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

Latest version published by SCAR - Microbial Antarctic Resource System on Mar 26, 2019 SCAR - Microbial Antarctic Resource System

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

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How to cite

Researchers should cite this work as follows:

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

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 9b846f85-327e-412d-abb7-2eef49b6fae4.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

A. Lopez-Bueno
Universidad Autónoma de Madrid Madrid ES
A. Rastrojo
Universidad Autónoma de Madrid Madrid ES
R. Peiro
Universidad Autónoma de Madrid Madrid ES
M. Arenas
Universidad Autónoma de Madrid Madrid ES
A. Alcami
Universidad Autónoma de Madrid Madrid ES

Who can answer questions about the resource:

A. Alcami
Universidad Autónoma de Madrid Madrid ES

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences Rue Vautier 29 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Limnopolar lake, Livingston Island, South Shetland Islands, Antarctica

Bounding Coordinates South West [-62.38, -61.06], North East [-62.38, -61.06]

Taxonomic Coverage

RNA-Viruses targeted with RNA-shotgun sequencing (454 pyrosequencing)

Temporal Coverage

Start Date / End Date 2007-11-27 / 2010-02-01

Project Data

No Description available

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

The personnel involved in the project:

A. Alcami

Sampling Methods

Samples were taken aseptically.

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.

Method step description:

  1. 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).

Bibliographic Citations

  1. 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