Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: Towards an automated reconstruction of the green algal tree of life

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Buchheim, Mark A ^a   Keller, Alexander ^b   Koetschan, Christian ^b   Förster, Frank ^b   Merget, Benjamin ^b   Wolf, Matthias ^b  

^a UNIVERSITY OF TULSA   (United States)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; INTERNAL TRANSCRIBED SPACER 2; RIBOSOME RNA;

ARTICLE; AUTOMATION; CHLOROPHYCEAE; CONTROLLED STUDY; DNA BARCODING; GENE CONSTRUCT; GENETIC VARIABILITY; GREEN ALGA; MOLECULAR PHYLOGENY; NEIGHBOR JOINING METHOD; NONHUMAN; PHYLUM; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TREBOUXIOPHYCEAE; TREE OF LIFE; ULVOPHYCEAE; CLASSIFICATION; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ALGAE; CHLOROPHYTA; EMBRYOPHYTA; TREBOUXIOPHYCEAE; ULVOPHYCEAE;

AUTOMATION; BASE SEQUENCE; CHLOROPHYTA; DNA BARCODING, TAXONOMIC; PHYLOGENY; RNA, RIBOSOMAL;

EID: 79951837282     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016931     Document Type: Article

References (115)

1. Wheeler QD, (2005) Losing the plot: DNA "barcodes" and taxonomy. Cladistics 21: 405-407.
2. Will KW, Mishler BD, Wheeler QD, (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54.
3. Ebach MC, Holdrege C, (2005) More Taxonomy, Not DNA Barcoding. BioScience 55: 823-824.
4. DeSalle R, Egan MG, Siddall M, (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society of London B Biological Sciences 360: 1905-1916.
5. Smith VS, (2005) DNA barcoding: Perspectives from a "Partnerships for Enhancing Expertise in Taxonomy" (PEET) debate. Systematic Biology 54: 841-844.
6. Holdrege C, Ebach MC, (2006) Response from Holdrege and Ebach: What about Taxa? Bioscience 56: 93.
7. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R, (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society of London B Biological Sciences 360: 1805-1811.
8. Hollingsworth ML, Clark AA, Forrest LL, Richardson J, Pennington RT, et al. (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Molecular Ecology Resources 9: 439-457.
9. Jakupciak JP, Colwell RR, (2009) Biological agent detection technologies. Molecular Ecology Resources 9: 51-57.
10. Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, et al. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society of London B Biological Sciences 360: 1935-1943.
11. Blaxter ML, (2004) The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society of London B Biological Sciences 359: 669-679.
12. Engelmann JC, Rahmann S, Wolf M, Schultz J, Fritzilas E, et al. (2009) Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources 9: 83-93.
13. Hebert PDN, Gregory TR, (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852-859.
14. Seberg O, Petersen G, (2009) How many loci does it take to DNA barcode a Crocus? PLoS ONE 4: e4598.
15. Chase MW, Fay MF, (2009) Barcoding of plants and fungi. Science 325: 682-683.
16. Wolf M, Schultz J, (2009) ITS better than its reputation. Science (E-Letter, 10 December 2009).
17. Buchheim MA, Kirkwood A, Buchheim JA, Verghese B, Henley WJ, (2010) Hypersaline soil supports a diverse community of Dunaliella (Chlorophyceae). Journal of Phycology 46: 1038-1047.
18. Buchheim MA, Buchheim JA, Carlson T, Braband A, Hepperle D, et al. (2005) Phylogeny of the Hydrodictyaceae (Chlorophyceae): Inferences from rDNA data. Journal of Phycology 41: 1039-1054.
19. Buchheim MA, Buchheim JA, Carlson T, Kugrens P, (2002) Phylogeny of Lobocharacium (Chlorophyceae) and allies: A study of 18S and 26S rDNA data. Journal of Phycology 38: 376-383.
20. Buchheim MA, Buchheim JA, Chapman RL, (1997) Phylogeny of the VLE-14 Chlamydomonas (Chlorophyceae) group. A study of 18S rRNA gene sequences. Journal of Phycology 33: 1024-1030.
21. Buchheim MA, Buchheim JA, Chapman RL, (1997) Phylogeny of Chloromonas (Chlorophyceae): A study of 18S ribosomal RNA gene sequences. Journal of Phycology 33: 286-293.
22. Buchheim MA, Chapman RL, (1991) Phylogeny of the colonial green flagellates: A study of 18S and 26S ribosomal RNA sequence data. BioSystems 25: 85-100.
23. Buchheim MA, Chapman RL, (1992) Phylogeny of Carteria (Chlorophyceae) inferred from molecular and organismal data. Journal of Phycology 28: 362-374.
24. Buchheim MA, Lemieux C, Otis C, Gutell RR, Chapman RL, et al. (1996) Phylogeny of the Chlamydomonadales (Chlorophyceae): A comparison of ribosomal RNA gene sequences from the nucleus and the chloroplast. Molecular Phylogenetics and Evolution 5: 391-402.
25. Buchheim MA, Michalopulos EA, Buchheim JA, (2001) Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: A study of 18S and 26S rDNA data. Journal of Phycology 37: 819-835.
26. Wolf M, Buchheim M, Hegewald E, Krienitz L, Hepperle D, (2002) Phylogenetic position of the Sphaeropleaceae (Chlorophyta). Plant Systematics and Evolution 230: 161-171.
27. 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.
28. Krienitz L, Hegewald EH, Hepperle D, Huss VAR, Rohr T, et al. (2004) Phylogenetic relationship of Chlorella and Parachlorella gen. nov. (Chlorophyta, Trebouxiophyceae). Phycologia 43: 529-542.
29. Wolf M, Hepperle D, Krienitz L, (2003) On the phylogeny of Radiococcus, Planktosphaeria and Schizochlamydella (Radiococcaceae, Chlorophyta). Biologia 58: 759-765.
30. Wolf M, Hegewald E, Hepperle D, Krienitz L, (2003) Phylogenetic position of the Golenkiniaceae (Chlorophyta) as inferred from 18S rDNA sequence data. Biologia 58: 433-436.
31. Wolf M, Krienitz L, Hepperle D, (2002) Phylogenetic position of Actinastrum hantzschii Lagerheim 1882 (Chlorophyta, Trebouxiophyceae). Algological Studies 104: 59-67.
32. Hegewald E, Wolf M, (2003) Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons. Plant Systematics and Evolution 241: 185-191.
33. Hegewald E, Hanagata N, (2000) Phylogenetic studies on Scenedesmaceae (Chlorophyta). Archiv für Hydrobiologie Supplement 136: 29-49.
34. Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L, (2010) ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus. Phycologia 49: 325-335.
35. Müller T, Philippi N, Dandekar T, Schultz J, Wolf M, (2007) Distinguishing species. RNA 13: 1469-1472.
36. An SS, Friedl T, Hegewald E, (1999) Phylogenetic relationships of Scenedesmus and Scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons. Plant Biology 1: 418-428.
37. Bakker FT, Olsen JL, Stam WT, (1995) Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta). Journal of Molecular Evolution 40: 640-651.
38. Coat G, Dion P, Noailles MC, De Reviers B, Fontaine JM, et al. (1998) Ulva armoricana (Ulvales, Chlorophyta) from the coasts of Brittany (France): II. Nuclear rDNA ITS sequence analysis. European Journal of Phycology 33: 81-86.
39. Coleman AW, (2001) Biogeography and speciation in the Pandorina/Volvulina (Chlorophyta) superclade. Journal of Phycology 37: 836-851.
40. Fabry S, Koehler A, Coleman AW, (1999) Intraspecies analysis: Comparison of ITS sequence data and gene intron sequence data with breeding data for a worldwide collection of Gonium pectorale. Journal of Molecular Evolution 48: 94-101.
41. Lewis LA, Flechtner VR, (2004) Cryptic species of Scenedesmus (Chlorophyta) from desert soil communities of Western North America. Journal of Phycology 40: 1127-1137.
42. Pillmann A, Woolcott GW, Olsen JL, Stam WT, King RJ, (1997) Inter- and intraspecific genetic variation in Caulerpa (Chlorophyta) based on nuclear rDNA ITS sequences. European Journal of Phycology 32: 379-386.
43. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madrinan S, et al. (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295-299.
44. Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, et al. (2005) Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society of London B Biological Sciences 360: 1889-1895.
45. Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, et al. (2008) Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well. PLoS ONE 3: e2802.
46. Kress WJ, Erickson DL, (2007) A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLoS One 2: Article No.: e508.
47. Newmaster SG, Fazekas AJ, Ragupathy S, (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany 84: 335-341.
48. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH, (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369-8374.
49. Ledford H, (2008) Botanical identities: DNA barcoding for plants comes a step closer. Nature 451: 616.
50. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106: 12794-12797.
51. Chen S, Yao H, Han J, Liu C, Song J, et al. (2010) Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS ONE 5: e8613.
52. Sanders ER, Karol KG, McCourt RM, (2003) Occurrence of matK in a trnK group II intron in Charophyte green algae and phylogeny of the Characeae. American Journal of Botany 90: 628-633.
53. Lemieux C, Otis C, Turmel M, (2000) Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 403: 649-652.
54. Turmel M, Otis C, De Cambiaire J-C, Pombert J-F, Lemieux C, (2002) The complete chloroplast DNA sequence of Chlorokybus atmophyticus: evidence that charophycean green algae from an early-diverging lineage adapted to terrestrial life. Botany 2002. Madison, WI.
55. Nozaki H, (2001) Chloroplast multigene phylogeny and systematics of the advanced genera of the Volvocaceae (Chlorophyceae). Phycologia 40: 37.
56. Nozaki H, Misawa K, Kajita T, Kato M, Nohara S, et al. (2000) Origin and evolution of the colonial Volvocales (Chlorophyceae) as inferred from multiple, chloroplast gene sequences. Molecular Phylogenetics and Evolution 17: 256-268.
57. Nozaki H, Motomi I, Ryosuke S, Hidenobu U, Makoto MW, et al. (1995) Phylogenetic relationships within the colonial Volvocales (Chlorophyta) inferred from rbcL gene sequence data. Journal of Phycology 31: 970-979.
58. Nozaki H, Ohta N, Takano H, Watanabe MM, (1999) Reexamination of phylogenetic relationships within the colonial Volvocales (Chlorophyta): An analysis of atpB and rbcL gene sequences. Journal of Phycology 35: 104-112.
59. White TJ, Bruns T, Lee S, Taylor J, (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR Protocols San Diego Academic Press pp. 315-322.
60. Mai JC, Coleman AW, (1997) The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. Journal of Molecular Evolution 44: 258-271.
61. Coleman AW, (2003) ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics 19: 370-375.
62. Coleman AW, (2007) Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research 35: 3322-3329.
63. Hershkovitz MA, Lewis LA, (1996) Deep-level diagnostic value of the rDNA-ITS region. Molecular Biology and Evolution 13: 1276-1295.
64. Schultz J, Maisel S, Gerlach D, Müller T, Wolf M, (2005) A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11: 361-364.
65. Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, et al. (2006) The internal transcribed spacer 2 database- a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research 34: W704-W707.
66. Schultz J, Wolf M, (2009) ITS2 sequence-structure analysis in phylogenetics: A how-to manual for molecular systematics. Molecular Phylogenetics and Evolution 52: 520-523.
67. Wolf M, Achtziger M, Schultz J, Dandekar T, Müller T, (2005) Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA 11: 1616-1623.
68. Keller A, Förster F, Müller T, Dandekar T, Schultz J, et al. (2010) Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct 5: 4.
69. Wiemers M, Keller A, Wolf M, (2009) ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus). BMC Evolutionary Biology 9: 300.
70. Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M, (2006) 4SALE- A tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7: 498.
71. Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T, (2008) ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics 24: 2401-2402.
72. Müller T, Rahmann S, Dandekar T, Wolf M, (2004) Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology 4: 20.
73. Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, et al. (2010) The ITS2 Database III- sequences and structures for phylogeny. Nucleic Acids Research 38: D275-279.
74. Friedrich J, Dandekar T, Wolf M, Müller T, (2005) ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics 21: 2108-2109.
75. Rahmann S, Müller, T, Dandekar, T, Wolf, M, (2006) Efficient and robust analysis of large phylogenetic datasets. In: Hsu H-H, editors. Advanced Data Mining Technologies in Bioinformatics Hershey, PA Idea Group, Inc pp. 104-117.
76. Angeler DG, Schagerl M, Coleman AW, (1998) Does the infraspecific disjunct occurrence of the carotenoid loroxanthin reflect phylogenetical relationships within syngens of Pandorina morum (Volvocales, Chlorophyta)? Biologia 53: 567-575.
77. Angeler DG, Schagerl M, Coleman AW, (1999) Phylogenetic relationships among isolates of Eudorina species (Volvocales, Chlorophyta) inferred from molecular and biochemical data. Journal of Phycology 35: 815-823.
78. Coleman AW, Mai JC, (1997) Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness. Journal of Molecular Evolution 45: 168-177.
79. Coleman AW, (2009) Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution 50: 197-203.
80. Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, et al. (2008) ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evolutionary Biology 8: 218.
81. McManus HA, Lewis LA, (2005) Molecular phylogenetics, morphological variation and colony-form evolution in the family Hydrodictyaceae (Sphaeropleales, Chlorophyta). Phycologia 44: 582-595.
82. Pocock T, Lachance M-A, Pröschold T, Priscu JC, Kim SS, et al. (2004) Identification of a psychrophilic green alga from Lake Bonney Antarctica: Chlamydomonas raudensis Ettl. (UWO 241) Chlorophyceae. Journal of Phycology 40: 1138-1148.
83. van Hannen EJ, Fink P, Lurling M, (2002) A revised secondary structure model for the internal transcribed spacer 2 of the green algae Scenedesmus and Desmodesmus and its implication for the phylogeny of these algae. European Journal of Phycology 37: 203-208.
84. Friedl T, (1996) Evolution of the polyphyletic genus Pleurastrum (Chlorophyta): Inferences from nuclear-encoded ribosomal DNA sequences and motile cell ultrastructure. Phycologia 35: 456-469.
85. Hepperle D, Hegewald E, Krienitz L, (2000) Phylogenetic position of the Oocystaceae (Chlorophyta). Journal of Phycology 36: 590-595.
86. Nakada T, Misawa K, Nozaki H, (2008) Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses. Molecular Phylogenetics and Evolution 48: 281-291.
87. Pröschold T, Marin B, Schloesser UG, Melkonian M, (2001) Molecular phylogeny and taxonomic revision of Chlamydomonas (chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist 152: 265-300.
88. Mei H, Liu G-X, Hu Z-Y, (2007) Phylogenetic studies of Oedogoniales (Chlorophyceae, Chlorophyta) based on 28S rDNA sequences. Acta Hydrobiologica Sinica 31: 492-498.
89. Leliaert F, Rousseau F, de Reviers B, Coppejans E, (2003) Phylogeny of the Cladophorophyceae (Chlorophyta) inferred from partial LSU rRNA gene sequences: Is the recognition of a separate order Siphonocladales justified? European Journal of Phycology 38: 233-246.
90. Nakazawa A, Yamada T, Nozaki H, (2004) Taxonomic study of Asterococcus (Chlorophyceae) based on comparative morphology and rbcL gene sequences. Phycologia 43: 711-721.
91. Loughnane CJ, McIvor LM, Rindi F, Stengel DB, Guiry MD, (2008) Morphology, rbcL phylogeny and distribution of distromatic Ulva (Ulvophyceae, Chlorophyta) in Ireland and southern Britain. Phycologia 47: 416-429.
92. Nozaki H, (2003) Origin and evolution of the genera Pleodorina and Volvox (Volvocales). Biologia 58: 425-431.
93. Nozaki H, Misumi O, Kuroiwa T, (2003) Phylogeny of the quadriflagellate Volvocales (Chlorophyceae) based on chloroplast multigene sequences. Molecular Phylogenetics and Evolution 29: 58-66.
94. Zechman FW, (2003) Phylogeny of the Dasycladales (Chlorophyta, Ulvophyceae) based on analyses of RUBISCO large subunit (rbcL) gene sequences. Journal of Phycology 39: 819-827.
95. Yao H, Song J, Liu C, Luo K, Han J, et al. (2010) Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5: e13102.
96. Edlind TD, Sharetsky C, Cha ME, (1990) Ribosomal RNA of the primitive eukaryote Giardia lamblia: large subunit domain I and potential processing signals. Gene 96: 289-293.
97. Zimmer EA, Martin SL, Beverly SM, Kan YW, Wilson AC, (1980) Rapid duplication and loss of genes coding for the α chains of hemoglobin. Proceedings of the National Academy of Sciences of the United States of America 77: 2518-2162.
98. Arnheim N, (1983) Concerted evolution of multigene families. In: Nei M, Koehn M, editors. Evolution of Genes and Proteins Sunderland, MA Sinauer Associates pp. 38-61.
99. Harpke D, Peterson A, (2006) Non-concerted ITS evolution in Mammillaria (Cactaceae). Molecular Phylogenetics and Evolution 41: 579-593.
100. Famà P, Olsen JL, Stam WT, Procaccini G, (2000) High levels of intra- and inter-individual polymorphism in the rDNA ITS1 of Caulerpa recemosa (Chlorophyta). European Journal of Phycology 35: 349-356.
101. Feliner GN, Rosseló JA, (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44: 911-919.
102. Gile GH, Stern RF, James ER, Keeling PJ, (2010) DNA Barcoding of the Chlorarachniophytes using nucleomorph ITS sequences. Journal of Phycology 46: 743-750.
103. Chase MW, Fay MF, (2009) Response to J. Schultz and M. Wolf's E-Letter. Science Online.
104. Chase MW, Knapp S, Cox AV, Clarkson JJ, Butsko Y, et al. (2003) Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae). Annals of Botany (London) 92: 107-127.
105. Harpke D, Peterson A, (2008) 5.8S motifs for the identification of pseudogenic ITS regions. Botany 86: 300-305.
106. Kapraun DF, (1993) Karyology of marine green algae. Phycologia 32: 1-21.
107. Kapraun DF, (1994) Cytophotometric estimation of nuclear DNA contents in thirteen species of the Caulerpales (Chlorophyta). Cryptogamic Botany 4: 410-418.
108. Kapraun DF, Buratti JR, (1998) Evolution of genome size in the Dasycladales (Chlorophyta) as determined by DAPI cytophotometry. Phycologia 37: 176-183.
109. Durand C, Manuel M, Boudouresque CF, Meinesz A, Verlaque M, et al. (2002) Molecular data suggest a hybrid origin for the invasive Caulerpa recemosa (Caulerpales, Chlorophyta) in the Mediterranean Sea. Journal of Evolutionary Biology 15: 122-133.
110. Verbruggen H, De Clerck O, Schils T, Kooistra WHCF, Coppejans E, (2005) Evolution and phylogeography of Halimeda section Halimeda (Bryopsidales, Chlorophyta). Molecular Phylogenetics and Evolution 37: 789-803.
111. Selig C, Wolf M, Müller T, Dandekar T, Schultz J, (2008) The ITS2 Database II: homology modeling RNA structure for molecular systematics. Nucleic Acids Research 36: D377-380.
112. Seibel P, Müller T, Dandekar T, Wolf M, (2008) Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes 1: 91.
113. Rambaut A, (2009) FigTree v1.2.3. Program distributed by the author.
114. Price MN, Dehal PS, Arkin AP, (2010) FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
115. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.