Multiple Gene Phylogenies Support the Monophyly of Cryptomonad and Haptophyte Host Lineages

Current Biology

Volumn 17, Issue 10, 2007, Pages 887-891

  Patron, Nicola J ^a,b   Inagaki, Yuji ^c   Keeling, Patrick J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

EVO_ECOL

Indexed keywords

ALGAL PROTEIN;

ALGA; ARTICLE; CLASSIFICATION; CRYPTOPHYTA; EXPRESSED SEQUENCE TAG; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PLASTID; RED ALGA; SYMBIOSIS;

ALGAE; ALGAE, RED; ALGAL PROTEINS; CRYPTOPHYTA; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASTIDS; SYMBIOSIS;

ALGAE; CRYPTOPHYTA; EUKARYOTA; GUILLARDIA THETA; HAPTOPHYCEAE; RHODOPHYTA;

EID: 34247899047     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2007.03.069     Document Type: Article

References (39)

1. Falkowski P.G., Katz M.E., Knoll A.H., Quigg A., Raven J.A., Schofield O., and Taylor F.J. The evolution of modern eukaryotic phytoplankton. Science 305 (2004) 354-360
2. Douglas S., Zauner S., Fraunholz M., Beaton M., Penny S., Deng L.T., Wu X., Reith M., Cavalier-Smith T., and Maier U.G. The highly reduced genome of an enslaved algal nucleus. Nature 410 (2001) 1091-1096
3. Patron N.J., Rogers M.B., and Keeling P.J. Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Euk. Cell 3 (2004) 1169-1175
4. Rice D.W., and Palmer J.D. 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. 4 (2006) 31
5. Yoon H.S., Hackett J.D., Pinto G., and Bhattacharya D. The single, ancient origin of chromist plastids. Proc. Natl. Acad. Sci. USA 99 (2002) 15507-15512
6. Bachvaroff T.R., Sanchez Puerta M.V., and Delwiche C.F. Chlorophyll c-containing plastid relationships based on analyses of a multigene data set with all four chromalveolate lineages. Mol. Biol. Evol. 22 (2005) 1772-1782
7. Bodyl A. Do plastid-related characteristics support the chromalveolate hypothesis?. J. Phycol. 41 (2005) 712
8. Cavalier-Smith T. A revised six-kingdom system of life. Biol. Rev. Camb. Philos. Soc. 73 (1998) 203-266
9. Dougherty E.C., and Allen M.B. Is pigmentation a clue to protistan phylogeny?. In: Allen M.B. (Ed). Comparative Biochemistry of Photoreactive Systems (1960), Academic Press, New York 129-144
10. Douglas S.E., Murphy C.A., Spencer D.F., and Gray M.W. Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature 350 (1991) 148-151
11. Bhattacharya D., and 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. 31 (1997) 439-446
12. Cavalier-Smith T., Allsopp M.T., and Chao E.E. Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?. Proc. Natl. Acad. Sci. USA 91 (1994) 11368-11372
13. Harper J.T., and Keeling P.J. Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol. 20 (2003) 1730-1735
14. Keeling P.J., Deane J.A., Hink-Schauer C., Douglas S.E., Maier U.G., and McFadden G.I. The secondary endosymbiont of the cryptomonad Guillardia theta contains alpha-, beta-, and gamma-tubulin genes. Mol. Biol. Evol. 16 (1999) 1308-1313
15. Liaud M.F., Brandt U., Scherzinger M., and Cerff R. Evolutionary origin of cryptomonad microalgae: two novel chloroplast/cytosol-specific GAPDH genes as potential markers of ancestral endosymbiont and host cell components. J. Mol. Evol. 44 Suppl 1 (1997) S28-S37
16. Fast N.M., Kissinger J.C., Roos D.S., and Keeling P.J. Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids. Mol. Biol. Evol. 18 (2001) 418-426
17. Cavalier-Smith T. Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Philos. Trans. R. Soc. Lond. B Biol. Sci. 358 (2003) 109-133
18. Palmer J.D. The symbiotic birth and spread of plastids: how many times and whodunit?. J. Phycol. 39 (2004) 4-11
19. Parfrey L.W., Barbero E., Lasser E., Dunthorn M., Bhattacharya D., Patterson D.J., and Katz L.A. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet. 2 (2006) e220 10.1371/journal.pgen.0020220
20. Rodriguez-Ezpeleta N., Brinkmann H., Burey S.C., Roure B., Burger G., Loffelhardt W., Bohnert H.J., Philippe H., and Lang B.F. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr. Biol. 15 (2005) 1325-1330
21. Jeffroy O., Brinkmann H., Delsuc F., and Philippe H. Phylogenomics: the beginning of incongruence?. Trends Genet. 22 (2006) 225-231
22. Rokas A., Williams B.L., King N., and Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425 (2003) 798-804
23. Patron N.J., Waller R.F., and Keeling P.J. A tertiary plastid uses genes from two endosymbionts. J. Mol. Biol. 357 (2006) 1373-1382
24. Delsuc F., Brinkmann H., and Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6 (2005) 361-375
25. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
26. Pupko T., Huchon D., Cao Y., Okada N., and Hasegawa M. Combining multiple data sets in a likelihood analysis: which models are the best?. Mol. Biol. Evol. 19 (2002) 2294-2307
27. Simpson A.G., Inagaki Y., and Roger A.J. Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol. Biol. Evol. 23 (2006) 615-625
28. Takishita K., Inagaki Y., Tsuchiya M., Sakaguchi M., and Maruyama T. A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, α-tubulin, and β-tubulin). Gene 362 (2005) 153-160
29. Cavalier-Smith T. The tiny enslaved genome of a rhizarian alga. Proc. Natl. Acad. Sci. USA 103 (2006) 9379-9380
30. Okamoto N., and 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 156 (2005) 163-179
31. Kim E., Simpson A.G., and Graham L.E. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol. Biol. Evol. 23 (2006) 2455-2466
32. Not F., Valentin K., Romari K., Lovejoy C., Massana R., Tobe K., Vaulot D., and Medlin L.K. Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315 (2007) 253-255
33. Okamoto N., and Inouye I. Hatena arenicola gen. et sp. nov., a katablepharid undergoing probable plastid acquisition. Protist 157 (2006) 401-419
34. McFadden G.I., Gilson P.R., and Hill D.R.A. Goniomonas: rRNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur. J. Phycol. 29 (1994) 29-32
35. Rogers M.B., Gilson P.R., Su V., McFadden G.I., and Keeling P.J. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol. Biol. Evol. 24 (2007) 54-62
36. Waller R.F., Patron N.J., and Keeling P.J. Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra. Int. J. Syst. Evol. Microbiol. 56 (2006) 1439-1447
37. Hillis D.M., Pollock D.D., McGuire J.A., and Zwickl D.J. Is sparse taxon sampling a problem for phylogenetic inference?. Syst. Biol. 52 (2003) 124-126
38. Rokas A., and Carroll S.B. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22 (2005) 1337-1344
39. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W., and Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21 (2004) 1740-1752