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

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INTRODUCTION 11 Figure 7. The estimated divergence time between Streptophyta and Chlorophyta, which are based on molecular clock studies, vary considerably among studies. The split between these lineages is generally situated in the Neoproterozoic to late Mesoproterozoic (between 1200 and 700 million years ago). The best characterized Precambrian fossils which most likely are green algae are Proterocladus and Palaeastrum at Svanbergfjellet, Tasmanites and Pterospermella at Thule and Spiromorpha at Ruyang. The oldest reliable fossil green algae are 540 million years old (Dasycladales). Other fossil Ulvophyceae are found more recently. Evolution of nuclear markers One of the major challenges when using nuclear genes for phylogenetic purposes is to assess orthology. Gene duplications lead to the formation of gene families (e.g. actin gene family, and GapA/B gene duplication in Streptophytes and the prasinophyte Ostreococcus), in which case extreme caution should be taken to ensure that the same orthologues gene is used in each species (An et al. 1999, Petersen et al. 2006, Robbens et al. 2007). Apart from difficulties in assessing orthology, there are indications of the occurrence of lateral gene transfer between eukayotes (Andersson 2005, Keeling and Palmer 2008). Two key genes of the translational apparatus, elongation factor-1 alpha (EF-1α) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia (Dasycladales, Ulvophyceae) where EF-1α is found, and the Streptophyta possess EF-1α except Mesostigma, which has EFL (Noble et al. 2007). The punctuated distribution of these two genes make it worth to further explore their distribution and evolutionary patterns of gain and loss within the green plant lineage. In this context it is interesting that Acetabularia not only has a different elongation factor gene compared to the rest of the Chlorophyta but also uses a different genetic code. In Acetabularia, and its close relative Batophora, stop codons TAG and TAA code for the amino acid glutamine (Schneider et al. 1989, Schneider and de Groot 1991). It is interesting to see if other green algae, especially close relatives of Acetabularia, also have the EF-1α gene or use the same alternative (non-canonical) code.
12 CHAPTER 1 Designing primers for low-copy nuclear markers For phylogenetic analyses we will concentrate on the development of low-copy nuclear markers. There are several alternative approaches to isolate and characterize novel low-copy nuclear markers: 1) the design of new primers from information in sequence databases (e.g., GenBank), 2) obtaining novel sequences via cDNA cloning 3) isolation of homologous DNA using a gene probe from another organism, and 4) characterization of sequence markers from DNA fingerprints (Schluter et al. 2005). In order to find suitable nuclear markers we first searched the literature for potentially useful lowcopy nuclear markers and then applied the first two approaches (Fig. 8). When designing new primers from information already available in GenBank, we used genomic sequences of two unicellular green algae (Chlamydomonas reinhartii and Ostreococcus tauri) and aligned them with Genbank sequences from land plants and other green algae if available. For the second approach we made an EST library for the siphonocladous ulvophyte Cladophora coelothrix. All Cladophora coelothrix EST sequences were blasted against the GenBank protein database (blastx) for annotating the genes. Only genes with a certain annotation (hits to Swiss-Prot database) were retained and aligned with GenBank sequences from other green algae and land plant. If those genes were long enough and contained conserved regions, primers were designed and tested on a variety of green algae. Figure 8. Flow chart showing three different methods to select suitable nuclear markers in green algae for which primers can be designed and tested on a wide range of green algae.
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 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 48 and 49: PHYLOGENY OF GREEN ALGAE 41 Table S
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
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Additional file 4 GAIN AND LOSS OF
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Additional file 6 Table S2. GenBank
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atpB rbcL SSU rDNA EF-1α EFL Chlor
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atpB rbcL SSU rDNA EF-1α EFL choan
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4 Complex phylogenetic distribution
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NON-CANONICAL GENENTIC CODE 71 addi
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Figure 1. The occurrence of a non-c
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NON-CANONICAL GENENTIC CODE 75 Figu
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Multiple independent gains NON-CANO
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Acknowledgements NON-CANONICAL GENE
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82 CHAPTER 5 Introduction The genet
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84 CHAPTER 5 The goal of this study
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86 CHAPTER 5
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88 CHAPTER 5 Codon usage bias and G
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6 A multi-locus time-calibrated phy
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A MULTI-LOCUS TIME-CALIBRATED PHYLO
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Time-calibrated phylogeny A MULTI-L
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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
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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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