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Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis… Gavelis, Gregory S; White, Richard A; Suttle, Curtis A; Keeling, Patrick J; Leander, Brian S Jul 17, 2015

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RESEARCH ARTICLESingle-cell transcriptomicsmke2In recent decades, we have become increasingly awareof the complex history of plastids, with red algae andtions can be difficult to study genetically, as even smallamounts of contamination can provide false impressionsthe fact thatlar, and havetive group ofophic, photo-re recognizedudocolonies,”algal bloomsGavelis et al. BMC Genomics  (2015) 16:528 DOI 10.1186/s12864-015-1636-8and P. hartmanii, have plastids with three membranesV6T1Z4, CanadaFull list of author information is available at the end of the articleby grazing on toxic dinoflagellates [7, 8]. Early-branching polykrikoids, such as Polykrikos geminatum* Correspondence: zoark0@gmail.com†Equal contributors1Department of Zoology, University of British Columbia, Vancouver, BCplastids from a single ancient cyanobacterium, and redalgae subsequently lending “secondary” plastids to mosteukaryotic phytoplankton (e.g., haptophytes, crypto-phytes, diatoms, dinoflagellates), and kelps [1, 2]. Somedinoflagellates even possess “tertiary” plastids derivedfrom haptophytes, cryptophytes, and diatoms [3, 4], andother organisms sequester plastids temporarily, withgenome. This is further complicated bymany of these organisms are rare, unicelluyet to be cultured in lab.Polykrikoid dinoflagellates are a distincuncultivated eukaryotes, including heterotrsynthetic, and mixotrophic species. They aby their large, multinucleated cells or “pseand include species that regulate harmfulgreen algae (including land plants) harnessing “primary” of photosynthetic gene transfer to the host’s nuclearBackground: 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 suggestedthat these plastids stem from a novel symbiosis with either a diatom or haptophyte, but this hypothesis has beendifficult 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-cellisolates of P. lebouriae from marine sediments. Polykrikos lebouriae expressed nuclear-encoded photosynthetic genesthat were characteristic of the peridinin-plastids of dinoflagellates, rather than those from a diatom of haptophyte. Weconfirmed these findings at the genomic level using multiple displacement amplification (MDA) to obtain a partialplastome of P. lebouriae.Conclusion: From these data, we infer that P. lebouriae has retained the peridinin plastids ancestral for dinoflagellatesas a whole, while its closest relatives have lost photosynthesis multiple times independently. We discuss these losseswith reference to mixotrophy in polykrikoid dinoflagellates. Our findings demonstrate new levels of variation associatedwith 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 differentsplice-leader bearing groups.Keywords: Chloroplast, Dinoflagellates, Endosymbiosis, Mixotrophy, Peridinin, Polykrikos, Spliced leaderBackground uncertain degrees of integration [5, 6]. Plastid acquisi-leader PCR: Evidence forphotosynthesis in polykridinoflagellatesGregory S. Gavelis1*†, Richard A. White III2†, Curtis A. SuttlAbstract© 2015 Gavelis et al. This is an Open Access a(http://creativecommons.org/licenses/by/4.0),provided the original work is properly creditedcreativecommons.org/publicdomain/zero/1.0/Open Accessusing splicedultiple losses ofoid,3,4, Patrick J. Keeling3 and Brian S. Leander1,3rticle distributed under the terms of the Creative Commons Attribution Licensewhich permits unrestricted use, distribution, and reproduction in any medium,. The Creative Commons Public Domain Dedication waiver (http://) applies to the data made available in this article, unless otherwise stated.Gavelis et al. BMC Genomics  (2015) 16:528 Page 2 of 9and triple-stacked thylakoids that are characteristic ofthe secondary peridinin-type plastids of most dinoflagel-lates [9, 10] (Fig. 1). The plastids of P. lebouriae, how-ever, are unusual; they are reported to be enveloped byonly two membranes, a trait that is more consistent withprimary plastids, and to contain double-stacked thyla-koids similar to those found in haptophytes and diatoms[11]. P. lebouriae also has a conspicuous phylogeneticposition, as a plastid-bearing mixotroph nested amongthree heterotrophic species (P. herdmanae, P. schwartziiand P. kofoidii) (Fig. 1). Leander and Hoppenrath (2007b)interpreted this as evidence of either multiple losses ofphotosynthesis among P. herdmanae, P. schwartzii andP. kofoidii, or a single loss at the base of this group,followed by acquisition of tertiary plastids in P. lebouriaefrom a diatom or haptophyte [12]. These hypothesesremain untested, as several attempts to cultivate P. lebour-iae have been unsuccessful (Aika Yamaguchi, MonaHoppenrath, personal communication), and PCR amplifi-cation of plastid genes in P. lebouriae has consistentlyfailed with PCR primers used successfully in other taxa.Multiple displacement amplification is a powerful toolfor whole-genome amplification from small amounts oftemplate DNA, but it is nonspecific and therefore proneFig. 1 Maximum likelihood (ML) tree inferred from the 31-taxon alignmentribosomal rDNA sequences using the GTR + Γ substitution model. Bootstraplisted above each branch The illustrations depict the pseudocolonies of pogray indicates a non-photosynthetic pseudocolonyto contamination [13]. We employed this technique toamplify a partial plastid genome of Polykrikos lebouriae,and supplemented this with a dinoflagellate-specifictranscriptomic approach, both to ensure that our plastidamplification did not stem from non-dinoflagellate en-vironmental contaminants (i.e.; diatoms, haptophytes orother algae that share the same habitat as P. lebouriae),and to test whether the plastids are functionally inte-grated into the cell (ie; if the nucleus expresses plastid-targeted genes) rather than being simply retainedas kleptoplastids. We synthesized cDNA from singleP. lebouriae cells, which we primed for PCR with a 21 bpspliced leader sequence specific to dinoflagellates, viaSLPCR. Previous researchers have established the effective-ness of SLPCR for amplifying dinoflagellate transcripts froma large volume of wild-caught plankton [14] or coral tissue[15], and this is the first study to apply SLPCR at the scaleof single cells (Additional file 1).MDA and SLPCR allowed us to illuminate regions ofthe plastid genome in P. lebouriae as well as nucleargene expression. In concert, these methods provided evi-dence of the presence and provenance of functionalplastids in P. lebouriae, and allowed us to test hypoth-eses for plastid evolution in this uncultivated group.(1,915 unambiguously aligned sites) of concatenated small and largesupport values 65 or higher and Bayesian posterior probabilities arelykrikoid species; orange indicates a photosynthetic pseudocolony, andResultsGenes for plastid-targeted proteins obtained from asingle-cell transcriptomePolykrikos lebouriae was identified by morphology inmarine sand, and single cells were manually isolated fortranscriptome and genome sequencing (see below). Theidentification was confirmed by comparing DNAfragments of HSP90 and LSU rRNA genes from singlecell sequence data to sequences obtained from previousisolates of Polykrikos lebouriae (LSU rDNA sequencesshared 96.8 % identity and HSP90 sequences shared98.9 % identity). In order to sequence the transcriptome,transcripts were reverse transcribed and amplifiedusing dinoflagellate spliced leader and polyA primers.For transcripts over 500 base pairs, the average length,after assembly, was 725 base pairs (Table 1). Estimatesof genome coverage were not possible as no sequencedgenome is available for Polykrikos lebouriae or anyspecies within its more inclusive clade (i.e., thePlastid-encoded genes obtained from single cellgenomic dataIn order to examine the genome of the plastid itself,we also sequenced a genomic library created by multipledisplacement amplification (MDA) from a single cell.Unlike the dinoflagellate specificity achieved throughSLPCR, our total genomic amplification through MDAyielded a majority of reads (64 %) from bacteria, withmost of the remainder (34 %) stemming from dinoflagel-lates, and a small fraction of viral or uncertain proven-ance (2 %). Of the eukaryotic reads, 5 % were fromplastids, with most other reads originating from themassive dinoflagellate nuclear genome. Bacterial se-quences were primarily from delta proteobacteria, specif-ically Francisella sp., which is known from cosmopolitanmarine and freshwater strains as well as symbiotic strainsfound among animals and protists [16, 17]. The eukaryoticsequences were most similar to dinoflagellates, as ex-pected, and we identified and assembled three protein-bGavelis et al. BMC Genomics  (2015) 16:528 Page 3 of 9Gymnodiniales).SLPCR amplified a diverse array of nuclear transcriptsfrom P. lebouriae (Fig. 2), suggesting that the cellexpressed genes spanning a broad range of functions, in-cluding photosynthesis. Fourteen transcripts over 600base pairs long were associated with photosynthesis, andall were most closely related to dinoflagellates (Table 1).These were all nucleus-encoded, plastid-targeted genes,supporting the presence of a plastid that is functionallyintegrated with the cell. Among these transcripts weretwo peridinin-chlorophyll a-binding precursor proteins,which are restricted to the peridinin-type plastids ofdinoflagellates.Table 1 Nuclear-encoded plastid-targeted genes transcripts (>600using BLASTX queries against all proteins in GenbankGenbank Predicted Plastid-Targeted Proteins #chloroplast ferredoxin 8chloroplast light harvesting complex protein 8chloroplast acyl carrier protein 5plastid C1 class II fructose bisphosphate aldolase 4chloroplast carbonic anhydrase 4chloroplast ATP synthase subunit C 4chloroplast phosphoribulokinase 3chloroplast ribose-5-phosphate isomerase 3chloroplast peridinin-chlorophyll a-binding protein precursor 2chloroplast ATP synthase gamma subunit 2chloroplast ferredoxin-NADP{+) reductase 1chloroplast photosystem I, subunit III 1chloroplast photosystem II 12 kDa extrinsic protein 1chloroplast photosystem I subunit XI 1coding genes from the plastid photosystem that areuniversally plastid-encoded: complete PsaA and PsbCgenes and a partial plastid AtpA gene. After confirmingthe identity of each plastid photosystem gene using mo-lecular phylogenetic analyses of the individual proteins(Additional file 3-5, Figures 3–5), the three proteins wereconcatenated and added to a 44-taxon alignment contain-ing diverse dinoflagellates and other photosynthetic eu-karyotes. Both Bayesian analysis and maximum likelihoodmethods demonstrated that the P. lebouriae plastidsequences branch with homologues from peridinin-typeplastids of other unarmored dinoflagellates (Fig. 3). Thesequences from P. lebouriae were highly divergent, butp) expressed by Polykrikos lebourae. Identifies were assignedTop Hit E value Coverage IdentityAlexandrium fundyense 6.00E-41 65 % 68 %Symbiodinium sp. 1.00E-60 45 % 61 %Heterocapsa triquetra 2.00E-31 54 % 65 %H. triquetra 0 68 % 85 %H. triquetra 7.00E-72 53 % 71 %A. affine 2.00E-32 60 % 100 %Lingulodinium polyedrum 7.00E-164 93 % 79 %H. triquetra 5.00E-96 71 % 69 %A. tamarense 5.00 E-103 99 % 82 %H. triquetra 3.00E-125 87 % 57 %H. triquetra 1.00E-167 73 % 70 %H. triquetra 2.00E-42 43 % 51 %H. triquetra 7.00E-42 69 % 62 %H. triquetra 1.00E-85 74 % 50 %e. TredGavelis et al. BMC Genomics  (2015) 16:528 Page 4 of 9branched with strong support after the Amphidiniumclade and before the clade consisting of Togula jolla andall armored dinoflagellates. Thus, the phylogenetic rela-tionships inferred from the alignment of concatenatedFig. 2 Transcripts expressed by a single cell isolate of Polykrikos lebouriaaccording to Level 1 Subsystem hierarchical classification in MG-RAST. Pplastid-protein sequences are generally consistent with theplacement of P. lebouriae as inferred from ribosomal genesequences (Figs. 1, 3).DiscussionThe majority of microbial species are not available inculture, and therefore the application of single cellmethods at the genomic level is highly desirable [18]. Inthis case, we used both single cell transcriptomics andsingle cell genomics to investigate the biology of plastidsin P. lebouriae and test hypotheses for their origin,which were otherwise difficult to resolve. Single-cellspliced-leader transcriptomics was particularly powerful,and using this method we were able to obtain a diversityof nuclear-encoded transcripts from P. lebouriae, despitethe presence of environmental contamination from bac-teria (as seen in the MDA results) and potentially evenother non-dinoflagellate eukaryotes. Both nucleus-encodedtranscripts and plastid-encoded genes consistently demon-strated that P. lebouriae is photosynthetic, with all photo-synthesis related genes and transcripts grouping with thosefound in dinoflagellates with peridinin-type plastids, in-cluding a protein with the principle function of binding thepigment peridinin. No abnormalities were seen in the plas-tid targeting sequences to suggest that P. lebouriae, whichwe found to bear typical Type I and II presequences(Additional file 6: Figure S6), as described in dinoflagellateswith triple membrane bound peridinin plastids [20–22].Thus is it unclear whether the two plastid membranesreported by Hoppenrath and Leander were an accurateranscripts are ranked from values 0 to 1 in abundance, and annotatedicted photosynthetic transcripts are shown in greeninterpretation, a misinterpretation, or an artefact.Peridinin plastids in Polykrikos lebouriaeWhile we cannot falsify the possibility of transient orhidden plastids in some polykrikoids, our findings arecontrary to the hypothesis that Polykrikos lebouriaeacquired photosynthesis from diatoms or haptophytesand support the presence of peridinin-type plastidsin P. lebouriae. The most parsimonious source forthese plastids is direct inheritance from ancestralpolykrikoids. Polykrikoid phylogeny, though lackingstrong support at some deeper nodes, shows an un-equivocal sisterhood between P. lebouriae and hetero-trophic P. herdmaniae—which necessitates a recent loss ofphotosynthesis in P. herdmaniae. A second loss is evidentin the P. kofoidii - P. schwartzii clade, as they are stronglysupported sister lineages, and therefore represent a lossindependent from that found in P. herdmaniae.Hypothesis for polykrikoid plastid evolutionSeveral losses of photosynthesis have previously beenestablished in dinoflagellates [19], primarily among para-sitic stem groups or within groups of questionablemonophyly (e.g., the Gymnodiniales). Interestingly, mul-tiple losses of photosynthesis appear to have occurredwithin polykrikoids alone, and the evolutionary reasonsGavelis et al. BMC Genomics  (2015) 16:528 Page 5 of 9for this are worth considering. A prominent trend inpolykrikoid evolution is a gradual increase in size [12](Fig. 1). This makes polykrikoids effective predators, asthey are able to consume groups of dinoflagellates linkedin defensive chain formations [23]. Yet size is known tomake photosynthesis less effective for single cells, aschloroplast self-shading increases, and absorptive surfacearea diminishes relative to volume [24]. As a mixotroph,P. lebouriae is known to prey on other dinoflagellates(Aika Yamaguchi, personal communication), and our iso-late possessed extrusive organelles such as nematocystsand taeniocysts. The presence of such specialized preda-tory features, as well as mixotrophy and large cell size,may have predisposed polykrikoids to multiple losses ofphotosynthesis, as seen in P. herdmaniae, a sister speciesthat shares the same habitat as P. lebouriae [11]. FactorsFig. 3 Maximum likelihood (ML) tree inferred from the 44-taxon alignmentgenes PsaA, PsbC, and AtpA using the PROTGAMMA model in RaxML. Bootare listed above each branch. The inset depicts a differential image contrassingle-cell transcriptomics; this cell was undergoing mitosis when the imagallowing the loss of photosynthesis probably vary bylineage, as losses have also occurred among smaller free-living and parasitic dinoflagellates.Dinoflagellates are fascinating models for the studyof organelle evolution, for in addition to plastid loss,they represent many stages in the process of plastid ac-quisition [1]. For instance, “dinotoms” house virtually in-tact diatom symbionts [4]; Pfiesteria piscicida scavengestemporary kleptoplastids with a limited lifespan [25];and Karenia and Karlodinium have haptophyte-derivedplastids that are nearly as integrated as native peridinin-type plastids [26, 27]. The challenge in studying endo-symbiosis at the earlier stages (where the symbiont re-tains some genetic autonomy) lies partly indifferentiating symbiont-expressed transcripts fromthose of the host. SLPCR circumvents this problem by(1,595 unambiguously aligned amino acids) of concatenated plastidstrap support values 65 or higher and Bayesian posterior probabilitiest (DIC) micrograph of the pseudocolony of Polykrikos lebouriae used fore was captured (scale bar = 10 μm)Gavelis et al. BMC Genomics  (2015) 16:528 Page 6 of 9ensuring dinoflagellate specificity [14, 15]. In the future,this approach is expected to grant insight into endosym-bioses in other uncultivated dinoflagellates, such as theplastid or symbiont-bearing Noctilucales [28] and newlineages of dinoflagellates with cryptophyte or pelago-phyte symbionts [29–31].ConclusionsUnderstanding trends in the evolution of microbial eu-karyotes will require a synthesis of ecology, phyloge-netics, and genomics—the last of which has beenparticularly limited in its applications to uncultivatedgroups. While SLPCR has previously been applied tobulk RNA samples [14, 15, 32], we show here that it isapplicable to single cells. In principle, this method isapplicable to any system with uniform spliced leaders,as found in dinoflagellates, euglenids, kinetoplastids,and a growing number of invertebrates [33]. SLPCRshows promise not only in avoiding contaminants inenvironmental isolates, but in capturing gene expres-sion of a single cell at a given point in time, such asstages of the cell cycle, cells perturbed my experimen-tal stimuli, or simply cells in the dynamism of theirnatural habitats.MethodsCollection of organismsSamples of the upper 1-cm of marine sand were col-lected during low tide from the mid intertidal zone inCannon Beach, Oregon during early October. Within36 h, the samples were transported to the University ofBritish Columbia, kept in an open dish of moist sandand exposed to natural day/night rhythms. Uhlig's sea-water ice method was used to draw cells from the sandinto a petri dish, where they were collected individuallyby micropipette [34]. Cells were visually identified basedon the presence of two-nuclei, eight zooid segments,and plastids, and later confirmed through analysisof the LSU ribosomal gene. To reduce the chance ofgenetic contamination from prey, we selected cells ofP. lebouriae in which no food vacuoles were evident.Pseudocolonies of P. lebouriae were washed five times,once in filtered seawater, twice in PBS buffer, and twicein distilled nuclease-free water. For transcriptomics, asingle cell (Fig. 3, inset) was processed for RNA extrac-tion immediately; other single cell isolates were frozenat −80 °C and thawed later that week for genomics pro-cessing using MDA.Single cell transcriptomicsFor cell lysis, 0.5 μl of proteinase K was added to thetubes, followed by incubation at 65 °C for 10 min, anddenaturation at 90 °C for 2 min, then rapid coolingat 4 °C. First strand cDNA was primed using a GeneRacerOligodT primer (1 μl at 10 μM) RNAse Out (0.5 μl),dNTPs – (2 μl at 10 μM) and incubated at 65 °C for 5 min.After this annealing step, DTT (1 μl at 10 μM), RnaseOut (0.5 μl), and 1 μl of Superscript III reverse tran-scriptase (Life Technologies, Carlsbad CA) were addedand incubated according to the manufacturer’s protocol,allowing for reverse transcription, along with T4 gene32 (0.5 μl) to maximize contact between the reversetranscriptase and RNA template. Afterwards, DNA/RNAhybrids were removed with 1 μl of RNAseH, incubated37 °C for 20 min.Polyadenylated transcripts were amplified with a aGeneRacer 3’ nested primer (5’-CGCTACGTAACGGCATGACAGTG-3’), and dinoflagellate specificity as-sured with the a dinoflagellate spliced-leader primer(5’-TCCGTAGCCATTTTGGCTCAAG-3’) and (LifeTechnologies, Carlsbad CA). Thermocycling proceededthrough a “touchdown PCR” program, as this was effectivefor Zhang et al. (2007). This program progressed through95 °C for 20 s, 72 °C for 2.5 min for 5 cycles; 95 °C for20 s, 65 °C for 30 s, 72 °C for 2 min for 5 cycles; 95 °C for20 s, 60 °C for 30 s, 72 °C for 2 min for 5 cycles; and 95 °Cfor 20 s, 58 °C for 30 s, 72 °C for 2 min for 25 cycles. Be-cause we were amplifying from a single cell, our PCR reac-tion program had ten more amplification steps than thatof Zhang et al. (2007). In order to reduce amplificationbias, we divided each SLPCR reaction into eight sub-reactions, which ran in parallel, and were pooled at theend. Reads were quality checked using a Bioanalyzer(Agilent, Santa Clara, CA).Single cell genomicsA frozen cell was thawed on ice then lysed as above.Multiple Displacement Amplification (MDA) was carriedout using the Repli-G mini kit (Qiagen, Venlo, Linburg,Netherlands) as per manufacturer’s instructions, at themaximum recommended time of 15 hours. The reactionwas divided into four sub-reactions to minimize amplifi-cation bias and then pooled at the end. Genomic DNAwas amplified non-specifically, including the plastidgenes of P. lebouriae.Sequencing, assembly and annotationDNA for libraries was sheared to ~300-400 bp by aCovaris Ultrasonicater (M220) using the manufacturer’sprotocol (Covaris, Woburn, MA). Libraries were indexedwith TruSeqTm adapter barcodes using Lucigen NxSeqlibrary prep without PCR enrichment to avoid amplifica-tion bias. Libraries were washed with two rounds ofAMPureXP magnetic beads (Beckman Coulter, Danvers,MA) at a beads to DNA ratio of 0.8:1 to remove freeadapters by size screening. To ensure sufficient adapterligation, a sample of the libraries were tested with real-timeqPCR (primed to the library indexes), and measuredGavelis et al. BMC Genomics  (2015) 16:528 Page 7 of 9against a digital standard curve [35]. Libraries werescreened for purity using a Nanodrop (ThermoFisher,Wilmington, DE) and length and purity using a BioanalyzerHighSens DNA chip (Agilent, Palo Alto, CA). Librarieswere sequenced with 250 bp paired-end reads on anIllumina MiSeq (GenoSeq UCLA Los Angeles, CA).A phiX library was used as a quality standardduring sequencing. From the output sequences, phiXwas screened and removed, paired ends were merged (ifoverlapping >30 bp), and non-overlapping reads wereinterleaved. Merged reads were checked for a minimumQscore (Q > 30). De novo assembly was performed withRay [36] using a variety of kmer sizes, with 31 chosen asthe optimal kmer size for assembling our genomic readsand 53 for reads from SLPCR. Resulting contigs wereuploaded to the MG-RAST server, which performedautomated annotations and protein predictions [37].Multiple sequence alignmentsSeveral alignments were constructed in this studyfor molecular phylogenetic analysis. For analysis of ribo-somal genes, we concatenated small and large subunitrDNA sequences, and aligned them across 31 unar-moured dinoflagellates, with Akashiwo sanguinea as theoutgroup. This nucleotide alignment consisted of 1,915unambiguously aligned sites, once gaps and ambiguouslyaligned regions were removed. A second alignment wasassembled for LSU rDNA sequences alone, in order toconfirm that the single cell isolate was Polykrikos lebouriae.This alignment included 25 dinoflagellate taxa, with 1,229unambiguously aligned bases (Additional file 2).The remaining alignments were for protein analyses,translated plastid genes PsaA, PsbC and AtpA. Predictedproteins were aligned with MUSCLE, followed by re-moval of gaps and ambiguously aligned bases. Using100 boostraps of RAxML and the substitution modelPROTGAMMA, preliminary trees were generated fromMUSCLE [38] alignments of 715 amino acids for PsaA(Additional file 3: Figure S3), 453 aligned amino acids forPsbC (Additional file 4: Figure 4), and 427 aligned aminoacids for AtpA (Additonal file 5 Figure 5). Having vali-dated these proteins as dinoflagellate plastid-type pro-teins, we manually concatenated these three alignmentsinto a supermatrix with 1,595 unambiguously aminoacids for the final analysis. This alignment incorporated44 taxa, including representatives of all major groupsof photosynthetic eukaryotes, including glaucophytes,red algae, green algae, land plants, haptophytes crypto-phytes, stramenopiles, dinoflagellates with peridinin-typeplastids, as well Lepidodinium, Karenia, Karlodinium,Durinskia, Kryptoperidinium and six species of cyano-bacteria. We chose dinoflagellate taxa for which two ormore of the plastid proteins were available in Genbankor CAMERA. Among dinoflagellates, Symbiodinium,Togula, Lingulodinium, Lepidinodinium, Kryptoperidi-nium, Durinskia, Aphidinium carterae, Heterocapsarotundata, and Polykrikos lebouriae had all three pro-teins, and dinoflagellates with two proteins were incorpo-rated as they led to higher resolution of the dinoflagellaterelationships.Molecular phylogenetic analysesMaximum likelihood analysis was run with 1,000bootstraps using RAxML and PROTGAMMAJTT orGRTGAMMA substitution models for protein and nu-cleotide sets, respectively [39]. Bayesian posterior prob-abilities were calculated for all alignments using thefollowing parameters on the program MrBayes 3.2.2(GTR [Lset nst = 6]; gamma distribution [of rate amongsites]; and Monte Carlo Markov Chains [starting trees = 4;heating (nchains = 4), default temperature = 0.2; genera-tions = 6,000,000; sample frequency = 100; prior burn-in = 500,000 trees] [40, 41].Presequence analysis of plastid targeted genesThe n-terminal region of nuclear encoded, putativelyplastid targeted genes was analysed for signal peptidesusing the Hidden Markov Model of SignalP3.0 [42, 43]using default settings. Transmembrane helices were pre-dicted using TMHMM v.2.0 [44], and their hydrophobi-city scores were calculated with the Kyte-Doolittle aminoacid scale from Protscale (http://web.expasy.org/protscale/,last accessed April 22, 2015) using default settings. Proteinsequences were manually aligned, in Mega 5.2.2 [45], andimported into Jalview [45], where the charge and hydro-phobicity of amino acids were color coded.Data availabilityAll plastid genes that we sequenced and employed inour phylogenetic analysis were submitted to Genbank,with accession numbers KP259913 to KP259915. Nuclear-encoded plastid targeted proteins were given the accessionnumbers KR134302 to KR134310.Additional filesAdditional file 1: Figure 1. Diagram of the basic steps in splice leaderprimed PCR (SLPCR).Additional file 2: Figure 2. Maximum likelihood (ML) tree inferred froma 25-taxon alignment of LSU rDNA sequences (1,229 unambiguouslyaligned bases) using the GTRGAMMA model in RAxML. Bootstrap supportvalues and Bayesian posterior probabilities are listed above each branch.Additional file 3: Figure 3. Maximum likelihood (ML) tree inferredfrom a 39-taxon alignment of PsaA (photosystem 1 P700 chlorophyll aapoprotein A1) sequences (715 unambiguously aligned amino acids)using the PROTGAMMA model in RAxML. Bootstrap support values arelisted above each branch.Additional file 4: Figure 4. Maximum likelihood (ML) tree inferred froma 44-taxon alignment of PsbC (photosystem II CP43 protein) sequencesGavelis et al. BMC Genomics  (2015) 16:528 Page 8 of 9(453 unambiguously aligned amino acids) using the PROTGAMMA modelin RAxML. Bootstrap support values are listed above each branch.Additional file 5: Figure 5. Maximum likelihood (ML) tree inferred froma 34-taxon alignment of AtpA (Atp synthase CF1 alpha chain) sequences(427 unambiguously aligned amino acids) using the PROTGAMMA modelin RAxML. Bootstrap support values are listed above each branch.Additional file 6: Figure 6. Transcripts in Polykrikos lebouriae haveplastid-targeted sequences typical of dinoflagellates with triple-membranebound peridinin plastids. A. Class I transit peptides, each containinga transmembrane domain, which have been manually aligned, ashave their “FVAP” motifs. Boxed proteins are previously published [22], typicalClass I transit peptides from Heterocapsa triquetra (AAW79309, AY826901,AY826898), for comparison. All other proteins are from P. lebouriae(KR134302 – KR134310). The average hydrophobicity score of eachcolumn in the transmembrane domain and neighboring regions have beenplotted above the alignment. Amino acid color code: Yellow = hydrophobic,blue = polar, green = negatively charged, red = positively charged. B. Class IItransit peptides: These presequences lack a transmembrane domain, butcontain the typical “FVAP” motif. For both classes of transit peptides, the“FVAP” cleavage-site (or nearly cleavage-site) motifs are listed to theright of the sequence alignment.AbbreviationsAtpA: Atp synthase CF1 alpha chain; LSU rDNA: Large subunit ribosomalDNA; MDA: Multiple displacement amplification; ML: Maximum likelihood;PsaA: Photosystem 1 P700 chlorophyll a apoprotein A1; PsbC: Photosystem IICP43 protein; SL: Spliced leader; SLPCR: Spliced leader polymerase chainreaction; SSU rDNA: Small subunit ribosomal DNA.Competing interestsThe authors declare that they have no competing interests.Authors’ contributionsGSG, RAW, PJK and BSL designed the experiment. GSG and RAW adaptedSLPCR for single cells and carried out the SLPCR and MDA reactions. RAWprepared samples for sequencing and performed post-sequencing qualitycontrol. GSG and RAW assembled genomic reads and analysed transcriptomicdata. GSG performed phylogenetic analyses. GSG and BSL wrote the manuscriptand all authors participated in the drafting process. Funding and lab support forGSG was provided by BSL and PJK. Funding and lab support for RAW wasprovided by CAS. All authors read and approved the final manuscript.AcknowledgementsThis work was supported by a Four-Year Fellowship granted to GSG from theDepartment of Zoology, University of British Columbia. Support for RAW wasprovided by an NSERC Discovery Grant to CAS. Research operating fundswere provided by a grant to BSL from the National Science and EngineeringResearch Council of Canada (NSERC 283091–09). PJK, CAS and BSL are SeniorFellows of the Canadian Institute for Advanced Research, Program in IntegratedMicrobial Biodiversity.Author details1Department of Zoology, University of British Columbia, Vancouver, BCV6T1Z4, Canada. 2Department of Microbiology & Immunology, University ofBritish Columbia, Vancouver, BC V6T1Z4, Canada. 3Department of Botany,University of British Columbia, Vancouver, BC V6T1Z4, Canada. 4Departmentof Earth, Ocean and Atmospheric Sciences, Vancouver, BC V6T1Z4, Canada.Received: 19 December 2014 Accepted: 18 May 2015References1. Keeling PJ. The number, speed, and impact of plastid endosymbioses ineukaryotic evolution, in Annual Review of Plant Biology, Vol 64, S.S.Merchant, Editor. Annual Reviews, Palo Alto, CA. 2013. p. 583–607.2. Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, et al. Algalgenomes reveal evolutionary mosaicism and the fate of nucleomorphs.Nature. 2012;492(7427):59–65.3. Archibald JM. 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