Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Project Information
• Funding

This dataset contains data related to RNA sequence genetic accessions at the National Center for Biotechnology Information (NCBI) including information about the host organism, collection location, and collection date.  

The accessions are the unprocessed Illumina MiSeq reads for the Ross Sea Dinoflagellate RNA-Seq experiments, Phaeocystis antarctica RNA-Seq experiments, and Pyramimons tychotreta & Micromonas polaris (CCMP 2099) mixotrophy experiments.

Pyramimonas tychotreta & Micromonas polaris (CCMP 2099) mixotrophy RNA sequences are available through the NCBI Sequence Read Archive (SRA) under the SRA accession number SRP090401 (BioProject PRJNA342459)

Ross Sea Dinoflagellate RNA sequences are available through the NCBI Sequence Read Archive (SRA) under the accession number SRP132912 (BioProject PRJNA428208).

Phaeocystis antarctica RNA sequences are available through the NCBI Sequence Read Archive (SRA) under the accession number SRP133243 (BioProject PRJNA434497).

Pyramimonas tychotreta and Micromonas polaris (CCMP 2099) mixotrophy RNA-Seq

Replicate cultures (n=4 for each isolate and treatment) were incubated under high- and reduced-nutrient conditions for a week.  High-nutrient treatments were full strength f/2+Si (i.e., the maintenance media), while low-nutrient treatments were a 10-fold dilution of f/2 + Si culture media with filter-sterilized seawater. The low-nutrient conditions were previously found to elicit increases in ingestion by these two species.

Ross Sea Dinoflagellate and Phaeocystis antarctica RNA-Seq

The Ross Sea Dinoflagellate (RSD) was enriched away from the prey and grown in f/2 + Si at 0C under 14/10hr light dark cycle at 26.2 µmol/m2/sec. For the temperature experiment, flasks with approximately 450,000 cells each incubated at 0C (4 replicates) or 5C (4 replicates) for 5 days.  For the different light conditions, flasks of approximately 450,000 cells each were incubated under constant illumination of 371 µmol/m2/sec (surface; 4 replicates), 48 µmol/m2/sec (DCM; 4 replicates) or darkness (4 replicates) at 0C for 5 days.

Phaeocystis antarctica was grown under the same experimental conditions with 4 replicates per treatment.  Approximately 3.3 x 10^6 cells per replicate were used in the 0C incubation, 2.6 x 10^6 cells per replicate in the 5C incubation, and 1.4 x 10^7 cells per replicate in the different light exposure treatments.

Sampling and analytical procedures:

Pyramimonas and Micromonas were collected on 25mm 0.2 µm polycarbonate filters, frozen at -80°C, then extracted using the Qiagen Mini RNA kit, with confirmation of nucleic acid abundance and quality assessed by Bioanalyzer. Replicate samples were sent to the Sulzberger Genome Center at Columbia University for poly-A selection, library construction and sequencing by Illumina Mi-Seq (150bp paired-end reads, 30 million reads per sample).

RSD and Phaeocystis cultures were fixed with RNALater and harvested by filtration onto 0.8 micron pore size 25 mm polycarbonate filters. Cells were lysed using the Qiagen RNeasy Mini Kit.  DNA was removed by DNase treatment on the purification column.  mRNA was isolated using ribosomal depletion (Ribo-Zero™ rRNA Removal Kit for Plant Leaf).  RNA quality was checked by Bioanalyzer and sent to Sulzberger Columbia Genome Center for library preparation and RNA-Seq (150bp paired-end reads, 30 million reads per sample).

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values replaced with no data value 'nd' for "no data" so they are recognized in our system
* metadata for runs obtained with sra run selector results at NCBI to download files that have the biosample, bioproject, sra project and sample info in them.
* split lat_lon into lat,lon in decimal degrees
* commas replaced with ;
* added link to each BioProject at NCBI

Description from NSF award abstract:
Kleptoplasty, the temporary acquisition and use of functional chloroplasts derived from algal prey, is viewed as an important model for the early evolution of the permanent, endosymbiotically-derived chloroplasts found in all permanently photosynthetic eukaryotes. This project will study the evolutionary history and expression of plastid-targeted genes in an abundant Antarctic dinoflagellate that steals chloroplasts from an ecologically important alga, the haptophyte Phaeocystis. Algae play an important role in the fixation and export of CO2 in the Southern Ocean, and this project will explore the genetic basis for the function of these chimeric cells with regard to their functional adaptation to extreme environments and will study the evolutionary history and expression of plastid-targeted genes in both the host and recipient. The project seeks to determine whether the kleptoplastidic dinoflagellate utilizes ancestral plastid proteins to regulate its stolen plastid, and how their transcription is related to environmental factors that are relevant to the Southern Ocean environment (temperature and light). To accomplish these goals, the project will utilize high throughput transcriptome analysis and RNA-sequencing experiments with the dinoflagellate and Phaeocystis.

This work will help biologists understand the environmental success of this alternative nutritional strategy, and to assess the potential impact of anthropogenic climate change on the organism. The project will also contribute to the maintenance of a culture collection of heterotrophic, phototrophic and mixotrophic Antarctic protists that are available to the scientific community, and it will support the mentoring of a graduate student and a postdoctoral fellow. The work is being accomplished as an international collaboration between US and Canadian scientists, and in addition to publishing results in peer-reviewed journals, the investigators will incorporate aspects of this work into public outreach activities. These include field data analysis opportunities for middle school students and science-based art projects with local schools and museums.