Archibald, J. M. (2009). The puzzle of plastid evolution. Curr. Biol. 19, R81–R88. doi: 10.1016/j.cub.2008.11.067
Barbrook, A. C., Howe, C. J., and Nisbet, R. E. R. (2019). Breaking up is hard to do: the complexity of the dinoflagellate chloroplast genome. Perspect. Phycol. 6, 31–37. doi: 10.1127/pip/2018/0084
Baurain, D., Brinkmann, H., Petersen, J., Rodriguez-Ezpeleta, N., Stechmann, A., Demoulin, V., et al. (2010). Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Mol. Biol. Evol. 27, 1698–1709. doi: 10.1093/molbev/msq059
Bentlage, B., Rogers, T. S., Bachvaroff, T. R., and Delwiche, C. F. (2016). Complex ancestries of isoprenoid synthesis in dinoflagellates. J. Eukaryot. Microbiol. 63, 123–137. doi: 10.1111/jeu.12261
Bjørnland, T., Haxo, F. T., and Liaaen-Jensen, S. (2003). Carotenoids of the Florida red tide dinoflagellate Karenia brevis. Biochem. Syst. Ecol. 31, 1147–1162. doi: 10.1016/S0305-1978(03)00044-9
Boisvert, S., Laviolette, F., and Corbeil, J. (2010). Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol. 17, 1519–1533. doi: 10.1089/cmb.2009.0238
Burki, F., Imanian, B., Hehenberger, E., Hirakawa, Y., Maruyama, S., and Keeling, P. J. (2014). Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. Eukaryot. Cell 13, 246–255. doi: 10.1128/EC.00299-13
Cai, C., Wang, L., Zhou, L., He, P., and Jiao, B. (2017). Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis. PLoS One 12:e0184196. doi: 10.1371/journal.pone. 0184196
Carpenter, E. J., Matasci, N., Ayyampalayam, S., Wu, S., Sun, J., Yu, J., et al. (2019). Access to RNA-sequencing data from 1,173 plant species: the 1000 Plant transcriptomes initiative (1KP). GigaScience 8:giz126. doi: 10.1093/gigascience/ giz126
Carty, S., and Parrow, M. W. (2015). “Dinoflagellates,” in Freshwater Algae of North America, ed. J. D. Wehr (Amsterdam: Elsevier), 773–807.
Cauz-Santos, L. A., da Costa, Z. P., Callot, C., Cauet, S., Zucchi, M. I., Bergès, H., et al. (2020). A repertory of rearrangements and the loss of an inverted repeat region in Passiflora chloroplast genomes. Genome Biol. Evol. 12, 1841–1857. doi: 10.1093/gbe/evaa155
Ceriotti, L. F., Roulet, M. E., and Sanchez-Puerta, M. V. (2021). Plastomes in the holoparasitic family Balanophoraceae: extremely high AT content, severe gene content reduction, and two independent genetic code changes. Mol. Phylogenet. Evol. 162:107208. doi: 10.1016/j.ympev.2021.107208
Chan, P. P., and Lowe, T. M. (2019). “tRNAscan-SE: searching for tRNA genes in genomic sequences,” in Gene Prediction, Methods in Molecular Biology, ed. M. Kollmar (New York, NY: Springer), 1–14.
Chen, S., Zhou, Y., Chen, Y., and Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. doi: 10.1093/bioinformatics/bty560 Choi, I.-S., Jansen, R., and Ruhlman, T. (2019). Lost and found: return of the inverted repeat in the legume clade defined by its absence. Genome Biol. Evol.
11, 1321–1333. doi: 10.1093/gbe/evz076
Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., et al. (2021). Twelve years of SAMtools and BCFtools. GigaScience 10:giab008. doi: 10.1093/gigascience/giab008
Dang, Y., and Green, B. R. (2009). Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA. Gene 442, 73–80. doi: 10.1016/j.gene.2009.04.006
Donaher, N., Tanifuji, G., Onodera, N. T., Malfatti, S. A., Chain, P. S. G., Hara, Y., et al. (2009). The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol. Evol. 1, 439–448. doi: 10.1093/gbe/ evp047
Dorrell, R. G., and Howe, C. J. (2012). Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors. Proc. Natl. Acad. Sci. U.S.A. 109, 18879–18884. doi: 10.1073/pnas.12122 70109
Gabrielsen, T. M., Minge, M. A., Espelund, M., Tooming-Klunderud, A., Patil, V., Nederbragt, A. J., et al. (2011). Genome evolution of a tertiary dinoflagellate plastid. PLoS One 6:e19132. doi: 10.1371/journal.pone.0019132
Gockel, G., and Hachtel, W. (2000). Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. Protist 151, 347–351. doi: 10.1078/S1434-4610(04)70033-4
Guisinger, M. M., Kuehl, J. V., Boore, J. L., and Jansen, R. K. (2011). Extreme reconfiguration of plastid genomes in the Angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol. Biol. Evol. 28, 583–600. doi: 10.1093/molbev/msq229
Hallick, R. B., Hong, L., Drager, R. G., Favreau, M. R., Monfort, A., Orsat, B., et al. (1993). Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res. 21, 3537–3544. doi: 10.1093/nar/21.15.3537
Hao, W., Liu, G., Wang, W., Shen, W., Zhao, Y., Sun, J., et al. (2021). RNA editing and its roles in plant organelles. Front. Genet. 12:757109. doi: 10.3389/fgene. 2021.757109
Jackson, C., Knoll, A. H., Chan, C. X., and Verbruggen, H. (2018). Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids. Sci. Rep. 8:1523. doi: 10.1038/s41598-017-18805-w
Jackson, C. J., Gornik, S. G., and Waller, R. F. (2013). A tertiary plastid gains RNA editing in its new host. Mol. Biol. Evol. 30, 788–792. doi: 10.1093/molbev/ mss270
Jeffrey, S. W., Sielicki, M., and Haxo, F. T. (1975). Chloroplast pigment patterns in dinoflagellates. J. Phycol. 11, 374–384. doi: 10.1111/j.1529-8817.1975.tb02799.x Jin, D.-M., Wicke, S., Gan, L., Yang, J.-B., Jin, J.-J., and Yi, T.-S. (2020). The loss of the inverted repeat in the Putranjivoid clade of Malpighiales. Front. Plant Sci.
11:942. doi: 10.3389/fpls.2020.00942
Kamikawa, R., Tanifuji, G., Kawachi, M., Miyashita, H., Hashimoto, T., and Inagaki, Y. (2015). Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biol. Evol. 7, 1133–1140. doi: 10.1093/gbe/evv060
Karnkowska, A., Bennett, M. S., and Triemer, R. E. (2018). Dynamic evolution of inverted repeats in Euglenophyta plastid genomes. Sci. Rep. 8:16071. doi: 10.1038/s41598-018-34457-w
Katoh, K. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066. doi: 10.1093/ nar/gkf436
Keeling, P. J. (2010). The endosymbiotic origin, diversification and fate of plastids.
Philos. Trans. R. Soc. B Biol. Sci. 365, 729–748. doi: 10.1098/rstb.2009.0103 Kim, D., Paggi, J. M., Park, C., Bennett, C., and Salzberg, S. L. (2019). Graph-based
genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915. doi: 10.1038/s41587-019-0201-4
Klinger, C. M., Paoli, L., Newby, R. J., Wang, M. Y.-W., Carroll, H. D., Leblond,
J. D., et al. (2018). Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends. Genome Biol. Evol. 10, 1019–1038. doi: 10.1093/gbe/evy057
Kodama, Y., Shumway, M., Leinonen, R., and International Nucleotide Sequence Database Collaboration (2012). The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res. 40, D54–D56. doi: 10.1093/nar/gkr854
Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie
2. Nat. Methods 9, 357–359. doi: 10.1038/nmeth.1923
Lartillot, N., Brinkmann, H., and Philippe, H. (2007). Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 7:S4. doi: 10.1186/1471-2148-7-S1-S4
Lartillot, N., and Philippe, H. (2004). A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095–1109. doi: 10.1093/molbev/msh112
Lartillot, N., and Philippe, H. (2006). Computing bayes factors using thermodynamic integration. Syst. Biol. 55, 195–207. doi: 10.1080/1063515 0500433722
Lemieux, C., Otis, C., and Turmel, M. (2014). Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae. BMC Evol. Biol. 14:211. doi: 10.1186/s12862-014-0211-2
Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993. doi: 10.1093/bioinformatics/ btr509
Li, J., Gao, L., Chen, S., Tao, K., Su, Y., and Wang, T. (2016). Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae. Sci. Rep. 6:20934. doi: 10.1038/srep20934
Matsumoto, T., Ishikawa, S. A., Hashimoto, T., and Inagaki, Y. (2011). A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Mol. Phylogenet. Evol. 60, 68–72. doi: 10.1016/j.ympev.2011.04. 010
Matsumoto, T., Kawachi, M., Miyashita, H., and Inagaki, Y. (2012). Prasinoxanthin is absent in the green-colored dinoflagellate Lepidodinium chlorophorum strain NIES-1868: pigment composition and 18S rRNA phylogeny. J. Plant Res. 125, 705–711. doi: 10.1007/s10265-012-0486-6
Matsuo, E., and Inagaki, Y. (2018). Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non- photosynthetic periods prior to plastid replacements in dinoflagellates. PeerJ 6:e5345. doi: 10.7717/peerj.5345
Minge, M. A., Shalchian-Tabrizi, K., Tørresen, O. K., Takishita, K., Probert, I., Inagaki, Y., et al. (2010). A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum. BMC Evol. Biol. 10:191. doi: 10.1186/1471-2148-10-191
Mühlhausen, S., Findeisen, P., Plessmann, U., Urlaub, H., and Kollmar, M. (2016). A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes. Genome Res. 26, 945–955. doi: 10.1101/gr.200931. 115
Mungpakdee, S., Shinzato, C., Takeuchi, T., Kawashima, T., Koyanagi, R., Hisata, K., et al. (2014). Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome. Genome Biol. Evol. 6, 1408–1422. doi: 10.1093/ gbe/evu109
Nakayama, T., Takahashi, K., Kamikawa, R., Iwataki, M., Inagaki, Y., and Tanifuji,
G. (2020). Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms. Commun. Integr. Biol. 13, 84–88. doi: 10.1080/19420889.2020.1776568
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., and Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274. doi: 10.1093/molbev/msu300
Nosenko, T., Lidie, K. L., Van Dolah, F. M., Lindquist, E., Cheng, J.-F., Us Department of Energy–Joint Genome Institute, et al. (2006). Chimeric plastid proteome in the Florida “red tide” dinoflagellate Karenia brevis. Mol. Biol. Evol. 23, 2026–2038. doi: 10.1093/molbev/msl074
One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685. doi: 10.1038/s41586-019-1693-2
Osawa, S., and Jukes, T. H. (1989). Codon reassignment (codon capture) in evolution. J. Mol. Evol. 28, 271–278. doi: 10.1007/BF02103422
Palmer, J. D., and Thompson, W. F. (1981). Rearrangements in the chloroplast genomes of mung bean and pea. Proc. Natl. Acad. Sci. U.S.A. 78, 5533–5537. doi: 10.1073/pnas.78.9.5533
Palmer, J. D., and Thompson, W. F. (1982). Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29, 537–550. doi: 10.1016/0092-8674(82)90170-2
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., and Korobeynikov, A. (2020). Using SPAdes de novo assembler. Curr. Protoc. Bioinform. 70:102. doi: 10.1002/ cpbi.102
Ruhlman, T. A., Zhang, J., Blazier, J. C., Sabir, J. S. M., and Jansen, R. K. (2017). Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. Am. J. Bot. 104, 559–572. doi: 10.3732/ajb.1600453
Saldarriaga, J. F., Taylor, F. J. R., Keeling, P. J., and Cavalier-Smith, T. (2001). Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J. Mol. Evol. 53, 204–213. doi: 10.1007/s002390010210
Santos, M. A. S., Cheesman, C., Costa, V., Moradas-Ferreira, P., and Tuite,
M. F. (1999). Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp. Mol. Microbiol. 31, 937–947. doi: 10.1046/j.1365-2958.1999.01233.x
Sarai, C., Tanifuji, G., Nakayama, T., Kamikawa, R., Takahashi, K., Yazaki, E., et al. (2020). Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis. Proc. Natl. Acad. Sci. U.S.A. 117, 5364–5375. doi: 10.1073/ pnas.1911884117
Schultz, D. W., and Yarus, M. (1994). Transfer RNA mutation and the malleability of the genetic code. J. Mol. Biol. 235, 1377–1380. doi: 10.1006/jmbi.1994.1094
Sengupta, S., and Higgs, P. G. (2005). A unified model of codon reassignment in alternative genetic codes. Genetics 170, 831–840. doi: 10.1534/genetics.104. 037887
Shalchian-Tabrizi, K., Minge, M. A., Cavalier-Smith, T., Nedreklepp, J. M., Klaveness, D., and Jakobsen, K. S. (2006). Combined heat shock protein 90 and ribosomal RNA sequence phylogeny supports multiple replacements of dinoflagellate plastids. J. Eukaryot. Microbiol. 53, 217–224. doi: 10.1111/j.1550- 7408.2006.00098.x
Shikanai, T. (2006). RNA editing in plant organelles: machinery, physiological function and evolution. Cell. Mol. Life Sci. 63, 698–708. doi: 10.1007/s00018- 005-5449-9
Sibbald, S. J., and Archibald, J. M. (2020). Genomic insights into plastid evolution.
Genome Biol. Evol. 12, 978–990. doi: 10.1093/gbe/evaa096
Su, H.-J., Barkman, T. J., Hao, W., Jones, S. S., Naumann, J., Skippington, E., et al. (2019). Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora. Proc. Natl. Acad. Sci.
U.S.A. 116, 934–943. doi: 10.1073/pnas.1816822116
Takano, Y., Hansen, G., Fujita, D., and Horiguchi, T. (2008). Serial replacement of diatom endosymbionts in two freshwater dinoflagellates, Peridiniopsis spp. (Peridiniales, Dinophyceae). Phycologia 47, 41–53. doi: 10.2216/07-36.1
Tanifuji, G., Kamikawa, R., Moore, C. E., Mills, T., Onodera, N. T., Kashiyama, Y., et al. (2020). Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biol. Evol. 12, 3926–3937. doi: 10.1093/gbe/evaa001
Tengs, T., Dahlberg, O. J., Shalchian-Tabrizi, K., Klaveness, D., Rudi, K., Delwiche,
C. F., et al. (2000). Phylogenetic analyses indicate that the 19r hexanoyloxy- fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin. Mol. Biol. Evol. 17, 718–729. doi: 10.1093/oxfordjournals.molbev. a026350
Turmel, M., Gagnon, M.-C., O’Kelly, C. J., Otis, C., and Lemieux, C. (2009a). The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol. Biol. Evol. 26, 631–648. doi: 10.1093/molbev/msn285
Turmel, M., Otis, C., and Lemieux, C. (2009b). The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales. Mol. Biol. Evol. 26, 2317–2331. doi: 10.1093/molbev/msp138
Uthanumallian, K., Iha, C., Repetti, S. I., Chan, C. X., Bhattacharya, D., Duchene, S., et al. (2022). Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis. Mol. Biol. Evol. 39:msab295. doi: 10.1093/molbev/msab295
Wang, H.-C., Minh, B. Q., Susko, E., and Roger, A. J. (2018). Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67, 216–235. doi: 10.1093/sysbio/ syx068
Watanabe, M. M., Suda, S., Inouya, I., Sawaguchi, T., and Chihara, M. (1990). Lepidodinium viride gen. et sp. nov. (Gymnodinaiales, Dinophyta), a green dinoflagellate with a chlorophyll a- and b-containing endosymbiont. J. Phycol. 26, 741–751. doi: 10.1111/j.0022-3646.1990.00741.x
Watanabe, M. M., Takeda, Y., Sasa, T., Inouye, I., Suda, S., Sawaguchi, T., et al. (1987). A green dinoflagellate with chlorophylls a and b: morphology, fine structure of the chloroplast and chlorophyll composition. J. Phycol. 23, 382–389. doi: 10.1111/j.1529-8817.1987.tb04148.x
Wu, C.-S., Wang, Y.-N., Hsu, C.-Y., Lin, C.-P., and Chaw, S.-M. (2011).
Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and Cupressophytes and influence of heterotachy on the evaluation of Gymnosperm phylogeny. Genome Biol. Evol. 3, 1284–1295. doi: 10.1093/gbe/ evr095
Yamada, N., Sym, S. D., and Horiguchi, T. (2017). Identification of highly divergent diatom-derived chloroplasts in dinoflagellates, including a description of Durinskia kwazulunatalensis sp. nov. (Peridiniales, Dinophyceae). Mol. Biol. Evol. 34, 1335–1351. doi: 10.1093/molbev/msx054
Zapata, M., Fraga, S., Rodríguez, F., and Garrido, J. (2012). Pigment-based chloroplast types in dinoflagellates. Mar. Ecol. Prog. Ser. 465, 33–52. doi: 10. 3354/meps09879
Zauner, S., Greilinger, D., Laatsch, T., Kowallik, K. V., and Maier, U.-G. (2004). Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridum. FEBS Lett. 577, 535–538. doi: 10.1016/ j.febslet.2004.10.060
Zhang, Z., Green, B. R., and Cavalier-Smith, T. (1999). Single gene circles in dinoflagellate chloroplast genomes. Nature 400, 155–159. doi: 10.1038/22099
論文の公開元へ
