Study Extent
Lake Limnopolar (Livingston Island, Antarctica) was sampled for cyanobacteria mats on the 27th of November 2006, the 22nd of January 2007 and the 1st of February 2010.Sampling
Samples were taken aseptically.Method steps
- Cyanobacterial mat samples (2.5 g) were homogenized in SM buffer (50 mm Tris‐HCl pH 7.5, 100 mm NaCl and 8 mm MgSO4.7H2O) by three cycles of vigorous vortex and sonication in a water bath during 20 and 10 s, respectively, then centrifuged at 3000 g for 5 min. This process was repeated twice. The resulting supernatants were combined and centrifuged at 8000 g for 1 h and then filtered through a 0.45‐μm syringe filter (Millex, Durapore PVDF) to remove cellular organisms. The resulting viral fractions, as well as those from lake water samples, were purified as described previously (López‐Bueno et al. 2009). In the case of the water sample collected in 2010, 0.45 μm filtration was carried out by TFF using two 0.093 m2 polyethersulfone filter cassettes (Pall) and nuclease treatment of purified viral particles included 100 U/mL of nuclease S7 (Roche). RNA viral genomes were purified with Trizol‐LS (Invitrogen) followed by DNAseI RNAse‐free (Roche) treatment before randomly amplification by sequence independent single primer amplification (SISPA) (Victoria et al. 2008; Djikeng et al. 2009; Culley et al. 2010). Briefly, Superscript II or III and the Klenow fragment (3′–>5′exo‐) enzyme (NEBiolabs) were used to convert RNA into dsDNA using 60 pmol of pseudo‐degenerated primers FR26‐RV (5′‐GCCGGAGCTCTGCAGATATCNNNNNN‐3) for the water sample collected in 2007 and primer A (5′‐GTTTCCCAGTCACGATANNNNNNNNN‐3) for samples collected in 2006 and 2010. After 40 cycles of PCR amplification with FastStart high fidelity polymerase (Roche), DNA fragments between 500 and 3000 bp were gel‐extracted with QIAquick Gel Extraction kit (Qiagen) and sequenced in the 454 GS FLX titanium platforms (Roche‐454) from LifeSequencing (Valencia, Spain) or from Parque Científico de Madrid (Spain).
Taxonomic Coverages
RNA-Viruses targeted with RNA-shotgun sequencing (454 pyrosequencing)
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Viricommon name: viruses
Geographic Coverages
Limnopolar lake, Livingston Island, South Shetland Islands, Antarctica
Bibliographic Citations
- López‐Bueno, A., Rastrojo, A., Peiró, R., Arenas, M., & Alcamí, A. (2015). Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Molecular ecology, 24(19), 4812-4825. - https://doi.org/10.1111/mec.13321
Contacts
A. Lopez-Buenooriginator
Universidad Autónoma de Madrid
Madrid
ES
A. Rastrojo
originator
Universidad Autónoma de Madrid
Madrid
ES
R. Peiro
originator
Universidad Autónoma de Madrid
Madrid
ES
M. Arenas
originator
Universidad Autónoma de Madrid
Madrid
ES
A. Alcami
originator
Universidad Autónoma de Madrid
Madrid
ES
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
A. Alcami
administrative point of contact
Universidad Autónoma de Madrid
Madrid
ES