Dataset: NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri

Data not availableVersion 1 (2024-06-13)Dataset Type:experimental

Principal Investigator: George McManus (University of Connecticut)

Co-Principal Investigator: Laura A. Katz (Smith College)

Co-Principal Investigator: Luciana Santoferrara (Hofstra University)

BCO-DMO Data Manager: Shannon Rauch (Woods Hole Oceanographic Institution)


Project: Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates (Ciliate Omics)


Abstract

Many ciliates express their genes only after "unscrambling" them from the genome (portions of the gene may be reversed in the genome or expressed in a different order from what is in the genome). Because the scrambling process would have to be unique to a given species, we can use genome/transcriptome comparisons of single cells to define species boundaries. We showed that two tintinnid ciliate species that look almost identical, Schmidingerella arcuata and S. meunieri, scramble and unscramble t...

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This project required sequencing whole genomes and transcriptomes from single cells picked from two cultures. One was Schmidingerella arcuata (urn:lsid:marinespecies.org:taxname:732664), isolated from the East Coast of the United States in Long Island Sound; the other was Schmidingerella meunieri (urn:lsid:marinespecies.org:taxname:732864), isolated by S. Strom from Puget Sound on the West Coast of the United States. S. arcuata was collected from the surface waters of northeastern Long Island Sound, CT (41.31°N, 72.06°W), using a 20-micrometer (µm) mesh plankton net. Single cells were isolated with drawn capillaries and moved to six-well culture plates with 0.2-µm-filtered sample water. The goal was to quantify the degree of difference in genome architecture for these two close congeners.

The cultures were grown in filtered seawater at 18 degrees Celsius (°C) on a 12:12 light cycle and fed the dinoflagellate Heterocapsa triquetra and the prymnesiophyte Isochrysis galbana. Individual cells were picked with a drawn capillary pipette and processed for sequencing as detailed below (from Smith et al 2020).

The SMART-Seq2 v4 Ultra Low input RNA kit (Cat: 634889; Takara, Mountain View, CA) was used for whole transcriptome amplification (WTA) following the manufacturer's protocols, with the exception that we quartered the reaction volumes. For whole-genome amplification (WGA), the Repli-g single-cell kit (Cat: 150343; Qiagen, Hilden, Germany) was used following the manufacturer’s protocols. The products (cDNA for WTA, gDNA for WGA) were quantified with the dsDNA Qubit assay (Invitrogen, Waltham, MA) and polymerase chain reaction-checked with eukaryotic 18S rDNA and genus-specific ITS primers. Minimum bacterial contamination was confirmed by polymerase chain reaction with 16S rDNA primers Sequencing libraries were prepared with the Illumina Nextera XT kit (Cat: FC1311096; Illumina, San Diego, CA), then processed with Illumina HiSeq 2500 at Macrogen Sequencing (Geumcheon-gu, Seoul, South Korea).

The isolation/cultivation was done in 2014-2015. The sequencing work was all completed and analyzed by the suummer of 2020.


Related Datasets

IsRelatedTo

Dataset: https://doi.org/10.6084/m9.figshare.16892893
Smith, S., Santoferrara, L. F., Katz, L., &amp; McManus, G. B. (2022). <i>Genome architecture used to supplement species delineation in two cryptic marine ciliates (study on congeneric tintinnid ciliates Schmidingerella arcuata and Schmidingerella meunieri (published as Smith et al. 2022 in Molecular Ecology Resources)</i> [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.16892893
IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA829814
University of Connecticut. Schmidingerella arcuata isolate:LIS Genome sequencing and assembly. 2022/06. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA829814. NCBI:BioProject: PRJNA829814.
IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA626068
University of Connecticut. Schmidingerella arcuata isolate:SAS-2020, Genome and transcriptome of marine ciliate Schmidingerella arcuata. 2020/09. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA626068. NCBI:BioProject: PRJNA626068.
IsRelatedTo

Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA828278
University of Connecticut. Schmidingerella meunieri isolate:PAC Genome sequencing and assembly. 2022/06. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA828278. NCBI:BioProject: PRJNA828278.

Related Publications

Results

Smith, S. A., Maurer-Alcalá, X. X., Yan, Y., Katz, L. A., Santoferrara, L. F., & McManus, G. B. (2020). Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion. Genome Biology and Evolution, 12(9), 1616–1622. https://doi.org/10.1093/gbe/evaa185
Results

Smith, S. A., Santoferrara, L. F., Katz, L. A., & McManus, G. B. (2022). Genome architecture used to supplement species delineation in two cryptic marine ciliates. Molecular Ecology Resources, 22(8), 2880–2896. Portico. https://doi.org/10.1111/1755-0998.13664
Methods

Fischer, S., Brunk, B. P., Chen, F., Gao, X., Harb, O. S., Iodice, J. B., Shanmugam, D., Roos, D. S., & Stoeckert, C. J. (2011). Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups. Current Protocols in Bioinformatics, 35(1). Portico. https://doi.org/10.1002/0471250953.bi0612s35
Software

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
Software

Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner. Lawrence Berkeley National Laboratory. LBNL Report #: LBNL-7065E. Retrieved from https://escholarship.org/uc/item/1h3515gn