Research ArticleEVOLUTIONARY BIOLOGY

An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

See allHide authors and affiliations

Science Advances  24 Apr 2019:
Vol. 5, no. 4, eaav1110
DOI: 10.1126/sciadv.aav1110
  • Fig. 1 Multiprotein phylogeny of Amoebophrya isolated from three separate hosts, 15 other dinoflagellates, and 13 related eukaryotes.

    (A) Free-living stage of the parasite Amoebophrya. Fl, flagellum. (B) The best maximum likelihood tree (IQ-TREE) under the LG + G4 + I + F model with ultrafast/nonparametric bootstrap supports at branches (black circles denote 100/100 support). (C) Relationships among Amoebophrya isolates in a PhyloBayes GTR + CAT + G4 inference with posterior probabilities at branches; the rest of the tree is identical to (B) and is fully supported at all branches.

  • Fig. 2 Shikimate (g6770) and tryptophan (g13589) synthesis pathway multidomain genes.

    (A) Individual domains of the shikimate pathway are illustrated by colored boxes, and domains of the tryptophan pathway are represented with differently shaded gray boxes. (B) Schematic view of the biosynthetic pathway for tryptophan in A. ceratii. Circles represent intermediates that can be synthesized in A. ceratii, and arrows indicate the respective enzymatic activities. Arrows without circles indicate missing pathway components in A. ceratii. The colors for the shikimate enzymatic activities are as in (A). For simplicity, all tryptophan pathway steps are depicted in gray.

  • Fig. 3 Investigation of mitochondria in A. ceratii cells.

    (A) Electron microscopy transmission image of A. ceratii dinospore showing the fine structure of the mitochondrion (Mi), nucleus (Nc), and flagella (Fl). Confocal microscopy images showing (B) SYTO-13–stained DNA of the nucleus (Nc), (C) mitochondria stained with MitoTracker, (D) an image of a free-swimming biflagellate dinospore cell, and (E) overlay of images.

  • Fig. 4 CoxI fragment alignment.

    Scaffold fragment, gene model, gDNA PCR amplicon sequence, and cDNA sequence with and without intron sequence. The predicted coxI domain is marked with a shaded background.

  • Fig. 5 Model of mitochondrial functions in A. ceratii based on the genome gene content.

    The C. velia model from (11) was taken as a template. Mitochondrial complex I has been replaced by an alternative NADH dehydrogenase (DH), which reduced the NADH from the tricarboxylic acid (TCA) cycle. Both alternative NADH dehydrogenase and succinate dehydrogenase (complex II) channel electrons through the carrier ubiquinone (Q) to the alternative oxidase (yellow arrows). Electrons may also be passed by other sources, such as d-lactate:cytochrome c oxidoreductase (d-LDH) and galacto-1,4-lactone:cytochrome c oxidoreductase (G-1,4-LDH) to cytochrome c (yellow arrows), which passes them on to complex IV (cytochrome c oxidase). Stippled yellow arrows indicate alternative pathways of electron flow as proposed in Chromera (11).

  • Table 1 Features of A. ceratii and other dinoflagellate genomes.

    CDS, coding regions. N50 measures assembly quality as a weighted median of contig length. Higher N50 values denote greater contiguity.

    A. ceratiiSymbiodinium
    minutum*
    Symbiodinium
    kawagutii
    Symbiodinium
    microadriaticum
    Hematodinium sp.§
    Genome
    Size (Mb)87.7~1,500 (assembled
    ~616)
    ~1,180 (assembled
    ~935.07)
    ~1,100 (assembled
    ~808.25)
    ~4,800
    Scaffolds (number)2,35121,89930,0409,695118,385 (>10 kbp)
    GC content (%)55.9%43.6%43.97%50.5%
    N50 value (kb)8462.747.134.817.2
    Genes
    Predicted CDS19,92541,92536,85049,109
    Average protein length
    (amino acids)
    6431,6681,041
    Predicted tRNAs39
    CDS with transcript
    data
    4,85632,36626,83437,470
    CDS with domain
    annotation
    8,768
    Introns
    Predicted number51,06695.3%61.1%98.2%
    Median size (bases)184499893504.7
    Intronless CDS5,464

    *From (22).

    †From (21).

    ‡From (20).

    §From (14).

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/5/4/eaav1110/DC1

      Fig. S1. Flow cytometry.

      Fig. S2. Alignment of 5′ ends of transcripts of A. ceratii showing SL and relict SL repeats.

      Fig. S3. The distribution of intron sizes in A. ceratii genes.

      Fig. S4. Expansion of gene numbers per metabolic pathway in A. ceratii.

      Fig. S5. Phylogenetic analysis of prokaryotic and eukaryotic PKS and FAS.

      Fig. S6. Predicted evolution of tetrapyrrole biosynthesis in A. ceratii and other dinoflagellates.

      Fig. S7. Confocal microscopy images of A. ceratii and A. catenella as a control.

      Fig. S8. CoxI phylogeny.

      Fig. S9. Plot obtained by assembling the PE dataset including spike-in mitochondrial reads of P. polycephalum.

      Fig. S10. Plot obtained by assembling the PE dataset including spike-in mitochondrial reads of P. polycephalum.

      Fig. S11. Model of the mitochondrial respiratory chain in A. ceratii.

      Table S1. Enriched gene families.

      Table S2. Number of genes encoding transcription factors in genomes/transcriptomes of 48 genera.

      Table S3. SL detected in the genome of A ceratii.

      Table S4. Illumina RNAseq reads of A. ceratii at 6 and 96 hours during the infection.

      Table S5. A list of enzymes involved in various metabolic pathways in the A. ceratii genome.

      Table S6. Mitochondrion respiration assay.

      Table S7. The search for components of the electron transport system of A. ceratii.

      Table S8. Mitochondrial functions encoded in the genome of A. ceratii.

      Table S9. Primers used in this study to amplify cox from A. ceratii cDNA.

      Table S10. Primers used to amplify various shikimate pathway transcripts from A. ceratii cDNA.

      Data file S1. Contigs of the A. ceratii AT5.2 genome.

      Data file S2. Scaffolds of the A. ceratii AT5.2 genome.

      Data file S3. GFF of the A. ceratii AT5.2 genome.

      Data file S4. Predicted protein sequences of the A. ceratii AT5.2 genome.

      Data file S5. Assembly statistics of the A. ceratii AT5.2 genome.

      Data file S6. Annotation table generated via Trinotate for the A. ceratii AT5.2 genome.

    • Supplementary Materials

      The PDF file includes:

      • Fig. S1. Flow cytometry.
      • Fig. S2. Alignment of 5′ ends of transcripts of A. ceratii showing SL and relict SL repeats.
      • Fig. S3. The distribution of intron sizes in A. ceratii genes.
      • Fig. S4. Expansion of gene numbers per metabolic pathway in A. ceratii.
      • Fig. S5. Phylogenetic analysis of prokaryotic and eukaryotic PKS and FAS.
      • Fig. S6. Predicted evolution of tetrapyrrole biosynthesis in A. ceratii and other dinoflagellates.
      • Fig. S7. Confocal microscopy images of A. ceratii and A. catenella as a control.
      • Fig. S8. CoxI phylogeny.
      • Fig. S9. Plot obtained by assembling the PE dataset including spike-in mitochondrial reads of P. polycephalum.
      • Fig. S10. Plot obtained by assembling the PE dataset including spike-in mitochondrial reads of P. polycephalum.
      • Fig. S11. Model of the mitochondrial respiratory chain in A. ceratii.
      • Table S1. Enriched gene families.
      • Table S2. Number of genes encoding transcription factors in genomes/transcriptomes of 48 genera.
      • Table S3. SL detected in the genome of A ceratii.
      • Table S4. Illumina RNAseq reads of A. ceratii at 6 and 96 hours during the infection.
      • Table S5. A list of enzymes involved in various metabolic pathways in the A. ceratii genome.
      • Table S6. Mitochondrion respiration assay.
      • Table S7. The search for components of the electron transport system of A. ceratii.
      • Table S8. Mitochondrial functions encoded in the genome of A. ceratii.
      • Table S9. Primers used in this study to amplify cox from A. ceratii cDNA.
      • Table S10. Primers used to amplify various shikimate pathway transcripts from A. ceratii cDNA.

      Download PDF

      Other Supplementary Material for this manuscript includes the following:

      • Data file S1 (.gz format). Contigs of the A. ceratii AT5.2 genome.
      • Data file S2 (.bz2 format). Scaffolds of the A. ceratii AT5.2 genome.
      • Data file S3 (.bz2 format). GFF of the A. ceratii AT5.2 genome.
      • Data file S4 (.gz format). Predicted protein sequences of the A. ceratii AT5.2 genome.
      • Data file S5 (.pdf format). Assembly statistics of the A. ceratii AT5.2 genome.
      • Data file S6 (Microsoft Excel format). Annotation table generated via Trinotate for the A. ceratii AT5.2 genome.

      Files in this Data Supplement:

    Stay Connected to Science Advances

    Navigate This Article