Role of diatoms in biogeochemical cycles

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Table of contents

Chapter I: Introduction
1.1 Diatoms, marine genomics, and the marine ecosystem
1.1.1 First glance
1.1.2 Diatom biology
1.1.3 Classification and habitats
1.1.4 Role of diatoms in biogeochemical cycles
1.1.5 Evolutionary history
1.1.6 Diatom and (algal) genomics
1.1.7 The diatom Phaeodactylum tricornutum
1.2 Transposable elements
1.2.1 Introduction
1.2.2 Diversity
1.2.2.1 Class I elements
1.2.2.2 Class II elements
1.2.3 Impact of TEs on genome evolution
1.2.3.1 Domestication
1.2.3.2 The generation of genetic variability in response to stress
1.2.3.3 TE-mediated recombination
1.2.3.4 Gene duplication
1.3References
Chapter II: Transcription factors in diatom genomes
2.1 Introduction
2.2 Results and Discussion
2.2.1 Transcription factor content in stramenopiles
2.2.2 Transcription factor complement among stramenopiles
2.2.3 Heat Shock Factors (HSFs)
2.2.4 Myb factors
2.2.5 bZIP domain factors
2.2.6 bHLH factors
2.2.7 Expression analysis
2.3 Material and Methods
2.4 References
Chapter III: Potential Impact of Stress Activated Retrotransposons on Genome Evolution in a Marine Diatom
3.1 Introduction
3.2 Results
3.2.1 Expansion of LTR Retrotransposons in the P. tricornutum genome
3.2.2 Classification of LTR retrotransposon sequences
3.2.3 Phylogenetic analysis
3.2.4 Expression of LTR retrotransposons in diatoms
3.2.5 Regulation of Blackbeard
3.2.6 Insertion polymorphism between P. tricornutum accessions
3.2.7 Two distinct haplotypes at loci containing TEs
3.2.8 TE-mediated recombination in the P. tricornutum genome
3.2.9 A high diversity of RT domains from micro-planktonic organisms
3.3 Discussion
3.4 Material and Methods
3.5 References
Chapter IV: Epigenetics in P. tricornutum
4.1 Introduction
4.2 Results and Discussion
4.2.1 Histone modifications
4.2.1.1 Histone modifiers
4.2.1.2 Effectors
4.2.1.3 Chromatin Extraction and Immunoprecipitation
4.2.2 DNA methylation
4.2.2.1 DNA methyltransferases in diatoms
4.2.2.2 DNA methylation in P. tricornutum
4.2.3 RNA silencing machinery in P. tricornutum
4.2.3.1 Diatom genes putatively involved in RNAi-related processes
4.2.3.2 RNA-directed DNA methylation (RdDM) in P. tricornutum
4.3 Material and Methods
4.4 References
Chapter V: Identification and analysis of transposable elements in the genome of the brown alga Ectocarpus siliculosus
5.1 Introduction
5.2 Results and discussion
5.2.1 Identification of repeated sequences in the E. siliculosus genome
5.2.2 Masking the E. siliculosus genome
5.2.3 Phylogeny of E. siliculosus LTR-retrotransposons
5.2.4 Expression analysis
5.2.5 DNA Methylation in Ectocarpus siliculosus
5.3 Material and Methods
5.4 References
Chapter VI: Conclusions and perspectives
6.1 Conclusions and perspectives
6.2 References
Supplementary Material