DNA extraction and fungal communities sequencing

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Table of contents

1 Introduction 
1.1 Community genetics
1.2 The phyllosphere
Definition of the term
Topography and microclimatic conditions
Microbial inhabitants of the phyllosphere
Microbiota functions in the phyllosphere
1.3 Plants strategy to cope with the diversity of biotic interactions might
select for specific networks of interacting species in the associated communities
1.4 Powdery mildew
1.5 Metabarcoding for studying microbial community
Fungi
Bacteria
1.6 Objectives of this work
1.7 Bibliography
2 Deciphering the pathobiome 
2.1 Introduction
2.2 Material and methods
Study site and sampling design
Leaf DNA extraction
Amplification and sequencing of the fungal assemblages
Amplification and sequencing of the bacterial assemblages
Processing of the fungal 454 pyrosequencing data
Processing of the bacterial Illumina data
Statistical analyses
2.3 Results
Taxonomic composition of oak foliar microbial communities
Relationship between the abundance of powdery mildew symptoms and the number of reads assigned to E. alphitoides
Relationship between the level of infection by E. alphitoides and the composition of foliar microbial communities
Inferred interactions between E. alphitoides and other members of the foliar community
2.4 Discussion
2.5 Acknowledgements
2.6 References
2.7 Supplementary methods S1 – Preliminary experiment aimed at assessing the effect of oak leaf storage on fungal community composition.
Study site and sampling design
DNA extraction and fungal communities sequencing
Statistical analyses
Results
Discussion
References
3 QTLs for microbial community descriptors 
3.1 Introduction
3.2 Material and Methods
Experimental site and leaf-sampling design
DNA extraction
Amplification and sequencing of the fungal assemblages
Amplification and sequencing of the bacterial assemblages
Processing of the fungal 454 pyrosequencing data
Processing of the bacterial Illumina data
Construction of foliar microbial networks
Choice of traits for QTL analysis
Genotyping and map construction
Number and type of markers
QTL analysis
3.3 Results
Sequencing data
Fungal data
Bacterial data
Correlation among traits
Chromosomal loci for the microbial community descriptors (QTLs) .
3.4 Discussion
3.5 Bibliography
4 Association mapping study 
4.1 Introduction
4.2 Material and Methods
Population structure and Sampling
DNA extraction
Amplification and sequencing of the fungal assemblages
Amplification and sequencing the bacterial assemblages
Processing of the fungal Ion Torrent sequencing data
Processing of the bacterial Illumina sequencing data
Statistical analysis and choice of traits
4.3 Results
Sequencing data
Fungal data
Bacterial data
Differences between maternal and offspring trees
4.4 Discussion
4.5 Bibliography
5 General discussion 
5.1 Recapitulation of the major findings
5.2 Possible evolutionary mechanisms
5.3 Bibliography
6 Appendix 122
6.1 Appendix A – An evolutionary ecology perspective to address forest pathology challenges of today and tomorrow
6.2 Appendix B – Learning Ecological Networks from Next-Generation Sequencing Data
6.3 Appendix C – Résumé en français