Dataset: Gene predictions for the complete TetV-1 genome sequence

Preliminary and in progressVersion 1 (2021-10-25)Dataset Type:Other Field Results

Principal Investigator: Grieg Steward (University of Hawaiʻi at Mānoa)

Co-Principal Investigator: Christopher Schvarcz (University of Hawaiʻi at Mānoa)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)


Project: Eating themselves sick? Ecological interactions among a mixotrophic flagellate, its prokaryotic prey, and an ingestible giant virus. (Giant virus ecology)

Note: The detailed protocols are described in Schvarcz and Steward, 2018. 

Shoreline sampling was carried out on September 2nd, 2010 in the coastal surface water of Kāneʻohe Bay, Oʻahu, Hawaiʻi.  Seawater (175 L) was filtered (0.8 µm polycarbonate track-etched), and particles in the filtrate concentrated by tangential flow filtration (TFF; 30 kDA molecular weight cut-off, regenerated cellulose). This was then used to challenge a culture of Tetraselmis species isolated previously from the same water. Lysate was serially diluted and used to challenge a new culture for several rounds using a dilution-to-extinction approach to ensure clonality of the virus. A large batch of lysate (40 L of culture) was filtered (0.45 PVDF over a Whatman glass-fiber GF/C). Viruses in the filtrate were concentrated by TFF (30 kDa) to 350 mL volume, further concentrated by polyethylene glycol precipitation, and purified in a CsCl buoyant density gradient. DNA was extracted from the virus peak in the gradient by buffer exchange into TE, treatment with hot SDS and proteinase K, followed by sequential selective precipitation of proteins (salting out), then DNA (alcohol precipitation) using the MasterPure DNA Purification Kit (Epicentre).

DNA was sequenced using PacBio P6-C4 chemistry platform.  The complete genome sequence was deposited in GenBank (Clark, 2015) with accession number KY322437 (https://www.ncbi.nlm.nih.gov/nuccore/KY322437).  The gene annotations were published as Supplementary Dataset S1 in Schvarcz & Steward, 2018. 


Related Datasets

Results

Dataset: https://www.ncbi.nlm.nih.gov/nuccore/KY322437.1/
Genome [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – . Accession No. KY322437.1, Tetraselmis virus 1, complete genome; [cited 2021 Nov 03]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/KY322437.1/

Related Publications

Methods, Results

Schvarcz, C. R., & Steward, G. F. (2018). A giant virus infecting green algae encodes key fermentation genes. Virology, 518, 423–433. doi:10.1016/j.virol.2018.03.010
General

Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2015). GenBank. Nucleic Acids Research, 44(D1), D67–D72. doi:10.1093/nar/gkv1276
Methods

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., … Pevzner, P. A. (2012). SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19(5), 455–477. doi:10.1089/cmb.2012.0021
Methods

Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., ..., Finn, R. D. (2020). The InterPro protein families and domains database: 20 years on. In Nucleic Acids Research (Vol. 49, Issue D1, pp. D344–D354). Oxford University Press (OUP). https://doi.org/10.1093/nar/gkaa977
Methods

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10(1). doi:10.1186/1471-2105-10-421