Making the most of phylogeny - OPUS - Universität Würzburg

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Internal transcribed spacer 2 Part I. Introduction Figure 2.: Ranges for often used phylogenetic markers. The bars indicate the range for which the corresponding DNA sequences are commonly utilised for phylogenetic comparisons. Abbreviations: ITS internal transcribed spacer; mtDNA non-coding regions of animal mitochondrial DNA; rbcL the large subunit of the chloroplast gene encoding ribulose bisphosphate carboxylase. The ITS2 bar represents the range possible by use of ITS2 secondary structure. Redrawn from Coleman (2003). Figure 3.: Organisation of a typical eukaryotic rRNA cistron. The drawing illustrates the organisation of the nuclear ribosomal cistrons (blue boxes) of a typical eukaryote composed of the 5 ′ ETS, the 18S-rRNA, internal transcribed spacer (ITS) 1, the 5.8S-rRNA, the ITS2, the 28S-rRNA and the 3 ′ ETS. Between all ribosomal cistrons are NTSs. Redrawn from Coleman (2003). 8
Part I. Introduction Internal transcribed spacer 2 C U U G C C C C G G G G G A U C G C U U U G G U A A G C G C G G C C G C C G C G C C C U G G G G U C C G U C U G G U G U A G C G U G C U G G C A U C G A U G C C G A U C G G C U G A U G C G U A U G C U A G U C G U G C G C G A C G G U A C G G G C A U G G C G G U A C U U C A C G G G C A U U G C C G G U U A U G A A C C C C A G G C A G G C A C G G C U U G G C U G U U C G G A A C A U G A C U A C G C A C A C C C U U U A U U G A A G U U G G U C G U U U U G U C C C U U A U U U A A A A A G U A C ITS2 C C A 5‘ 3‘ U U C G C C G U G U U U G U U G G G A C 5.8S 28S Figure 4.: Secondary structure of the ITS2 of Dahlia brevis. General ITS2 topology and visualisation of plant HMM motifs for the secondary structure of D. brevis (gi:31281745). Annotation from HMMs of 5.8S and 28S are displayed as dotted lines tracing the outline of their position, whereas the ITS2 motif HMMs are represented by coloured lines. In parts of these motifs, nucleotide frequencies are presented (Byun and Han 2009; Gorodkin et al. 1997). Nucleotides are coloured yellow in unpaired regions, whereas paired nucleotides are blue. CBCs between secondary structures of D. brevis and Dahlia iscapigeroides (gi:31281755) are shown in red. Image taken from Koetschan et al. (2010) 9
Page 1: Making the most of phylogeny: Uniqu
Page 4 and 5: Eingereicht am: . . . . . . . . . .
Page 7 and 8: Contents Acronyms xi I. Introductio
Page 9: List of Figures Contents List of Fi
Page 12 and 13: Acronyms Acronyms xii ITS2 internal
Page 15 and 16: Part I. Introduction Thesis outline
Page 17 and 18: Part I. Introduction The phylum Tar
Page 19: Part I. Introduction Internal trans
Page 23: Part II. Material and Methods 11
Page 27 and 28: Chapter 2. Methods 2.1. Bioinformat
Page 29 and 30: Part II. Material and Methods Bioin
Page 31 and 32: Part II. Material and Methods Bioin
Page 33: Part III. Results 21
Page 36 and 37: BMC Genomics BioMed Central Researc
Page 38 and 39: BMC Genomics 2009, 10:469 http://ww
Page 47 and 48: Chapter 4. Transcriptome survey of
Page 49 and 50: Mali et al. BMC Genomics 2010, 11:1
Page 59 and 60: Chapter 5. Transcriptome analyzed a
Page 61 and 62: Abstract Tardigrades are unique met
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Page 65 and 66: non-directional cDNA library. For t
Page 67 and 68: available ESTs from both species co
Page 69 and 70: Individual COG/KOGs: Among the COGs
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anches, but have only Lea 4 protein
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emains a question mark in Fig. 5. H
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(posttranslational modification) an
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other aspects of the adaptation pro
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tolerance in man. It is a recombina
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We used primer3 90 for the design o
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cathode buffer (25 mM Tris-HCl pH 9
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24. Ostareck-Lederer, A., Ostareck,
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59. Gaudermann, P., Vogl, I., Zient
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91. Bork, P. & Gibson, T. J. (1996)
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Fig. 2. PCR validation of heat shoc
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Fig. 7. Comparison of COGs/KOGs spe
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Table IIa. Subset of important COGs
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KOG0660:[T]Mitogen-activated protei
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Table III. Enzymes in metabolic pat
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ec:5.3.3.2 isopentenyl-diphosphate
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Table IVa. Specific stress pathway
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Chapter 6. Proteomic analysis of ta
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Figure 1. SEM images of M. tardigra
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listed in Table 2. The individual i
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Table 1. Overview of identified pro
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Table 2. Cont. Sequence coverage No
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Table 3. Identified proteins withou
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Table 3. Cont. Spot no. Accession n
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Table 3. Cont. Spot no. Accession n
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Figure 8. Detection of hsp60 and hs
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Unique proteins, when analyzed on t
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(version 56.1, September 2008, The
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Chapter 7. Stress response in tardi
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Due to the remarkable ability of ta
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Fig. 1 Alignment of two α-crystall
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active state. This leads to the ass
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Pfaffl MW, Horgan GW, Dempfle L (20
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Tardigrade bioinformatics: Molecula
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searched against the next more exte
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Concerted changes in tardigrade ada
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mit dynamischen Modellierungstechni
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Tables and Figures Table 1: Bioinfo
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Figure 1: Maximum likelihood tree f
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Chapter 9. The ITS2 Database III—
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D276 Nucleic Acids Research, 2010,
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D278 Nucleic Acids Research, 2010,
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Chapter 10. Including RNA Secondary
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Keller et al. Biology Direct 2010,
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BMC Evolutionary Biology Research a
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BMC Evolutionary Biology 2008, 8:21
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Chapter 12. Distinguishing species
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Abstract Distinguishing species in
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Distinguishing species in Paramacro
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ITS 2 gene amplification and sequen
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References Distinguishing species i
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Figure legends Distinguishing speci
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221
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Part IV. General Discussion and Con
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Summary succeeded to show the benef
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Zusammenfassung der internal transc
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Bibliography Bibliography Bavan, S.
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Bibliography Bibliography 146.4 (Ap
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Bibliography Bibliography Horikawa,
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Bibliography Bibliography Letunic,
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Bibliography Bibliography Pertea, G
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Bibliography Bibliography Schultz,
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Bibliography Bibliography Westh, P.
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Contributions Markus Grohme wrote t
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Contributions model and the ITS2 se
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List of Publications Publications a
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List of Publications Förster, F.,
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Making the most of phylogeny - OPUS - Universität Würzburg

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