Phylogeny and molecular evolution of green algae - Phycology ...

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PHYLOGENY OF GREEN ALGAE 41 Table S3. Primer sequences used for PCR amplification and sequencing. Primers were found in literature, adapted from existing primers or based on aligned Genbank sequence of green algae and land plants (Viridiplantae), often complemented with a Cladophora coelothrix cDNA sequence. Primer name Primer sequence (5’-3’) Primers based on Actin Actin_F GAC ATG GAR AAR ATN TGG CAC CAC AC 244F; An et al. (1999) Actin_R ATC CAC ATC TGY TGA AAR GTR G Ac3-R; Bhattacharya, Stickes, and Sogin (1993) Ac3-R GAA GCA YTT GCG RTG SAC RAT Bhattacharya, Stickes, and Sogin (1993) Fern5-F CTT GTY TGY GAC AAT GGA TCW GGA ATG GT An et al. (1999) Glucose-6-phosphate isomerase G6PI_F TTY GCR TTY TGG GAC TGG G Ostreococcus and land plants G6PI_R CCC CAC TGG TCR AAI GAR TT Ostreococcus and land plants Glyceraldehyde-3-phosphate dehydrogenase GapA_Fb GSN ATH AAY GGN TTY GG Petersen et al. (2006) GapA_Re CCA YTC RTT RTC RTA CCA Petersen et al. (2006) GapA_Fm GCI YSI TGC ACI ACY AAC TG green algae and land plants Oxygen-evolving enhancer protein, chloroplastic (OEE1) Oxy_F1 TGA CCT AYI TGC ARR TYA AGG G Viridiplantae and cDNA library Cladophora Oxy_F2 CIG GCI TKG CCA ACA CIT GCC C Viridiplantae and cDNA library Cladophora Oxy_R GAR CCA CCR CGG CCC TTG GGG TC Viridiplantae and cDNA library Cladophora 40S ribosomal protein S9 (RPS9) 40S_S9_F ATG CCG AAG ATC GSC YAK TAY CGC Viridiplantae and cDNA library Cladophora 40S_S9_R CAC KCK AGC GTG GTG GAT GGA CTT Viridiplantae and cDNA library Cladophora 40S_S9_3’UTR GTC TAT CCT GTC CAG CCT GAG CAG C Viridiplantae and cDNA library Cladophora 60S ribosomal protein L3 (RPL3) 60S_L3_F ATG TCI CAC AGI AAG TTT GAA CAC CC Viridiplantae and cDNA library Cladophora 60S_L3_R GTC TTG CGI GGM AGI CGG GTG AC Viridiplantae and cDNA library Cladophora 60S ribosomal protein L17 (RPL17) 60S_L17_F CAA GGC GCG CGG GTC GGA YCT Viridiplantae and cDNA library Cladophora 60S_L17_R CAT GTA CGG GTT GAT GCG RCC RTG CGC Viridiplantae and cDNA library Cladophora cDNA library pExCell primers M13_F GTA AAA CGA CGG CCA GT M13_R GGA AAC AGC TAT GAC CAT G
42 CHAPTER 2 Table S4. PCR conditions, expected length of PCR products and total length of the alignment used for phylogenetic inferences. primer combination Annealing Length of Total length Comment temperature PCR product alignment Actin 1122 bp Actin_F + Actin_R 55°C ≈ 850 bp Ac3-R + Fern5-F 55°C ≈ 1000 bp Closterium Glucose-6-phosphate isomerase 753 bp G6PI_F + G6PI_R 55°C ≈ 760 bp Glyceraldehyde-3-phosphate dehydrogenase 966 bp GapA_Fb + GapA_Re 50°C ≈ 1000 bp GapA_Fm +GapA_Re 50°C ≈ 550 bp Oxygen-evolving enhancer protein, chloroplastic 762 bp Oxy_F1 + Oxy_R 50°C ≈ 470 bp Oxy_F2 + Oxy_R 50°C ≈ 500 bp 40S ribosomal protein S9 (RPS9) 537 bp 40S_S9_F + 40S_S9_R 55°C ≈ 400 bp 40S_S9_F + 40S_S9_3’UTR 55°C ≈ 550 bp Ulva intestinalis 60S ribosomal protein L3 (RPL3) 1185 bp 60S_L3_F + 60S_L3_R 55°C ≈ 730 bp 60S ribosomal protein L17 (RPL17) 477 bp 60S_L17_F + 60S_L17_R 55°C ≈ 380 bp
Page 1 and 2: Phylogeny and molecular evolution o
Page 3 and 4: Promotor: Prof. Dr. O. De Clerck (U
Page 5 and 6: Aan de mensen van de plantkunde in
Page 8 and 9: 1 Introduction Algae Algae are a la
Page 10 and 11: Green lineage or Viridiplantae INTR
Page 12 and 13: INTRODUCTION 5 Figure 4. Variation
Page 14 and 15: INTRODUCTION 7 (shared gene losses
Page 16 and 17: INTRODUCTION 9 Sphaeropleales (dire
Page 18 and 19: INTRODUCTION 11 Figure 7. The estim
Page 20 and 21: Tree building methods Maximum likel
Page 22 and 23: INTRODUCTION 15 Figure 9. Flow char
Page 24 and 25: Removal of fast-evolving sites INTR
Page 26 and 27: 2 Ancient relationships among green
Page 28 and 29: PHYLOGENY OF GREEN ALGAE 21 environ
Page 30 and 31: PHYLOGENY OF GREEN ALGAE 23 Our phy
Page 32 and 33: PHYLOGENY OF GREEN ALGAE 25 Figure
Page 34 and 35: PHYLOGENY OF GREEN ALGAE 27 to the
Page 36 and 37: PHYLOGENY OF GREEN ALGAE 29 primers
Page 38 and 39: Topological hypothesis testing PHYL
Page 40 and 41: Additional files PHYLOGENY OF GREEN
Page 42 and 43: PHYLOGENY OF GREEN ALGAE 35 Figure
Page 44 and 45: actin G6PI GapA histone OEE1 40S_S9
Page 46 and 47: PHYLOGENY OF GREEN ALGAE 39 atpB rb
Page 50 and 51: 3 Gain and loss of elongation facto
Page 52 and 53: GAIN AND LOSS OF ELONGATION FACTOR
Page 60 and 61: Methods Algal strains GAIN AND LOSS
Page 64 and 65: Authors' contributions GAIN AND LOS
Page 66 and 67: Additional file 2 GAIN AND LOSS OF
Page 68 and 69: Additional file 4 GAIN AND LOSS OF
Page 70 and 71: Additional file 6 Table S2. GenBank
Page 72 and 73: atpB rbcL SSU rDNA EF-1α EFL Chlor
Page 74 and 75: atpB rbcL SSU rDNA EF-1α EFL choan
Page 76 and 77: 4 Complex phylogenetic distribution
Page 78 and 79: NON-CANONICAL GENENTIC CODE 71 addi
Page 80 and 81: Figure 1. The occurrence of a non-c
Page 82 and 83: NON-CANONICAL GENENTIC CODE 75 Figu
Page 84 and 85: Multiple independent gains NON-CANO
Page 86: Acknowledgements NON-CANONICAL GENE
Page 89 and 90: 82 CHAPTER 5 Introduction The genet
Page 91 and 92: 84 CHAPTER 5 The goal of this study
Page 93 and 94: 86 CHAPTER 5
Page 95 and 96: 88 CHAPTER 5 Codon usage bias and G
Page 98 and 99:
6 A multi-locus time-calibrated phy
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A MULTI-LOCUS TIME-CALIBRATED PHYLO
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Page 104 and 105:
Page 106 and 107:
Time-calibrated phylogeny A MULTI-L
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Page 112 and 113:
Page 114 and 115:
Acknowledgments A MULTI-LOCUS TIME-
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Dichotomosiphon tuberosus AB038487
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Table 3. List of calibration points
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116 CHAPTER 7 Introduction Green al
Page 125 and 126:
118 CHAPTER 7 ulvophycean order Ulo
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120 CHAPTER 7 10). Filaments that w
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122 CHAPTER 7 invaded freshwater ha
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124 CHAPTER 7 filaments, and the po
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126 CHAPTER 7 Type species: Okellya
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8 General discussion This thesis fo
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SSU nrDNA phylogenies GENERAL DISCU
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GENERAL DISCUSSION 133 copy nuclear
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GENERAL DISCUSSION 135 Figure 2. Su
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GENERAL DISCUSSION 137 Our site str
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GENERAL DISCUSSION 139 In the light
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GENERAL DISCUSSION 141 genomes (Rok
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144 REFERENCES Bartsch I and Kuhlen
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146 REFERENCES Derelle E, Ferraz C,
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148 REFERENCES Hanyuda T, Wakana I,
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150 REFERENCES Knight RD, Freeland
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152 REFERENCES Mattox K and Stewart
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154 REFERENCES Philippe H, Lartillo
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156 REFERENCES Sanderson MJ. 2002.
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158 REFERENCES Turmel M, Otis C, an
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160 REFERENCES Zechman FW, Theriot
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162 SUMMARY derived from a multinuc
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Samenvatting Groenwieren worden wer
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SAMENVATTING 167 kleine variaties o
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