title: Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates.
abstract: BACKGROUND
  Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but this hypothesis has been difficult to test as P. lebouriae dwells in marine sand rife with potential genetic contaminants.
  
  
  RESULTS
  We applied spliced-leader targeted PCR (SLPCR) to obtain dinoflagellate-specific transcriptomes on single-cell isolates of P. lebouriae from marine sediments. Polykrikos lebouriae expressed nuclear-encoded photosynthetic genes that were characteristic of the peridinin-plastids of dinoflagellates, rather than those from a diatom of haptophyte. We confirmed these findings at the genomic level using multiple displacement amplification (MDA) to obtain a partial plastome of P. lebouriae.
  
  
  CONCLUSIONS
  From these data, we infer that P. lebouriae has retained the peridinin plastids ancestral for dinoflagellates as a whole, while its closest relatives have lost photosynthesis multiple times independently. We discuss these losses with reference to mixotrophy in polykrikoid dinoflagellates. Our findings demonstrate new levels of variation associated with the peridinin plastids of dinoflagellates and the usefulness of SLPCR approaches on single cell isolates. Unlike other transcriptomic methods, SLPCR has taxonomic specificity, and can in principle be adapted to different splice-leader bearing groups.
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. zoark0@gmail.com.
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Gavelis
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. raw937@gmail.com.
authors.forename: Richard A
authors.initials: RA
authors.lastname: White
authors.affiliation: Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. suttle@science.ubc.ca.|Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. suttle@science.ubc.ca.|Department of Earth, Ocean and Atmospheric Sciences, Vancouver, BC, V6T1Z4, Canada. suttle@science.ubc.ca.
authors.forename: Curtis A
authors.initials: CA
authors.lastname: Suttle
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. pkeeling@mail.ubc.ca.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
authors.affiliation: Department of Zoology, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. bleander@mail.ubc.ca.|Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada. bleander@mail.ubc.ca.
authors.forename: Brian S
authors.initials: BS
authors.lastname: Leander
mesh_terms: D002338:Carotenoids / Q000378:metabolism; D004275:DNA, Ribosomal / Q000737:chemistry; D004141:Dinoflagellida / Q000235:genetics* / Q000378:metabolism; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D018087:Plastids / Q000145:classification / Q000235:genetics; D016133:Polymerase Chain Reaction; D020038:RNA, Spliced Leader / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013559:Symbiosis; D059467:Transcriptome
chemical_list: D004275:DNA, Ribosomal; D020038:RNA, Spliced Leader; C016040:peridinin; D002338:Carotenoids