Meta-algae are organisms with photosynthetic organelles of secondary or tertiary endosymbiotic origin, and their close non-photosynthetic, plastid-bearing, relatives. Apicomplexans are a secondarily non-photosynthetic group of chromalveoates which retain a reduced plastid organelle.
Photosynthetic chromalveolates
Dinoflagellate plastid genomes are not organised into a single circular DNA molecule like other plastid genomes, but into an array of mini-circles.
In some photosynthetic organisms that ability was acquired via symbiosis with a unicellular green alga (chlorophyte) or red alga (rhodophyte). In some such cases not only does the chloroplast of the former unicellular alga retain its own genome, but a remnant of the alga is also retained. When this retains a nucleus and a nuclear genome it is termed a nucleomorph.
The unicellular eukaryote Paulinella chromatophora possesses an organelle (the cyanelle) which represents an independent case of the acquisition of photosynthesis by cyanobacterial endosymbiosis. (Note: the term cyanelle is also applied to the plastids of glaucophytes.)
^Villarreal JC, Forrest LL, Wickett N, Goffinet B (March 2013). "The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain". American Journal of Botany. 100 (3): 467–77. doi:10.3732/ajb.1200429. PMID23416362.
^Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K (March 2007). "The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses". Journal of Plant Research. 120 (2): 281–90. doi:10.1007/s10265-006-0055-y. PMID17297557. S2CID7691300.
^ abcdefghijGuisinger et al, Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae, J Mol Evol 70: 149–166 (2010)
^Yan M, Moore MJ, Meng A, Yao X, Wang H (2016-09-21). "The first complete plastome sequence of the basal asterid family Styracaceae (Ericales) reveals a large inversion". Plant Systematics and Evolution. 303 (1): 61–70. doi:10.1007/s00606-016-1352-0. ISSN0378-2697. S2CID25942874.
^Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (September 2002). "The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation". Molecular Biology and Evolution. 19 (9): 1602–12. doi:10.1093/oxfordjournals.molbev.a004222. PMID12200487. S2CID1111063.
^ abcdHansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK (November 2007). "Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)". Molecular Phylogenetics and Evolution. 45 (2): 547–63. doi:10.1016/j.ympev.2007.06.004. PMID17644003.
^Goremykin V, Hirsch-Ernst KI, Wölfl S, Hellwig FH (2003). "The chloroplast genome of the basal angiosperm Calycanthus fertilis – structural and phylogenetic analyses". Plant Systematics and Evolution. 242 (1–4): 119–135. doi:10.1007/s00606-003-0056-4. S2CID44377635.
^Yang Y, Wang M, Lu Z, Xie X, Feng S (2017-01-04). "Characterization of the complete chloroplast genome of Carpinus tientaiensis". Conservation Genetics Resources. 9 (2): 339–341. doi:10.1007/s12686-016-0668-y. ISSN1877-7252. S2CID5184815.
^Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, Kolganova TV, Skyabin KG (June 2008). "Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms". Journal of Molecular Evolution. 66 (6): 555–64. Bibcode:2008JMolE..66..555M. doi:10.1007/s00239-008-9091-7. PMID18463914. S2CID10044367.
^Malé PJ, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, Lhuillier E, Scotti-Saintagne C, Tinaut A, Chave J (September 2014). "Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family". Molecular Ecology Resources. 14 (5): 966–75. doi:10.1111/1755-0998.12246. PMID24606032. S2CID26777683.
^Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, Buzgo M, Landherr LL, Hu Y, DiLoreto DS, Ilut DC, Field D, Tanksley SD, Ma H, Claude (2008). "An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron". Tree Genetics & Genomes. 4 (3): 419–433. doi:10.1007/s11295-007-0120-2. S2CID44266336.
^Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY (June 1989). "The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals". Molecular & General Genetics. 217 (2–3): 185–94. doi:10.1007/BF02464880. PMID2770692. S2CID36458326.
^Okumura S, Sawada M, Park YW, Hayashi T, Shimamura M, Takase H, Tomizawa K (October 2006). "Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts". Transgenic Research. 15 (5): 637–46. doi:10.1007/s11248-006-9009-3. PMID16952016. S2CID39294451.
^Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, Jeong WJ, Liu JR (December 2006). "The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence". Plant Cell Reports. 25 (12): 1369–79. doi:10.1007/s00299-006-0196-4. PMID16835751. S2CID24055793.
^Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG, Mache R (February 2001). "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization". Plant Molecular Biology. 45 (3): 307–15. doi:10.1023/A:1006478403810. PMID11292076. S2CID28271437.
^Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, et al. (2000). "Chinese Spring Wheat (Triticum aestivum L.) Chloroplast Genome: Complete Sequence and Contig Clones". Plant Molecular Biology Reporter. 18 (3): 243–253. doi:10.1007/BF02823995. S2CID41773993.
^Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H, Tsunewaki K (January 2002). "Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA". Molecular Genetics and Genomics. 266 (5): 740–6. doi:10.1007/s00438-001-0606-9. PMID11810247. S2CID22434780.
^Fajardo D, Senalik D, Ames M, Zhu H, Steffan SA, Harbut R, Polashock J, Vorsa N, Gillespie E, Kron K, Zalapa JE (2013). "Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing". Tree Genetics & Genomes. 9 (2): 489–498. doi:10.1007/s11295-012-0573-9. S2CID17130517.
^Maier RM, Neckermann K, Igloi GL, Kössel H (September 1995). "Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing". Journal of Molecular Biology. 251 (5): 614–28. doi:10.1006/jmbi.1995.0460. PMID7666415.
^Campbell, Matthew A.; Presting, Gernot; Bennett, Matthew S.; Sherwood, Alison R. (2014-02-21). "Highly conserved organellar genomes in the Gracilariales as inferred using new data from the Hawaiian invasive alga Gracilaria salicornia (Rhodophyta". Phycologia. 53 (2): 109–116. doi:10.2216/13-222.1. S2CID85867132.
^Hagopian JC, Reis M, Kitajima JP, Bhattacharya D, de Oliveira MC (October 2004). "Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids". Journal of Molecular Evolution. 59 (4): 464–77. Bibcode:2004JMolE..59..464H. CiteSeerX10.1.1.614.9150. doi:10.1007/s00239-004-2638-3. PMID15638458. S2CID19135480.
^Tajima N, Sato S, Maruyama F, Kurokawa K, Ohta H, Tabata S, Sekine K, Moriyama T, Sato N (May 2014). "Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum". Journal of Plant Research. 127 (3): 389–97. doi:10.1007/s10265-014-0627-1. PMID24595640. S2CID1420996.
^Salomaki ED, Nickles KR, Lane CE (April 2015). "The ghost plastid of Choreocolax polysiphoniae". Journal of Phycology. 51 (2): 217–21. doi:10.1111/jpy.12283. PMID26986516. S2CID30670447.
^Löffelhardt W, Bohnert HJ, Bryant DA (1997). "The complete sequence of the Cyanophora paradoxa cyanelle genome (Glaucocystophyceae)". Plant Systematics and Evolution. Vol. 11. Springer Vienna. pp. 149–162. doi:10.1007/978-3-7091-6542-3_8. ISBN9783211830352.
^Douglas SE, Penny SL (February 1999). "The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae". Journal of Molecular Evolution. 48 (2): 236–44. Bibcode:1999JMolE..48..236D. doi:10.1007/PL00006462. PMID9929392. S2CID2005223.
^Kowallik KV, Stoebe B, Schaffran I, Kroth-Pancic P, Freier U (December 1995). "The chloroplast genome of a chlorophylla+c-containing alga,Odontella sinensis". Plant Molecular Biology Reporter. 13 (4): 336–342. doi:10.1007/BF02669188. ISSN0735-9640. S2CID1515475.
^ abOudot-Le Secq MP, Grimwood J, Shapiro H, Armbrust EV, Bowler C, Green BR (April 2007). "Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage". Molecular Genetics and Genomics. 277 (4): 427–39. doi:10.1007/s00438-006-0199-4. PMID17252281. S2CID23192934.
^Dennis, R. D. (January 1976). "Insect morphogenetic hormones and developmental mechanisms in the nematode, Nematospiroides dubius". Comparative Biochemistry and Physiology. A, Comparative Physiology. 53 (1): 53–56. doi:10.1016/s0300-9629(76)80009-6. ISSN0300-9629. PMID184.