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Oenothera, a Unique Model to Study the Role of Plastids in Speciation

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Oenothera, a Unique Model to Study the Role of Plastids in Speciation Oenothera, a unique model to study the role of plastids in speciation Dissertation der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Stephan Greiner am 15. Mai 2008 Erstgutachter: Professor Reinhold G. Herrmann Zweitgutachter: Professor Wolfgang Stephan Tag der mündlichen Prüfung: 19. Juni 2008 Table of Contents Table of Contents 1. Introduction ...................................................................................................................... 1 1.1. Eukaryotic genomes are integrated and compartmentalized ...................................... 1 1.2. Dobzhansky-Muller incompatibilities and asymmetric hybridization barriers .......... 2 1.2.1. The model of Dobzhansky-Muller incompatibility .............................................. 4 1.2.2. “Speciation genes” have not yet been identified for PGI ..................................... 5 1.3. Hybridization barriers formed by plastids .................................................................. 6 1.4. The occurrence of PGI in natural populations is underestimated ............................ 10 1.5. Physiology and cell biology of PGI ......................................................................... 14 1.5.1. Albinotic phenotypes of PGI .............................................................................. 15 1.5.2. PGI phenotypes with affected cell growth and function .................................... 15 1.6. Oenothera as a molecular model to investigate PGI ................................................ 17 1.7. Oenothera genetics ................................................................................................... 19 1.7.1. Complete reciprocal translocations of whole chromosome arms in Oenothera .19 1.7.2. Maintenance of complete permanent translocation heterozygosis ..................... 22 1.7.3. Exchanging plastomes between species ............................................................. 23 1.8. Aims of this work ..................................................................................................... 25 2. Material and Methods .................................................................................................... 26 2.1. Material .................................................................................................................... 26 2.1.1. Chemicals ........................................................................................................... 26 2.1.2. Solutions, buffers and media .............................................................................. 26 2.1.3. Antibodies .......................................................................................................... 26 2.1.4. Oligonucleotides ................................................................................................. 27 2.1.5. Reference species for bioinformatic analysis ..................................................... 28 2.1.6. Oenothera strains ............................................................................................... 29 2.1.7. Arabidopsis strains ............................................................................................. 36 III Table of Contents 2.1.8. Bacterial strains .................................................................................................. 36 2.2. Methods .................................................................................................................... 36 2.2.1. Growth of biological material ............................................................................ 36 2.2.1.1. Oenothera growth conditions and breeding .................................................... 36 2.2.1.1.1. Axenic culture of seedlings ...................................................................... 36 2.2.1.1.2. Field experiments ..................................................................................... 36 2.2.1.1.3. Crossing experiments and seed storage .................................................... 37 2.2.1.2. Bacterial growth conditions ............................................................................ 37 2.2.2. Analysis of nucleic acids .................................................................................... 37 2.2.2.1. Isolation of nucleic acids ................................................................................. 37 2.2.2.1.1. Isolation of total DNA from Oenothera ................................................... 37 2.2.2.1.2. Isolation of plasmid DNA from Escherichia coli .................................... 38 2.2.2.1.3. RNA isolation from Oenothera ................................................................ 38 2.2.2.2. Agarose gel electrophoresis ............................................................................ 38 2.2.2.3. cDNA synthesis ............................................................................................... 38 2.2.2.4. PCR approaches .............................................................................................. 38 2.2.2.5. Sequencing approaches ................................................................................... 39 2.2.2.5.1. Direct PCR product sequencing ............................................................... 39 2.2.2.5.2. Sequencing of cloned PCR products ........................................................ 39 2.2.2.5.3. Sequencing of inversion breakpoints in the Oenothera plastome ............ 39 2.2.2.5.4. Plastome sequencing ................................................................................ 39 2.2.2.6. SNP mapping by Nuclease S digestion ........................................................... 40 2.2.2.7. Design, digestion and analysis of CAPS markers ........................................... 40 2.2.2.8. Gene expression analysis ................................................................................ 41 2.2.2.8.1. Generation and application of macroarrays ............................................. 41 2.2.2.8.2. Real-time PCR analysis ............................................................................ 42 2.2.2.8.2.1. Analysis of nuclear gene expression via Real-time PCR ...................... 42 2.2.2.8.2.2. Analysis of plastid gene expression via Real-time PCR ....................... 43 IV Table of Contents 2.2.3. Analysis of proteins ............................................................................................ 43 2.2.3.1. Preparation of thylakoid membranes ............................................................... 43 2.2.3.2. Chlorophyll absorption measurements ............................................................ 44 2.2.3.3. SDS polyacrylamide gel electrophoresis ......................................................... 44 2.2.3.4. Western analysis .............................................................................................. 44 2.2.4. Determination of chromosome configurations ................................................... 44 2.2.5. Chlorophyll a fluorescence analysis .................................................................. 45 2.2.6. Bioinformatic analysis ........................................................................................ 46 2.2.6.1. Calculation of genetic linkage ......................................................................... 46 2.2.6.2. Analysis of the Oenothera plastid genomes .................................................... 46 2.2.6.2.1. Repeat analysis ......................................................................................... 46 2.2.6.2.2. Analysis of variable amino acid sites ....................................................... 46 2.2.6.2.3. Computational prediction of sigma factor and T7 binding sites .............. 47 2.2.6.2.4. Prediction of Shine-Dalgarno sequences .................................................. 48 2.2.6.2.5. Calculation of phylogenetic trees ............................................................. 48 2.2.6.2.6. Determination of Ka/Ks-values ................................................................ 48 3. Results ............................................................................................................................. 49 3.1. Molecular approaches in Oenothera genetics .......................................................... 49 3.1.1. Marker systems for Oenothera genetics and breeding approaches .................... 50 3.1.1.1. Co-dominant markers discriminating A and B genomes ................................ 50 3.1.1.2. Genotyping of Renner complexes. .................................................................. 54 3.1.1.3. Markers for basic plastomes and subplastomes .............................................. 56 3.1.2. New combination of genetic compartments ....................................................... 59 3.1.2.1. Generation of interspecific AB-I and AB-III plastome-genome hybrids ........ 59 3.1.2.2. Generation of the interspecific incompatible BB-II hybrid ............................ 60 3.1.3. Correlation of classical and molecular Oenothera maps ................................... 64 3.1.3.1. The hybrid Stalbicans·htuscaloosa and its genetic behaviour ........................... 64 3.1.3.2. Identification of marker alleles between Stalbicans and htuscaloosa ............... 65 V Table of Contents 3.1.3.3. Assignment of coupling group 7 to chromosome 9·8 ..................................... 66 3.2. The complete sequences of the five basic Oenothera plastid genomes ..................
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