Supporting Information Smith and Keeling 10.1073/pnas.1422049112 Table S1. Mitochondrial and plastid genome architectural diversity and its extremes Mitochondrial genomes Plastid genomes Genomic trait Species (lineage) Notable feature Species (lineage) Notable feature Nucleotide Nakaseomyces bacillisporus GC poor (11%) Leucocytozoon caulleryi GC poor (15%) content (pathogenic yeast) (apicomplexan parasite) Selaginella moellendorffii GC rich (68%) Trebouxiophyceae sp. MX- GC rich (58%) (lycophyte) AZ01 (trebouxiophyte green alga) Conformation Ochromonas danica Linear-mapping genome with Chromera velia (autotrophic Linear-mapping genome with (stramenopile alga) inverted-repeat telomeres alveolate) inverted repeat telomeres Chlamydomonas moewusii Circular monomeric genome Nicotiana tabacum Multigenomic, linear-branched (chlorophycean green (angiosperm) chromosomal structure alga) Chromosome Diplonema papillatum >75 small (6–7 kb) circular Karlodinium veneficum Conventional plastid genome number (euglenozoan) DNAs with (dinoflagellate with with a satellite fraction of single-gene modules haptophyte-derived plastid) fragmented miniature chromosomes Amoebidium parasiticum Several hundred (0.3–8.3 kb) Symbiodinium sp. clade C3 Multiple mini (2–3 kb) circular (ichthyosporean protist) linear chromosomes with (dinoflagellate with chromosomes with one to one to multiple genes apiece peridinin-containing plastid) a few genes each Size Silene conica (angiosperm) 11,318-kb genome, ∼99% Floydiella terrestris 521 kb genome, ∼80% noncoding (chlorophycean green alga) noncoding DNA Babesia bovis 6-kb genome, >90% coding Helicosporidium sp. 37.5 kb genome, ∼95% coding (apicomplexan parasite) (nonphotosynthetic, parasitic trebouxiophyte) Introns Agaricus bisporus (button 43 group I and 3 group II Euglena gracilis (euglenozoan >150 introns, including 72 mushroom) introns distributed in 8 of 15 alga) group II and 46 group III protein-coding genes. introns, many of which are Introns represent 45% of the twintrons (introns within mtDNA sequence introns). Introns represent ∼40% of the ptDNA sequence Genes Andalucia godoyi (jakobid) MtDNA encodes 66 proteins Porphyra purpurea PtDNA encodes 212 proteins and 34 functional RNAs; no (multicellular red alga) and 41 functional RNAs; no introns introns Hematodinium sp. (deep- MtDNA encodes three proteins Heterocapsa triquetra PtDNA encodes 10 proteins, ∼3 branching, parasitic and two functional RNAs; no (dinoflagellate with functional RNAs; no introns dinoflagellate) introns peridinin-containing plastid) Fragmented Plasmodium falciparum LSU and SSU rRNA genes are Chlamydomonas reinhardtii psaA gene is split in three genes (apicomplexan parasite) fragmented and scrambled (chlorophycean green alga) separate exons in distant loci into ≥27 coding modules of the plastid genome Gene Saccharomyces cerevisiae Deviant genetic code: AUA is Lepidodinium chlorophorum One codon reassignment: AUA expression (yeast) read as methionine, UGA as (dinoflagellate with green is read as methionine instead tryptophan, and CUN as algal-derived plastid) of isoleucine threonine Trypanosoma brucei ∼90% of codons experience Anthoceros formosae 509 C-to-U and 433 U-to-C (kinetoplastid) uracil-insertion/deletion (hornwort) editing sites editing Foreign DNA Amborella trichopoda Contains six genome Daucus carota (carrot) Contains an ∼1.5 kb of (angiosperm) equivalents of foreign potential mitochondrial mtDNA, acquired from origin green algae, mosses, and other angiosperms Physarum polycephalum 14.5-kb linear plasmid with Ernodesmis verticillata Putative ∼2.2-kb plasmid (amboebozoan) defined telomeres in the (ulvophycean green alga) within the chloroplast mitochondrion Smith and Keeling www.pnas.org/cgi/content/short/1422049112 1of2 Table S1. Cont. Mitochondrial genomes Plastid genomes Genomic trait Species (lineage) Notable feature Species (lineage) Notable feature Genome loss Encephalitozoon cuniculi Mitochondrial-derived Polytomella spp. Genome and transcriptome (microsporidian fungus) organelle (mitosome) (nonphotosynthetic sequencing suggest without DNA chlorophycean green algae) complete loss of plastid genome Trichomonas vaginalis Mitochondrial-derived Rafflesia lagascae Genome sequencing data (parabasalid excavate) organelle (hydrogenosome) (nonphotosynthetic, suggest complete loss of without DNA parasitic angiosperm) plastid genome Table S2. Convergent mitochondrial and plastid genomic architectures within the same lineage or species Species (lineage) Mitochondrial genomic architecture Plastid genomic architecture Selaginella Elevated GC content (68%). Reduced tRNA Elevated GC content (52%). Reduced moellendorffii repertoire (none). Intron rich (37). Large number tRNA repertoire (13). Intron rich (11). (lycophyte) of C-to-U RNA-editing sites (thousands). Large number of C-to-U RNA-editing Recombinant structure (dynamic organization, sites (hundreds). Recombinant structure currently too complex to define). (circular-mapping chromosome that is highly rearranged compared with ptDNAs of close relatives). Amphidinium carterae Complex structure (dynamic organization Complex structure (multiple miniature strain CCAP 1102/6 of highly recombinant heterogeneous circular ptDNA molecules). Reduced gene (dinoflagellate with mtDNA molecules). Reduced gene repertoire (12 proteins, 3 functional RNAs, peridinin-containing plastid) repertoire (3 proteins, no identifiable no introns). Fragmented genes. Extensive rRNAs, tRNAs, or introns). Fragmented posttranscriptional modifications genes. Extensive posttranscriptional (poly-U tails, 5′ processing). modifications (Six types of RNA editing, transsplicing, and poly-A tails). Cyanidioschyzon merolae Genomic compaction (∼99% coding and Genomic compaction (∼90% coding (unicellular red alga) no introns or repeats). AT rich (27.1%). and no introns or repeats). AT rich (37.6%). Conventional architecture (circular-mapping Conventional architecture (circular-mapping monomeric genome, standard genetic monomeric genome, standard genetic code, code, and intact genes). and intact genes). Dunaliella salina (chlorophycean Genomic expansion (∼60% noncoding). Genomic expansion (∼65% noncoding). green alga) Large numbers of introns (∼1.5 introns/gene). Large numbers of introns (∼0.4 introns/gene). Repeat rich (similar repeats in mtDNA Repeat rich (similar repeats in mtDNA and ptDNA). Gene fragmentation and ptDNA). Gene fragmentation (rRNA genes). AT rich (34.4%). (psaA). AT rich (32.1%). Smith and Keeling www.pnas.org/cgi/content/short/1422049112 2of2.