RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)

A. Lopez-Bueno1, A. Rastrojo1, R. Peiro1, M. Arenas1, A. Alcami1, Maxime Sweetlove2

1 Universidad Autónoma de Madrid, Madrid, Spain; 2 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels, Belgium

Corresponding author(s): A. Lopez-BuenoA. RastrojoR. PeiroM. ArenasA. Alcami, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Lopez-Bueno A, Rastrojo A, Peiro R, Arenas M, Alcami A (2019): RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica). v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=virome_livingston_island_antarctica&v=1.0

Abstract

RNA shotgun sequencing (454 pyrosequencing) metagenome dataset of viruses in lake Limnopolar (Livingston Island, Antarctica), over a three-year period.

Keywords: Metadata

Project details

Project title: RNA-Virome (RNA shotgun sequencing) from lake Limnopolar on Livingston Island (Antarctica)
Personnel: A. Alcami
Funding: This project was funded by the Spanish Polar Programme and the Spanish Ministry of Economy and Competitiveness (CTM2008‐05134‐E/ANT and CTM2009‐08644‐E).

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=virome_livingston_island_antarctica

Taxonomic coverage

General taxonomic coverage description: RNA-Viruses targeted with RNA-shotgun sequencing (454 pyrosequencing)

Common names: viruses

Spatial coverage

General spatial coverage: Limnopolar lake, Livingston Island, South Shetland Islands, Antarctica
Coordinates: 62°22'48''S and 62°22'48''S Latitude; 61°3'36''W and 61°3'36''W Longitude 

Temporal coverage: November 27, 2007 - February 1, 2010

Methods

Method step description: 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).
Study extent description: 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 description: Samples were taken aseptically.

Metadata language: English
Date of metadata creation: 2019-03-26
Hierarchy level: Dataset

References
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