Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?
Abstract
Keywords
Full Text:
PDFReferences
Delwiche CF, Timme RE. Plants. Curr Biol. 2011;21(11):R417–R422. http://dx.doi.org/10.1016/j.cub.2011.04.021
Schenk HE. Glaucocystophytes. In: Encyclopedia of life sciences. Chichester: John Wiley & Sons; 2001. http://dx.doi.org/10.1038/npg.els.0003061
Thomas DN. Seaweeds. London: Natural History Museum; 2002.
Lewis LA, McCourt RM. Green algae and the origin of land plants. Am J Bot. 2004;91(10):1535–1556. http://dx.doi.org/10.3732/ajb.91.10.1535
Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005;52(5):399–451. http://dx.doi.org/10.1111/j.1550-7408.2005.00053.x
Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012;59(5):429–514. http://dx.doi.org/10.1111/j.1550-7408.2012.00644.x
Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, et al. The tree of eukaryotes. Trends Ecol Evol. 2005;20(12):670–676. http://dx.doi.org/10.1016/j.tree.2005.09.005
Gould SB, Waller RF, McFadden GI. Plastid evolution. Ann Rev Plant Biol. 2008;59(1):491–517. http://dx.doi.org/10.1146/annurev.arplant.59.032607.092915
Keeling PJ. The endosymbiotic origin, diversification and fate of plastids. Phil Trans R Soc Lond B. 2010;365(1541):729–748. http://dx.doi.org/10.1098/rstb.2009.0103
Reyes-Prieto A, Weber APM, Bhattacharya D. The origin and establishment of the plastid in algae and plants. Annu Rev Genet. 2007;41(1):147–168. http://dx.doi.org/10.1146/annurev.genet.41.110306.130134
Stoebe B, Kowallik KV. Gene-cluster analysis in chloroplast genomics. Trends Genet. 1999;15(9):344–347. http://dx.doi.org/10.1016/S0168-9525(99)01815-6
Stoebe B, Martin W, Kowallik KV. Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes. Plant Mol Biol Rep. 1998;16(3):243–255. http://dx.doi.org/10.1023/A:1007568326120
Besendahl A, Qiu YL, Lee J, Palmer JD, Bhattacharya D. The cyanobacterial origin and vertical transmission of the plastid tRNA(Leu) group-I intron. Curr Genet. 2000;37(1):12–23.
Pfanzagl B, Zenker A, Pittenauer E, Allmaier G, Martinez-Torrecuadrada J, Schmid ER, et al. Primary structure of cyanelle peptidoglycan of Cyanophora paradoxa: a prokaryotic cell wall as part of an organelle envelope. J Bacteriol. 1996;178(2):332–339.
Burey SC, Fathi-Nejad S, Poroyko V, Steiner JM, Löffelhardt W, Bohnert HJ. The central body of the cyanelles of Cyanophora paradoxa: a eukaryotic carboxysome? Can J Bot. 2005;83(7):758–764. http://dx.doi.org/10.1139/b05-060
Kies L, Kremer BP. Phylum Glaucocystophyta. In: Margulis L, editor. Handbook of protoctista. Boston, MA: Jones and Bartlett Publishers; 1990. p. 152–166.
Archibald JM. The puzzle of plastid evolution. Curr Biol. 2009;19(2):R81–R88. http://dx.doi.org/10.1016/j.cub.2008.11.067
Bodył A, Stiller JW, Mackiewicz P. Chromalveolate plastids: direct descent or multiple endosymbioses? Trends Ecol Evol. 2009;24(3):119–121. http://dx.doi.org/10.1016/j.tree.2008.11.003
Yusa F, Steiner JM, Loffelhardt W. Evolutionary conservation of dual Sec translocases in the cyanelles of Cyanophora paradoxa. BMC Evol Biol. 2008;8(1):304. http://dx.doi.org/10.1186/1471-2148-8-304
Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber APM, et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science. 2012;335(6070):843–847. http://dx.doi.org/10.1126/science.1213561
Chan CX, Gross J, Yoon HS, Bhattacharya D. Plastid origin and evolution: new models provide insights into old problems. Plant Physiol. 2011;155(4):1552–1560. http://dx.doi.org/10.1104/pp.111.173500
McFadden GI, van Dooren GG. Evolution: red algal genome affirms a common origin of all plastids. Curr Biol. 2004;14(13):R514–R516. http://dx.doi.org/10.1016/j.cub.2004.06.041
Reyes-Prieto A, Bhattacharya D. Phylogeny of Calvin cycle enzymes supports Plantae monophyly. Mol Phylogenet Evol. 2007;45(1):384–391. http://dx.doi.org/10.1016/j.ympev.2007.02.026
Cavalier-Smith T, Lee JJ. Protozoa as hosts for endosymbioses and the conversion of symbionts into organelles. J Eukaryot Microbiol. 1985;32(3):376–379. http://dx.doi.org/10.1111/j.1550-7408.1985.tb04031.x
Cavalier-Smith T. Membrane heredity and early chloroplast evolution. Trends Plant Sci. 2000;5(4):174–182. http://dx.doi.org/10.1016/S1360-1385(00)01598-3
Cavalier-Smith T. The origins of plastids. Bot J Linn Soc. 1982;17(3):289–306. http://dx.doi.org/10.1111/j.1095-8312.1982.tb02023.x
Palmer JD. The symbiotic birth and spread of plastids: how many times and whodunit? J Phycol. 2003;39(1):4–12. http://dx.doi.org/10.1046/j.1529-8817.2003.02185.x
Howe C, Barbrook A, Nisbet RE, Lockhart P, Larkum AW. The origin of plastids. Philos Trans R Soc Lond B Biol Sci. 2008;363(1504):2675–2685. http://dx.doi.org/10.1098/rstb.2008.0050
Nozaki H. A new scenario of plastid evolution: plastid primary endosymbiosis before the divergence of the “Plantae”, emended. J Plant Res. 2005;118(4):247–255. http://dx.doi.org/10.1007/s10265-005-0219-1
Larkum AWD, Lockhart PJ, Howe CJ. Shopping for plastids. Trends Plant Sci. 2007;12(5):189–195. http://dx.doi.org/10.1016/j.tplants.2007.03.011
Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol. 2009;53(3):872–880. http://dx.doi.org/10.1016/j.ympev.2009.08.015
Stiller JW, Reel DC, Johnson JC. A single origin of plastids revisited: convergent evolution in organellar genome content. J Phycol. 2003;39(1):95–105. http://dx.doi.org/10.1046/j.1529-8817.2003.02070.x
Stiller JW, Hall BD. The origin of red algae: implications for plastid evolution. Proc Natl Acad Sci USA. 1997;94(9):4520–4525.
Douglas SE, Turner S. Molecular evidence for the origin of plastids from a cyanobacterium-like ancestor. J Mol Evol. 1991;33(3):267–273. http://dx.doi.org/10.1007/BF02100678
Giovannoni SJ, Wood N, Huss V. Molecular phylogeny of oxygenic cells and organelles based on small-subunit ribosomal RNA sequences. In: Lewin RA, editor. Origins of plastids. New York, NY: Chapman and Hall; 1993. p. 159–170. http://dx.doi.org/10.1007/978-1-4615-2818-0_10
Olsen GJ, Woese CR, Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol. 1994;176(1):1–6.
Marin B, Nowack EC, Melkonian M. A plastid in the making: evidence for a second primary endosymbiosis. Protist. 2005;156(4):425–432. http://dx.doi.org/10.1016/j.protis.2005.09.001
Ochoa de Alda JAG, Esteban R, Diago ML, Houmard J. The plastid ancestor originated among one of the major cyanobacterial lineages. Nat Commun. 2014;5:4937. http://dx.doi.org/10.1038/ncomms5937
Delwiche C. Phylogenetic analysis of tufa sequences indicates a cyanobacterial origin of all plastids. Mol Phylogenet Evol. 1995;4(2):110–128. http://dx.doi.org/10.1006/mpev.1995.1012
Morden CW, Delwiche CF, Kuhsel M, Palmer JD. Gene phylogenies and the endosymbiotic origin of plastids. Biosystems. 1992;28(1–3):75–90. http://dx.doi.org/10.1016/0303-2647(92)90010-V
Palmer JD, Delwiche CF. The origin and evolution of plastids and their genomes. In: Soltis DE, Soltis PS, Doyle JJ, editors. Molecular systematics of plants II. Boston, MA: Kluwer Academic Publishers; 1998. p. 375–409. http://dx.doi.org/10.1007/978-1-4615-5419-6_13
Ohta N, Sato N, Nozaki H, Kuroiwa T. Analysis of the cluster of ribosomal protein genes in the plastid genome of a unicellular red alga Cyanidioschyzon merolae: translocation of the str cluster as an early event in the rhodophyte-chromophyte lineage of plastid evolution. J Mol Evol. 1997;45(6):688–695. http://dx.doi.org/10.1007/PL00006273
Adachi J, Waddell PJ, Martin W, Hasegawa M. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol. 2000;50(4):348–358.
Yoon HS, Hackett JD, Ciniglia C, Pinto G, Bhattacharya D. A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol. 2004;21(5):809–818. http://dx.doi.org/10.1093/molbev/msh075
Rodríguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Löffelhardt W, et al. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol. 2005;15(14):1325–1330. http://dx.doi.org/10.1016/j.cub.2005.06.040
Deschamps P, Moreira D. Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes. Mol Biol Evol. 2009;26(12):2745–2753. http://dx.doi.org/10.1093/molbev/msp189
Criscuolo A, Gribaldo S. Large-scale phylogenomic analyses indicate a deep origin of primary plastids within cyanobacteria. Mol Biol Evol. 2011;28(11):3019–3032. http://dx.doi.org/10.1093/molbev/msr108
Li B, Lopes JS, Foster PG, Embley TM, Cox CJ. Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins. Mol Biol Evol. 2014;31(7):1697–1709. http://dx.doi.org/10.1093/molbev/msu105
Chu KH, Qi J, Yu ZG, Anh V. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol. 2003;21(1):200–206. http://dx.doi.org/10.1093/molbev/msh002
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci USA. 2013;110(3):1053–1058. http://dx.doi.org/10.1073/pnas.1217107110
Marin B, Nowack EC, Glöckner G, Melkonian M. The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like γ-proteobacterium. BMC Evol Biol. 2007;7(1):85. http://dx.doi.org/10.1186/1471-2148-7-85
Sogin ML. The phylogenetic significance of sequence diversity and length variations in eukaryotic small subunit ribosomal RNA coding regions. In: Warren L, Koprowski H, editors. New perspectives on evolution. New York, NY: Wiley-Liss; 1991. p. 175–188. (Wistar symposium series; vol 4).
Sogin ML, Elwood HJ, Gunderson JH. Evolutionary diversity of eukaryotic small-subunit rRNA genes. Proc Natl Acad Sci USA. 1986;83(5):1383–1387.
Bhattacharya D, Medlin L. The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J Phycol. 1995;31(4):489–498. http://dx.doi.org/10.1111/j.1529-8817.1995.tb02542.x
Bhattacharya D, Helmchen T, Bibeau C, Melkonian M. Comparisons of nuclear-encoded small-subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol Biol Evol. 1995;12(3):415–420.
van de Peer Y, Rensing SA, Maier UG, de Wachter R. Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc Natl Acad Sci USA. 1996;93(15):7732–7736.
van de Peer Y, de Wachter R. Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. J Mol Evol. 1997;45(6):619–630.
van de Peer Y, Baldauf SL, Doolittle WF, Meyer A. An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. J Mol Evol. 2000;51(6):565–576.
Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 2002;52(2):297–354.
Cavalier-Smith T. Only six kingdoms of life. Proc Biol Sci. 2004;271(1545):1251–1262. http://dx.doi.org/10.1098/rspb.2004.2705
Okamoto N, Inouye I. The katablepharids are a distant sister group of the Cryptophyta: a proposal for Katablepharidophyta divisio nova/kathablepharida phylum novum based on SSU rDNA and beta-tubulin phylogeny. Protist. 2005;156(2):163–179. http://dx.doi.org/10.1016/j.protis.2004.12.003
Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, et al. Widespread distribution of a unique marine protistan lineage. Environ Microbiol. 2008;10(6):1621–1634. http://dx.doi.org/10.1111/j.1462-2920.2008.01580.x
Ishida K, Inagaki Y, Sakaguchi M, Oiwa A, Kai A, Suzuki M, et al. Comprehensive SSU rRNA phylogeny of eukaryota. Endocytobiosis Cell Res. 2010;20:81–88.
Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, et al. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science. 2011;332(6030):714–717. http://dx.doi.org/10.1126/science.1203163
Seenivasan R, Sausen N, Medlin LK, Melkonian M. Picomonas judraskeda gen. et sp. nov.: the first identified member of the Picozoa phylum nov., a widespread group of Picoeukaryotes, formerly known as “picobiliphytes”. PLoS ONE. 2013;8(3):e59565. http://dx.doi.org/10.1371/journal.pone.0059565
Moreira D, von der Heyden S, Bass D, López-García P, Chao E, Cavalier-Smith T. Global eukaryote phylogeny: combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata. Mol Phylogenet Evol. 2007;44(1):255–266. http://dx.doi.org/10.1016/j.ympev.2006.11.001
Zhao S, Burki F, Brate J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K. Collodictyon – an ancient lineage in the tree of eukaryotes. Mol Biol Evol. 2012;29(6):1557–1568. http://dx.doi.org/10.1093/molbev/mss001
Yabuki A, Inagaki Y, Ishida K. Palpitomonas bilix gen. et sp. nov.: a novel deep-branching heterotroph possibly related to Archaeplastida or Hacrobia. Protist. 2010;161(4):523–538. http://dx.doi.org/10.1016/j.protis.2010.03.001
Kim E, Simpson AGB, Graham LE. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol. 2006;23(12):2455–2466. http://dx.doi.org/10.1093/molbev/msl120
Bhattacharya D, Weber K. The actin gene of the glaucocystophyte Cyanophora paradoxa: analysis of the coding region and introns, and an actin phylogeny of eukaryotes. Curr Genet. 1997;31(5):439–446.
Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 2000;290(5493):972–977. http://dx.doi.org/10.1126/science.290.5493.972
Lartillot N. A bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 2004;21(6):1095–1109. http://dx.doi.org/10.1093/molbev/msh112
Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. 2007;56(3):389–399. http://dx.doi.org/10.1080/10635150701397643
Reeb VC, Peglar MT, Yoon HS, Bai JR, Wu M, Shiu P, et al. Interrelationships of chromalveolates within a broadly sampled tree of photosynthetic protists. Mol Phylogenet Evol. 2009;53(1):202–211. http://dx.doi.org/10.1016/j.ympev.2009.04.012
Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, Mylnikov AP, et al. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci USA. 2004;101(21):8066–8071. http://dx.doi.org/10.1073/pnas.0308602101
Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, et al. Broadly sampled multigene trees of eukaryotes. BMC Evol Biol. 2008;8(1):14. http://dx.doi.org/10.1186/1471-2148-8-14
Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison HG, Sogin ML, et al. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol. 2010;59(5):518–533. http://dx.doi.org/10.1093/sysbio/syq037
Kim E, Graham LE. EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS ONE. 2008;3(7):e2621. http://dx.doi.org/10.1371/journal.pone.0002621
Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, et al. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci USA. 2009;106(10):3859–3864. http://dx.doi.org/10.1073/pnas.0807880106
Cavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM, Lewis R. Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa. Mol Phylogenet Evol. 2014;81:71–85. http://dx.doi.org/10.1016/j.ympev.2014.08.012
Burki F, Okamoto N, Pombert JF, Keeling PJ. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci. 2012;279(1736):2246–2254. http://dx.doi.org/10.1098/rspb.2011.2301
Tekle YI, Grant J, Anderson OR, Nerad TA, Cole JC, Patterson DJ, et al. Phylogenetic placement of diverse amoebae inferred from multigene analyses and assessment of clade stability within “Amoebozoa” upon removal of varying rate classes of SSU-rDNA. Mol Phylogenet Evol. 2008;47(1):339–352. http://dx.doi.org/10.1016/j.ympev.2007.11.015
Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa M, et al. The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J Mol Evol. 2003;56(4):485–497. http://dx.doi.org/10.1007/s00239-002-2419-9
Hackett JD, Yoon HS, Li S, Reyes-Prieto A, Rummele SE, Bhattacharya D. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol Biol Evol. 2007;24(8):1702–1713. http://dx.doi.org/10.1093/molbev/msm089
Burki F, Shalchian-Tabrizi K, Pawlowski J. Phylogenomics reveals a new “megagroup” including most photosynthetic eukaryotes. Biol Lett. 2008;4(4):366–369. http://dx.doi.org/10.1098/rsbl.2008.0224
Burki F, Inagaki Y, Brate J, Archibald JM, Keeling PJ, Cavalier-Smith T, et al. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol. 2009;1:231–238. http://dx.doi.org/10.1093/gbe/evp022
Yabuki A, Kamikawa R, Ishikawa SA, Kolisko M, Kim E, Tanabe AS, et al. Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista. Sci Rep. 2014;4:4641. http://dx.doi.org/10.1038/srep04641
Zhao S, Shalchian-Tabrizi K, Klaveness D. Sulcozoa revealed as a paraphyletic group in mitochondrial phylogenomics. Mol Phylogenet Evol. 2013;69(3):462–468. http://dx.doi.org/10.1016/j.ympev.2013.08.005
Jackson CJ, Reyes-Prieto A. The mitochondrial genomes of the Glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multilocus phylogenetics suggests a monophyletic archaeplastida. Genome Biol Evol. 2014;6(10):2774–2785. http://dx.doi.org/10.1093/gbe/evu218
Stiller JW, Riley J, Hall BD. Are red algae plants? A critical evaluation of three key molecular data sets. J Mol Evol. 2001;52(6):527–539. http://dx.doi.org/10.1007/s002390010183
Roger AJ, Hug LA. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci. 2006;361(1470):1039–1054. http://dx.doi.org/10.1098/rstb.2006.1845
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005;6(5):361–375. http://dx.doi.org/10.1038/nrg1603
Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AGB, et al. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci. 2013;280(1769):20131755. http://dx.doi.org/10.1098/rspb.2013.1755
Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 1978;27(4):401. http://dx.doi.org/10.2307/2412923
Stiller JW, Harrell L. The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny. BMC Evol Biol. 2005;5(1):71. http://dx.doi.org/10.1186/1471-2148-5-71
Roure B, Baurain D, Philippe H. Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol. 2013;30(1):197–214. http://dx.doi.org/10.1093/molbev/mss208
Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol. 2004;21(9):1740–1752. http://dx.doi.org/10.1093/molbev/msh182
Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, et al. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol Biol Evol. 2007;24(8):1592–1595. http://dx.doi.org/10.1093/molbev/msm091
Inagaki Y, Nakajima Y, Sato M, Sakaguchi M, Hashimoto T. Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study. Mol Biol Evol. 2009;26(5):1171–1178. http://dx.doi.org/10.1093/molbev/msp036
Brinkmann H, van der Giezen M, Zhou Y, de Raucourt GP, Philippe H. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol. 2005;54(5):743–757. http://dx.doi.org/10.1080/10635150500234609
Susko E, Roger AJ. On reduced amino acid alphabets for phylogenetic inference. Mol Biol Evol. 2007;24(9):2139–2150. http://dx.doi.org/10.1093/molbev/msm144
Tuffley C, Steel M. Modeling the covarion hypothesis of nucleotide substitution. Math Biosci. 1998;147(1):63–91. http://dx.doi.org/10.1016/S0025-5564(97)00081-3
Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, et al. Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Curr Biol. 2011;21(4):328–333. http://dx.doi.org/10.1016/j.cub.2011.01.037
Maddison WP. Gene trees in species trees. Syst Biol. 1997;46(3):523–536. http://dx.doi.org/10.1093/sysbio/46.3.523
Page R. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol. 1997;7(2):231–240. http://dx.doi.org/10.1006/mpev.1996.0390
Chan CX, Bhattacharya D. Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mob Genet Elem. 2013;3(6):e27669. http://dx.doi.org/10.4161/mge.27669
Chan CX, Bhattacharya D, Reyes-Prieto A. Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life. Mob Genet Elem. 2012;2(2):101–105. http://dx.doi.org/10.4161/mge.20110
Huang J, Yue J. Horizontal gene transfer in the evolution of photosynthetic eukaryotes: HGT in plants. J Syst Evol. 2013;51(1):13–29. http://dx.doi.org/10.1111/j.1759-6831.2012.00237.x
Schönknecht G, Weber APM, Lercher MJ. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. BioEssays. 2014;36(1):9–20. http://dx.doi.org/10.1002/bies.201300095
Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 2008;9(8):605–618. http://dx.doi.org/10.1038/nrg2386
Keeling PJ. Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids. In: Gogarten MB, Gogarten JP, Olendzenski LC, editors. Horizontal gene transfer. Totowa, NJ: Humana Press; 2009. p. 501–515. (vol 532). http://dx.doi.org/10.1007/978-1-60327-853-9_29
Richardson AO, Palmer JD. Horizontal gene transfer in plants. J Exp Bot. 2006;58(1):1–9. http://dx.doi.org/10.1093/jxb/erl148
Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD. Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA. 2004;101(51):17747–17752. http://dx.doi.org/10.1073/pnas.0408336102
Bergthorsson U, Adams KL, Thomason B, Palmer JD. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature. 2003;424(6945):197–201. http://dx.doi.org/10.1038/nature01743
Woloszynska M, Bocer T, Mackiewicz P, Janska H. A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Mol Biol. 2004;56(5):811–820. http://dx.doi.org/10.1007/s11103-004-5183-y
Timmis JN, Ayliffe MA, Huang CY, Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 2004;5(2):123–135. http://dx.doi.org/10.1038/nrg1271
Kleine T, Maier UG, Leister D. DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol. 2009;60(1):115–138. http://dx.doi.org/10.1146/annurev.arplant.043008.092119
Lane CE, Archibald JM. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol. 2008;23(5):268–275. http://dx.doi.org/10.1016/j.tree.2008.02.004
Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008;57(1):104–115. http://dx.doi.org/10.1080/10635150801910436
Stiller JW. Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evol Biol. 2011;11(1):259. http://dx.doi.org/10.1186/1471-2148-11-259
Andersson JO, Roger AJ. A cyanobacterial gene in nonphotosynthetic protists – an early chloroplast acquisition in eukaryotes? Curr Biol. 2002;12(2):115–119.
Cavalier-Smith T. The origin, losses and gains of chloroplasts. In: Lewin RA, editor. Origins of plastids. New York, NY: Chapman and Hall; 1993. p. 291–348.
Dorrell RG, Smith AG. Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. Eukaryot Cell. 2011;10(7):856–868. http://dx.doi.org/10.1128/EC.00326-10
Vesteg M, Vacula R, Krajčovič J. On the origin of chloroplasts, import mechanisms of chloroplast-targeted proteins, and loss of photosynthetic ability – review. Folia Microbiol Praha. 2009;54(4):303–321. http://dx.doi.org/10.1007/s12223-009-0048-z
Krause K. From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants. Curr Genet. 2008;54(3):111–121. http://dx.doi.org/10.1007/s00294-008-0208-8
Borza T, Popescu CE, Lee RW. Multiple metabolic roles for the nonphotosynthetic plastid of the green alga Prototheca wickerhamii. Eukaryot Cell. 2005;4(2):253–261. http://dx.doi.org/10.1128/EC.4.2.253-261.2005
Mazumdar J, Wilson EH, Masek K, Hunter CA, Striepen B. Apicoplast fatty acid synthesis is essential for organelle biogenesis and parasite survival in Toxoplasma gondii. Proc Natl Acad Sci USA. 2006;103(35):13192–13197. http://dx.doi.org/10.1073/pnas.0603391103
Bodył A, Mackiewicz P, Gagat P. Organelle evolution: Paulinella breaks a paradigm. Curr Biol. 2012;22(9):R304–R306. http://dx.doi.org/10.1016/j.cub.2012.03.020
Gagat P, Bodył A, Mackiewicz P, Stiller JW. Tertiary plastid endosymbioses in dinoflagellates. In: Löffelhardt W, editor. Endosymbiosis. Vienna: Springer; 2014. p. 233–290. http://dx.doi.org/10.1007/978-3-7091-1303-5_13
Kies L, Kremer BP. Function of cyanelles in the tecamoeba Paulinella chromatophora. Naturewissenschaften. 1979;66:578–579.
Bodył A, Mackiewicz P, Stiller JW. The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles? Trends Microbiol. 2007;15(7):295–296. http://dx.doi.org/10.1016/j.tim.2007.05.002
Nowack ECM, Melkonian M, Glöckner G. Chromatophore genome sequence of Paulinella sheds light on acquisition of photosynthesis by eukaryotes. Curr Biol. 2008;18(6):410–418. http://dx.doi.org/10.1016/j.cub.2008.02.051
Reyes-Prieto A, Yoon HS, Moustafa A, Yang EC, Andersen RA, Boo SM, et al. Differential gene retention in plastids of common recent origin. Mol Biol Evol. 2010;27(7):1530–1537. http://dx.doi.org/10.1093/molbev/msq032
Nowack ECM, Vogel H, Groth M, Grossman AR, Melkonian M, Glockner G. Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora. Mol Biol Evol. 2011;28(1):407–422. http://dx.doi.org/10.1093/molbev/msq209
Nakayama T, Ishida K. Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora. Curr Biol. 2009;19(7):R284–R285. http://dx.doi.org/10.1016/j.cub.2009.02.043
Nowack ECM, Grossman AR. Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora. Proc Natl Acad Sci USA. 2012;109(14):5340–5345. http://dx.doi.org/10.1073/pnas.1118800109
Mackiewicz P, Bodył A, Gagat P. Protein import into the photosynthetic organelles of Paulinella chromatophora and its implications for primary plastid endosymbiosis. Symbiosis. 2012;58(1–3):99–107. http://dx.doi.org/10.1007/s13199-012-0202-2
Mackiewicz P, Bodył A, Gagat P. Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora. Theory Biosci. 2012;131(1):1–18. http://dx.doi.org/10.1007/s12064-011-0147-7
Bodył A, Mackiewicz P, Stiller JW. Comparative genomic studies suggest that the cyanobacterial endosymbionts of the amoeba Paulinella chromatophora possess an import apparatus for nuclear-encoded proteins. Plant Biol. 2009;12:639–649. http://dx.doi.org/10.1111/j.1438-8677.2009.00264.x
Carpenter EJ, Foster RA. Marine cyanobacterial symbioses. In: Rai AN, Bergman B, Rasmussen U, editors. Cyanobacteria in symbiosis. Dordrecht: Kluwer Academic Publishers; 2002. p. 11–17. http://dx.doi.org/10.1007/0-306-48005-0_2
Raven JA. Evolution of cyanobacterial symbioses. In: Rai AN, Bergman B, Rasmussen U, editors. Cyanobacteria in symbiosis. Dordrecht: Kluwer Academic Publishers; 2002. p. 329–346. http://dx.doi.org/10.1007/0-306-48005-0_16
Kneip C, Lockhart P, Voß C, Maier UG. Nitrogen fixation in eukaryotes – new models for symbiosis. BMC Evol Biol. 2007;7(1):55. http://dx.doi.org/10.1186/1471-2148-7-55
Kneip C, Voβ C, Lockhart PJ, Maier UG. The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution. BMC Evol Biol. 2008;8(1):30. http://dx.doi.org/10.1186/1471-2148-8-30
Rogers M, Keeling PJ. Lateral transfer and recompartmentalization of Calvin cycle enzymes of plants and algae. J Mol Evol. 2004;58(4):367–375. http://dx.doi.org/10.1007/s00239-003-2558-7
Durnford DG, Deane JA, Tan S, McFadden GI, Gantt E, Green BR. A phylogenetic assessment of the eukaryotic light-harvesting antenna proteins, with implications for plastid evolution. J Mol Evol. 1999;48(1):59–68.
Rissler HM, Durnford DG. Isolation of a novel carotenoid-rich protein in Cyanophora paradoxa that is immunologically related to the light-harvesting complexes of photosynthetic eukaryotes. Plant Cell Physiol. 2005;46(3):416–424. http://dx.doi.org/10.1093/pcp/pci054
Plancke C, Colleoni C, Deschamps P, Dauvillee D, Nakamura Y, Haebel S, et al. Pathway of cytosolic starch synthesis in the model glaucophyte Cyanophora paradoxa. Eukaryot Cell. 2008;7(2):247–257. http://dx.doi.org/10.1128/EC.00373-07
Deschamps P, Haferkamp I, d’Hulst C, Neuhaus HE, Ball SG. The relocation of starch metabolism to chloroplasts: when, why and how. Trends Plant Sci. 2008;13(11):574–582. http://dx.doi.org/10.1016/j.tplants.2008.08.009
Deschamps P, Colleoni C, Nakamura Y, Suzuki E, Putaux JL, Buleon A, et al. Metabolic symbiosis and the birth of the plant kingdom. Mol Biol Evol. 2008;25(3):536–548. http://dx.doi.org/10.1093/molbev/msm280
Ball S, Colleoni C, Cenci U, Raj JN, Tirtiaux C. The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis. J Exp Bot. 2011;62(6):1775–1801. http://dx.doi.org/10.1093/jxb/erq411
Cavalier-Smith T. Eukaryote kingdoms: seven or nine? Biosystems. 1981;14(3–4):461–481.
Delwiche CF, Palmer JD. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol Biol Evol. 1996;13(6):873–882.
Shibata M, Kashino Y, Satoh K, Koike H. Isolation and characterization of oxygen-evolving thylakoid membranes and photosystem II particles from a glaucocystophyte, Cyanophora paradoxa. Plant Cell Physiol. 2001;42(7):733–741. http://dx.doi.org/10.1093/pcp/pce092
Koike H, Shibata M, Yasutomi K, Kashino Y, Satoh K. Identification of photosystem I components from a glaucocystophyte, Cyanophora paradoxa: the PsaD protein has an N-terminal stretch homologous to higher plants. Photosynth Res. 2000;65(3):207–217. http://dx.doi.org/10.1023/A:1010734912776
Machida M, Takechi K, Sato H, Chung SJ, Kuroiwa H, Takio S, et al. Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss. Proc Natl Acad Sci USA. 2006;103(17):6753–6758. http://dx.doi.org/10.1073/pnas.0510693103
Takano H, Takechi K. Plastid peptidoglycan. Biochim Biophys Acta. 2010;1800(2):144–151. http://dx.doi.org/10.1016/j.bbagen.2009.07.020
Lockhart PJ, Howe CJ, Bryant DA, Beanland TJ, Larkum AWD. Substitutional bias confounds inference of cyanelle origins from sequence data. J Mol Evol. 1992;34(2):153–162. http://dx.doi.org/10.1007/BF00182392
Lockhart PJ, Penny D, Hendy MD, Howe CJ, Beanland TJ, Larkum AWD. Controversy on chloroplast origins. FEBS Lett. 1992;301(2):127–131. http://dx.doi.org/10.1016/0014-5793(92)81231-A
Okamoto N, Chantangsi C, Horák A, Leander BS, Keeling PJ. Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the hacrobia taxon nov. PLoS ONE. 2009;4(9):e7080. http://dx.doi.org/10.1371/journal.pone.0007080
Burki F, Shalchian-Tabrizi K, Minge M, Skjæveland Å, Nikolaev SI, Jakobsen KS, et al. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2007;2(8):e790. http://dx.doi.org/10.1371/journal.pone.0000790
Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol. 1999;46(4):327–338.
Reyes-Prieto A, Bhattacharya D. Phylogeny of nuclear-encoded plastid-targeted proteins supports an early divergence of glaucophytes within Plantae. Mol Biol Evol. 2007;24(11):2358–2361. http://dx.doi.org/10.1093/molbev/msm186
Qiu H, Yang EC, Bhattacharya D, Yoon HS. Ancient gene paralogy may mislead inference of plastid phylogeny. Mol Biol Evol. 2012;29(11):3333–3343. http://dx.doi.org/10.1093/molbev/mss137
Helmchen TA, Bhattacharya D, Melkonian M. Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids. J Mol Evol. 1995;41(2):203–210.
Yoon HS, Hackett JD, van Dolah FM, Nosenko T, Lidie KL, Bhattacharya D. Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol. 2005;22(5):1299–1308. http://dx.doi.org/10.1093/molbev/msi118
Yoon HS, Nakayama T, Reyes-Prieto A, Andersen RA, Boo SM, Ishida K, et al. A single origin of the photosynthetic organelle in different Paulinella lineages. BMC Evol Biol. 2009;9(1):98. http://dx.doi.org/10.1186/1471-2148-9-98
Falcón LI, Magallón S, Castillo A. Dating the cyanobacterial ancestor of the chloroplast. ISME J. 2010;4(6):777–783. http://dx.doi.org/10.1038/ismej.2010.2
Auch AF, Henz SR, Holland BR, Göker M. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics. 2006;7(1):350. http://dx.doi.org/10.1186/1471-2105-7-350
Nozaki H, Ohta N, Matsuzaki M, Misumi O, Kuroiwa T. Phylogeny of plastids based on cladistic analysis of gene loss inferred from complete plastid genome sequences. J Mol Evol. 2003;57(4):377–382. http://dx.doi.org/10.1007/s00239-003-2486-6
Sanchez-Puerta MV, Bachvaroff TR, Delwiche CF. Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids. Mol Phylogenet Evol. 2007;44(2):885–897. http://dx.doi.org/10.1016/j.ympev.2007.03.003
de Las Rivas J. Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res. 2002;12(4):567–583. http://dx.doi.org/10.1101/gr.209402
Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, et al. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr Biol. 2007;17(16):1420–1425. http://dx.doi.org/10.1016/j.cub.2007.07.036
Lopez P, Casane D, Philippe H. Heterotachy, an important process of protein evolution. Mol Biol Evol. 2002;19(1):1–7.
Vogl C, Badger J, Kearney P, Li M, Clegg M, Jiang T. Probabilistic analysis indicates discordant gene trees in chloroplast evolution. J Mol Evol. 2003;56(3):330–340. http://dx.doi.org/10.1007/s00239-002-2404-3
Ane C. Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol. 2005;22(4):914–924. http://dx.doi.org/10.1093/molbev/msi076
Whelan S, Blackburne BP, Spencer M. Phylogenetic substitution models for detecting heterotachy during plastid evolution. Mol Biol Evol. 2011;28(1):449–458. http://dx.doi.org/10.1093/molbev/msq215
Lockhart PJ, Steel MA, Barbrook AC, Huson DH, Charleston MA, Howe CJ. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol Biol Evol. 1998;15(9):1183–1188.
Lockhart P, Steel M. A tale of two processes. Syst Biol. 2005;54(6):948–951. http://dx.doi.org/10.1080/10635150500234682
Lockhart P. Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol. 2005;23(1):40–45. http://dx.doi.org/10.1093/molbev/msj005
Rice DW, Palmer JD. An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol. 2006;4(1):31. http://dx.doi.org/10.1186/1741-7007-4-31
Mackiewicz P, Bodył A, Moszczyński K. The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome. Mob Genet Elem. 2013;3(4):e25845. http://dx.doi.org/10.4161/mge.25845
Moszczynski K, Mackiewicz P, Bodyl A. Evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles. Mol Biol Evol. 2012;29(3):887–892. http://dx.doi.org/10.1093/molbev/msr276
Bachvaroff TR, Sanchez-Puerta MV, Delwiche CF. Chlorophyll c-containing plastid relationships based on analyses of a multigene data set with all four chromalveolate lineages. Mol Biol Evol. 2005;22(9):1772–1782. http://dx.doi.org/10.1093/molbev/msi172
Cuvelier ML, Allen AE, Monier A, McCrow JP, Messie M, Tringe SG, et al. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci USA. 2010;107(33):14679–14684. http://dx.doi.org/10.1073/pnas.1001665107
Hagopian JC, Reis M, Kitajima JP, Bhattacharya D, de Oliveira MC. 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. J Mol Evol. 2004;59(4):464–477. http://dx.doi.org/10.1007/s00239-004-2638-3
Janouskovec J, Horak A, Obornik M, Lukes J, Keeling PJ. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proc Natl Acad Sci USA. 2010;107(24):10949–10954. http://dx.doi.org/10.1073/pnas.1003335107
Janouškovec J, Horák A, Barott KL, Rohwer FL, Keeling PJ. Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Curr Biol. 2012;22(13):R518–R519. http://dx.doi.org/10.1016/j.cub.2012.04.047
Khan H, Parks N, Kozera C, Curtis BA, Parsons BJ, Bowman S, et al. Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Mol Biol Evol. 2007;24(8):1832–1842. http://dx.doi.org/10.1093/molbev/msm101
Kim E, Harrison JW, Sudek S, Jones MDM, Wilcox HM, Richards TA, et al. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proc Natl Acad Sci USA. 2011;108(4):1496–1500. http://dx.doi.org/10.1073/pnas.1013337108
Le Corguillé G, Pearson G, Valente M, Viegas C, Gschloessl B, Corre E, et al. Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids. BMC Evol Biol. 2009;9(1):253. http://dx.doi.org/10.1186/1471-2148-9-253
Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV. Gene transfer to the nucleus and the evolution of chloroplasts. Nature. 1998;393(6681):162–165. http://dx.doi.org/10.1038/30234
Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA. 2002;99(19):12246–12251. http://dx.doi.org/10.1073/pnas.182432999
Nelissen B, van de Peer Y, Wilmotte A, de Wachter R. An early origin of plastids within the cyanobacterial divergence is suggested by evolutionary trees based on complete 16S rRNA sequences. Mol Biol Evol. 1995;12(6):1166–1173.
Ohta N, Matsuzaki M, Misumi O, Miyagishima SY, Nozaki H, Tanaka K, et al. Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res. 2003;10(2):67–77. http://dx.doi.org/10.1093/dnares/10.2.67
Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol Biol Evol. 2007;24(1):54–62. http://dx.doi.org/10.1093/molbev/msl129
Sato N. Origin and evolution of plastids: genomic view on the unification and diversity of plastids. In: Wise RR, Hoober JK, editors. The structure and function of plastids. Dordrecht: Springer; 2006. p. 75–102. (Advances in photosynthesis and respiration). http://dx.doi.org/10.1007/978-1-4020-4061-0_4
Tengs T, Dahlberg OJ, Shalchian-Tabrizi K, Klaveness D, Rudi K, Delwiche CF, et al. Phylogenetic analyses indicate that the 19’Hexanoyloxy-fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin. Mol Biol Evol. 2000;17(5):718–729.
Wang Y, Joly S, Morse D. Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with red algal plastid genes. J Mol Evol. 2008;66(2):175–184. http://dx.doi.org/10.1007/s00239-008-9070-z
Baurain D, Brinkmann H, Petersen J, Rodriguez-Ezpeleta N, Stechmann A, Demoulin V, et al. Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Mol Biol Evol. 2010;27(7):1698–1709. http://dx.doi.org/10.1093/molbev/msq059
Minge MA, Silberman JD, Orr RJ, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, et al. Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc Biol Sci. 2009;276(1657):597–604. http://dx.doi.org/10.1098/rspb.2008.1358
Moreira D, Le Guyader H, Philippe H. The origin of red algae and the evolution of chloroplasts. Nature. 2000;405(6782):69–72. http://dx.doi.org/10.1038/35011054
Patron NJ, Inagaki Y, Keeling PJ. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol. 2007;17(10):887–891. http://dx.doi.org/10.1016/j.cub.2007.03.069
Tekle YI, Grant J, Cole JC, Nerad TA, Anderson OR, Patterson DJ, et al. A multigene analysis of Corallomyxa tenera sp. nov. suggests its membership in a clade that includes Gromia, Haplosporidia and Foraminifera. Protist. 2007;158(4):457–472. http://dx.doi.org/10.1016/j.protis.2007.05.002
Tekle YI, Parfrey LW, Katz LA. Molecular data are transforming hypotheses on the origin and diversification of eukaryotes. Bioscience. 2009;59(6):471–481. http://dx.doi.org/10.1525/bio.2009.59.6.5
DOI: https://doi.org/10.5586/asbp.2014.044
|
|
|