Analysis of a plastid multigene data set and the phylogenetic position of the marine macroalga caulerpa filiformis (chlorophyta)

Journal of Phycology

Volumn 45, Issue 5, 2009, Pages 1206-1212

  Zuccarello, G C ^a   Price, Natalie ^a   Verbruggen, Heroen ^b   Leliaert, Frederik ^b  

^a VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Caulerpa; Chlorophyta; Chloroplast genome; Phylogenetics; Systematics; Ulvophyceae

Indexed keywords

ALGAE; CAULERPA; CAULERPA FILIFORMIS; CHLORELLA (CHLORELLALES); CHLORELLA (PRASIOLALES); CHLORELLA (UNCLASSIFIED CHLOROPHYCEAE); CHLORELLA (UNCLASSIFIED TREBOUXIOPHYCEAE); CHLOROPHYCEAE; CHLOROPHYTA; OLTMANNSIELLOPSIS; PSEUDENDOCLONIUM; TREBOUXIOPHYCEAE; ULVOPHYCEAE;

EID: 70350169819     PISSN: 00223646     EISSN: 15298817     Source Type: Journal    
DOI: 10.1111/j.1529-8817.2009.00731.x     Document Type: Article

References (54)

1. Adachi, J., Waddell, P. J., Martin, W. Hasegawa, M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50 : 348 358.
2. Bremer, K. 1985. Summary of green plant phylogeny and classification. Cladistics 1 : 369 385.
3. de Cambiaire, J. C., Otis, C., Turmel, M. Lemieux, C. 2007. The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae. BMC Genomics 8 : 213.
4. Cavalier-Smith, T. 1981. Eukaryote kingdoms: seven or nine? Biosystems 14 : 461 481.
5. Chihara, M., Inouye, I. Takahata, N. 1986. Oltmannsiellopsis, a new genus of marine flagellate (Dunaliellaceae, Chlorophyceae). Arch. Protistenkd. 132 : 313 324.
6. Duminil, J., Grivet, D., Ollier, S., Jeandroz, S. Petit, R. J. 2008. Multilevel control of organelle DNA sequence length in plants. J. Mol. Evol. 66 : 405 415.
7. Famà, P., Wysor, B., Kooistra, W. H. C. F. Zuccarello, G. C. 2002. Molecular phylogeny of the genus Caulerpa (Caulerpales, Chlorophyta) inferred from chloroplast tufA gene. J. Phycol. 38 : 1040 1050.
8. Floyd, G. L. O'Kelly, C. J. 1990. Phylum Chlorophyta: class Ulvophyceae. In Margulis, L., Corliss, J. O., Melkonian, M. Chapman, D. J. [Eds.] Handbook of Protoctista. Jones and Bartlett Publishers, Boston, pp. 17 635.
9. Friedl, T. 1995. Inferring taxonomic positions and testing genus level assignments in coccoid green lichen algae: a phylogenetic analysis of 18S ribosomal RNA sequences from Dictyochloropsis reticulata and from members of the genus Myrmecia (Chlorophyta, Trebouxiophyceae cl. nov.). J. Phycol. 31 : 632 639.
10. Friedl, T. O'Kelly, C. J. 2002. Phylogenetic relationships of green algae assigned to the genus Planophila (Chlorophyta): evidence from 18S rDNA sequence data and ultrastructure. Eur. J. Phycol. 37 : 373 384.
11. Guillou, L., Eikrem, W., Chretiennot-Dinet, M. J., Le Gall, F., Massana, R., Romari, K., Pedros-Alio, C. Vaulot, D. 2004. Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist 155 : 193 214.
12. Guindon, S. Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 : 696 704.
13. Hargraves, P. E. Steele, R. L. 1980. Morphology and ecology of Oltmannsiella virida, sp. nov. (Chlorophyceae: Volvocales). Phycologia 19 : 96 102.
14. Heath, T. A., Hedtke, S. M. Hillis, D. M. 2008. Taxon sampling and the accuracy of phylogenetic analyses. J. Syst. Ecol. 46 : 239 257.
15. Hillis, D. M., Pollock, D. D., McGuire, J. A. Zwickl, D. J. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52 : 124 126.
16. van den Hoek, C., Mann, D. G. Jahns, H. M. 1995. Algae. An Introduction to Phycology. Cambridge University Press, Cambridge, UK, 623 pp.
17. Jobb, G., von Haeseler, A. Strimmer, K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4 : 18.
18. Koch, M. A., Dobes, C., Kiefer, C., Schmickl, R., Klimes, L. Lysak, M. A. 2007. Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. Mol. Biol. Evol. 24 : 63 73.
19. Krienitz, L., Hegewald, E., Hepperle, D. Wolf, M. 2003. The systematics of coccoid green algae: 18S rRNA gene sequence data versus morphology. Biologia 58 : 437 446.
20. Lehman, R. L. Manhart, J. R. 1997. A preliminary comparison of restriction fragment patterns in the genus Caulerpa (Chlorophyta) and the unique structure of the chloroplast genome in Caulerpa sertularioides. J. Phycol. 33 : 1055 1062.
21. Lemieux, C., Otis, C. Turmel, M. 2007. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol. 5 : 2.
22. Lewis, L. A. McCourt, R. M. 2004. Green algae and the origin of land plants. Am. J. Bot. 91 : 1535 1556.
23. Lokhorst, G. M., Star, W. Zuccarello, G. C. 2004. New genus Koliellopsis (Trebouxiophyceae, Chlorophyta): its phylogenetic position inferred from ultrastructure and nuclear ribosomal DNA sequences. Phycol. Res. 52 : 235 243.
24. Lopez-Bautista, J. M. Chapman, R. L. 2003. Phylogenetic affinities of the Trentepohliales inferred from small-subunit rDNA. Int. J. Syst. Evol. Microbiol. 53 : 2099 2106.
25. Lowe, T. M. Eddy, S. R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 : 955 964.
26. Manhart, J. R., Kelly, K., Dudock, B. S. Palmer, J. D. 1989. Unusual characteristics of Codium fragile chloroplast revealed by physical and gene mapping. Mol. Gen. Genet. 216 : 417 421.
27. Mattox, K. R. Stewart, K. D. 1984. Classification of the green algae: a concept based on comparative cytology. In Irvine, D. E. G. John, D. M. [Eds.] The Systematics of the Green Algae. Academic Press, London, pp. 29 72.
28. Nakayama, T., Suda, S., Kawachi, M. Inouye, I. 2007. Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov. Phycologia 46 : 680 697.
29. O'Kelly, C. J. Floyd, G. L. 1984. Flagellar apparatus absolute orientations and the phylogeny of the green algae. Biosystems 16 : 227 251.
30. O'Kelly, C. J., Wysor, B. Bellows, W. K. 2004. Gene sequence diversity and the phylogenetic position of algae assigned to the genera Phaeophila and Ochlochaete (Ulvophyceae, Chlorophyta). J. Phycol. 40 : 789 799.
31. Palmer, J. D. 1986. Isolation and structural analysis of chloroplast DNA. Methods Enzymol. 118 : 167 186.
32. Pombert, J. F., Lemieux, C. Turmel, M. 2006. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biol. 4 : 3.
33. Pombert, J. F., Otis, C., Lemieux, C. Turmel, M. 2004. The complete mitochondrial DNA sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the Chlorophyta and suggests a sister-group relationship between the Ulvophyceae and Chlorophyceae. Mol. Biol. Evol. 21 : 922 935.
34. Pombert, J. F., Otis, C., Lemieux, C. Turmel, M. 2005. Chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol. Biol. Evol. 22 : 1903 1918.
35. Pröschold, T. Leliaert, F. 2007. Systematics of the green algae: conflict of classic and modern approaches. In Brodie, J. Lewis, J. [Eds.] Unravelling the Algae: The Past, Present and Future of the Algae Systematics. CRC Press, Taylor & Francis, Boca Raton, Florida, pp. 123 153.
36. Provan, J., Murphy, S. Maggs, C. A. 2004. Universal plastid primers for Chlorophyta and Rhodophyta. Eur. J. Phycol. 39 : 43 50.
37. Rambaut, A. 1996. Se-Al: Sequence Alignment Editor. Available at http://evolve.zoo.ox.ac.uk/ (accessed 9 August 2002).
38. Robbens, S., Derelle, E., Ferraz, C., Wuyts, J., Moreau, H. Van de Peer, Y. 2007. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol. Biol. Evol. 24 : 956 968.
39. Ronquist, F. Huelsenbeck, J. P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 : 1572 1574.
40. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 : 492 508. (Pubitemid 35180700)
41. Shimodaira, H. Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 : 1114 1116.
42. Shimodaira, H. Hasegawa, M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 : 1246 1247.
43. Sluiman, H. J. 1989. The green algal class Ulvophyceae: an ultrastructural survey and classification. Cryptogam. Bot. 1 : 83 94.
44. Stam, W. T., Olsen, J. L., Zaleski, S. F., Murray, S. N., Brown, K. R. Walters, L. J. 2006. A forensic and phylogenetic survey of Caulerpa species (Caulerpales, Chlorophyta) from the Florida coast, local aquarium shops, and e-commerce: establishing a proactive baseline for early detection. J. Phycol. 42 : 1113 1124.
45. Steane, D. A. 2005. Complete nucleotide sequence of the chloroplast genome from the Tasmanian blue gum, Eucalyptus globulus (Myrtaceae). DNA Res. 12 : 215 220.
46. Steinkötter, J., Bhattacharya, D., Semmelroth, I., Bibeau, C. Melkonian, M. 1994. Prasionophytes form independent lineages within the Chlorophyta - evidence from ribosomal RNA sequence comparison. J. Phycol. 30 : 340 345.
47. Tsuji, S., Ueda, K., Nishiyama, T., Hasebe, M., Yoshikawa, S., Konagaya, A., Nishiuchi, T. Yamaguchi, K. 2007. The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses. J. Plant. Res. 120 : 281 290.
48. Turmel, M., Brouard, J. S., Gagnon, C., Otis, C. Lemieux, C. 2008. Deep division in the Chlorophyceae (Chlorophyta) revealed by chloroplast phylogenomic analyses. J. Phycol. 44 : 739 750.
49. Turmel, M., Otis, C. Lemieux, C. 1999. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc. Natl. Acad. Sci. U. S. A. 96 : 10248 10253.
50. Wakasugi, T., Nagai, T., Kapoor, M., Sugita, M., Ito, M., Ito, S., Tsudzuki, J., et al. 1997. Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc. Natl. Acad. Sci. U. S. A. 94 : 5967 5972.
51. Watanabe, S. Nakayama, T. 2007. Ultrastructure and phylogenetic relationships of the unicellular green algae Ignatius tetrasporus and Pseudocharacium americanum (Chlorophyta). Phycol. Res. 55 : 1 16.
52. Yang, Z. 2007. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol. Biol. Evol. 24 : 1586 1591.
53. Zechman, F. W., Theriot, E. C., Zimmer, E. A. Chapman, R. L. 1990. Phylogeny of the Ulvophyceae (Chlorophyta): cladistic analysis of nuclear-encoded rRNA sequence data. J. Phycol. 26 : 700 710.
54. Zuccarello, G. C. Lokhorst, G. M. 2005. Molecular phylogeny of the genus Tribonema (Xanthophyceae) using rbcL gene sequence data: monophyly of morphologically simple algal species. Phycologia 44 : 384 392.