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The nucleomorph genomes of cryptophytes and chlorarachniophytes
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Membrane heredity, symbiogenesis, and the multiple origins of algae
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Membrane heredity and early chloroplast evolution
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Cavalier-Smith T: Membrane heredity and early chloroplast evolution. Trends Plant Sci 2000, 5:174-182. This paper explains the concepts of membrane heredity and genetic membranes, with special reference to the origin of chloroplasts and their lateral transfer during secondary symbiogenesis to form the more complex cells of chromalveolate and cabozoan algae.
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Trends Plant Sci
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A revised six-kingdom system of life
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The highly reduced genome of an enslaved algal nucleus
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Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG: The highly reduced genome of an enslaved algal nucleus. Nature 2001, 410:1091-1096. This paper presents the first full DNA sequence of a nucleomorph genome (that of the cryptomonad G. theta), the smallest nuclear genome completely sequenced. It shows that most nucleomorph genes are genetic housekeeping genes that are needed only to enable the expression of the 30 nucleomorph-encoded chloroplast protein genes and a handful of other end-product genes, notably a few transporter proteins.
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Nature
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Ultrastuctural studies on Bigelowiella natans, gen. et sp. nov., a chlorarachniophyte flagellate
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Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinofiagellate, and sporozoan plastid origins and the eukaryote family tree
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Cavalier-Smith T: Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinofiagellate, and sporozoan plastid origins and the eukaryote family tree. J Euk Microbiol 1999, 46:347-366.
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Translocation of proteins across the multiple membranes of complex plastids
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The secondary endosymbiont of the cryptomonad Guillardia theta contains alpha-, beta-, and gamma-tubulin genes
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Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph
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Zauner S, Fraunholz M, Wastl J, Penny S, Beaton M, Cavalier-Smith T, Maier UG, Douglas S: Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph. Proc Natl Acad Sci USA 2000, 97:200-205. Together with [5], this paper provides evidence for several centrosomal proteins encoded by the cryptomonad nucleomorph, making it highly probable that it divides mitotically. This is even though the authors of [12,13] could not detect microtubules ultrastructurally within dividing nuclei, in which the envelope does not break down (that is, nucleomorphs probably use closed mitosis like some red algae). This paper shows that the telomere sequences are less typical than in chlorarachnean nucleomorphs.
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Evidence for nucleomorph to host nucleus gene transfer: Light-harvesting complex proteins from cryptomonads and chlorarachniophytes
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Deane JA, Fraunholz M, Su V, Maier UG, Martin W, Durnford DG, McFadden GI: Evidence for nucleomorph to host nucleus gene transfer: light-harvesting complex proteins from cryptomonads and chlorarachniophytes. Protist 2000, 151:239-252. It had long been deduced that hundreds, possibly thousands, of genes must have been transferred from nucleomorphs into the host nucleus. The light-harvesting complex (LHC) proteins are the first well-studied example. The bipartite cryptomonad targeting sequences are more similar to those of heterokonts than alveolates, supporting chromist monophyly. This study provides the first evidence for bipartite targeting sequences in chlorarachneans and suggests that their LHC protein is more similar to that of Tetraselmis than those of higher plants, corroborating other evidence that both chlorarachnean and euglenoid plastids came from a green alga belonging to the infraphylum Tetraphytae, which includes Tetraselmis, Ulvophyceae, Trebouxiophyceae and Chlorophyceae [4].
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Analyses of RNA Polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang
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A cyanobacterial gene in nonphotosynthetic protists - An early chloroplast acquisition in eukaryotes?
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The structure and gene repertoire of an ancient red algal plastid genome
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Glockner G, Rosenthal A, Valentin K: The structure and gene repertoire of an ancient red algal plastid genome. J Mol Evol 2000, 51:382-390. This paper shows unique features of the Cyanidium chloroplast genome that are not shared with that of other red algae or chromalveolates. It supports the idea that Cyanidiophyceae should be a distinct red algal class and that the primary divergence within red algae was between them and the other unicellular class, Rhodellophyceae [4]. It also indicates that the red alga enslaved by the ancestral chromalveolate to form the cryptomonad nucleomorph and periplastid membrane was not derived from a cyanidiophyte, but from a more typical rhodellophyte red alga.
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(2000)
J Mol Evol
, vol.51
, pp. 382-390
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Glockner, G.1
Rosenthal, A.2
Valentin, K.3
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43
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0036208071
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The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa
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Cavalier-Smith T: The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002, 52:297-354. This paper revises the phagotrophy theory of the origin of eukaryotes in the light of evidence that no extant eukaryotes are primitively amitochondrial. It revises protozoan higher classification, formally establishing the new infrakingdoms Rhizaria and Excavata, and expanding the phylum Cercozoa (to which Chlorarachnea belong) by including the parasitic Ascetosporea. It names the ancestrally biciliate bikont clade, which includes plants, chromaIveolates, excavates and Rhizaria, arguing that their complex ciliary transformation indicates that they are derived compared with the putatively primitively uniciliate Amoebozoa and opisthokonts.
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(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 297-354
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Cavalier-Smith, T.1
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44
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0034903594
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Foraminifera and Cercozoa are related in actin phylogeny: Two orphans find a home?
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Keeling PJ: Foraminifera and Cercozoa are related in actin phylogeny: Two orphans find a home? Mol Biol Evol 2001, 18:1551-1557.
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(2001)
Mol Biol Evol
, vol.18
, pp. 1551-1557
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Keeling, P.J.1
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45
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0032955849
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Topology of Euglena chloroplast protein precursors within endoplasmic reticulum to Golgi to chloroplast transport vesicles
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Sulli C, Fang Z, Muchhal U, Schwartzbach SD: Topology of Euglena chloroplast protein precursors within endoplasmic reticulum to Golgi to chloroplast transport vesicles. J Biol Chem 1999, 274:457-463.
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(1999)
J Biol Chem
, vol.274
, pp. 457-463
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Sulli, C.1
Fang, Z.2
Muchhal, U.3
Schwartzbach, S.D.4
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46
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0032989696
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Diversification of a chimaeric algal group, the chlorarachniophytes: Phylogeny of nuclear and nucleomorph small subunit rRNA genes
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Ishida K, Green BR, Cavalier-Smith T: Diversification of a chimaeric algal group, the chlorarachniophytes: Phylogeny of nuclear and nucleomorph small subunit rRNA genes. Mol Biol Evol 1999, 16:321-331.
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(1999)
Mol Biol Evol
, vol.16
, pp. 321-331
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Ishida, K.1
Green, B.R.2
Cavalier-Smith, T.3
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47
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0034490505
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Endomembrane structure and the chloroplast protein targeting pathway in Heterosigma akashiwo (Raphidophyceae, Chromista)
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Ishida K, Cavalier-Smith T, Green BR: Endomembrane structure and the chloroplast protein targeting pathway in Heterosigma akashiwo (Raphidophyceae, Chromista). J Phycol 2000, 36:1135-1144.
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(2000)
J Phycol
, vol.36
, pp. 1135-1144
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Ishida, K.1
Cavalier-Smith, T.2
Green, B.R.3
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48
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0034980405
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Phylogenetic analysis of phagotrophic, photomorphic and osmotrophic euglenoids by using the nuclear 18S rDNA sequence
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Mullner AN, Angeler DG, Samuel R, Linton EW, Triemer RE: Phylogenetic analysis of phagotrophic, photomorphic and osmotrophic euglenoids by using the nuclear 18S rDNA sequence. Int J Syst Evol Microbiol 2001, 51:783-791.
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(2001)
Int J Syst Evol Microbiol
, vol.51
, pp. 783-791
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Mullner, A.N.1
Angeler, D.G.2
Samuel, R.3
Linton, E.W.4
Triemer, R.E.5
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49
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0037154314
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Chloroplast evolution: Secondary symbiogenesis and multiple losses
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Cavalier-Smith T: Chloroplast evolution: Secondary symbiogenesis and multiple losses. Curr Biol 2002, 12:R62-64.
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(2002)
Curr Biol
, vol.12
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Cavalier-Smith, T.1
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50
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0037025197
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Rooting the eukaryote tree by using a derived gene fusion
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Stechmann A, Cavalier-Smith T: Rooting the eukaryote tree by using a derived gene fusion. Science 2002, 297:89-91. This paper shows that a secondarily derived gene fusion between dihydrofolate reductase and thymidylate synthetase (TS) is present in all bikont eukaryotes so far studied. If this gene fusion has never been reversed, the eukaryotic root must lie between bikonts (plants, chromalveolates, cabozoa, Heliozoa and Apusozoa) and opisthokonts (animals, choanozoan protozoa and fungi), which lack the fusion. The position of Amoebozoa with respect to the root remains ambiguous because it is unknown whether TS genes arnplified from them are truly separate or part of a fusion gene that simply would not amplify. As previous deductions of the position of the root using outgroup rooting of sequence trees were flawed by long-branch artefacts, this is the strongest available evidence regarding its true position.
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(2002)
Science
, vol.297
, pp. 89-91
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Stechmann, A.1
Cavalier-Smith, T.2
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51
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0036095568
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Retortamonad flagellates are closely related to diplomonads - Implications for the history of mitochondrial function in eukaryote evolution
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Silberman JD, Simpson AG, Kulda J, Cepicka I, Hampl V, Johnson PJ, Roger AJ: Retortamonad flagellates are closely related to diplomonads - Implications for the history of mitochondrial function in eukaryote evolution. Mol Biol Evol 2002, 19:777-786. This paper provides the first rRNA sequence evidence for the position of retortamonads, showing that they are either sisters of or derived from diplomonads. This supports the monophyly of the protozoan superclass Eopharyngia (diplomonads plus retortamonads) [4] and means that, like all other established groups of amitochondrial eukaryotes, they must be secondarily amitochondrial. Thus, no amitochondrial eukaryotes are primitive.
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(2002)
Mol Biol Evol
, vol.19
, pp. 777-786
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Silberman, J.D.1
Simpson, A.G.2
Kulda, J.3
Cepicka, I.4
Hampl, V.5
Johnson, P.J.6
Roger, A.J.7
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