Front Cover

Fungi

Copyright

Contents

Contributors

Preface

Fungal–Plant Interactions: A Never Ending Story of Friends and Foes

Acknowledgement

References

Chapter One: Fungal Genomics: Sequencing and Annotation

1. Introduction

2. What Is Genome Assembly, and How to Do It

2.1. Purpose of assembly

2.2. Challenges of assembly

2.3. Sequencing platforms

2.4. Assembly strategy and algorithms

2.5. Computational limitations on algorithm choice

2.6. Paired reads

2.7. Generation of contigs and scaffolds

2.8. Assembly quality evaluation

3. What Is Annotation, and Why Do It

3.1. The purpose of annotation

3.2. How to annotate

Gather inputs

Structural annotation

Functional annotation

Distribute outputs

3.2.1 Assessing and preparing the assembly

3.2.2. Finding the genes (structural annotation)

3.2.3. Characterizing the genes (functional annotation)

3.2.4. Using and distributing the annotation

4. What to Do with the Annotation Once You´ve Got It

4.1. Comparing the annotation to itself: Duplications and higher-order structure

4.2. Comparing the annotation with experimental data: other -omics

4.2.1. Transcriptomics

4.2.2. Proteomics

4.2.3. Metabolomics

4.2.4. Epigenomics

4.2.5. Population genomics

4.3. Comparing the annotation to those of other genomes

4.3.1. Comparative genomics

4.3.2. Phylogenomics

4.3.3. Ecogenomics

5. Genomics of Plant-Microbe Interactions: What´s Next?

5.1. Systems biology

5.2. Metagenomics

5.3. The 1000 Fungal Genomes Project

6. Conclusion

Acknowledgements

References

Chapter Two: Exploring the Transcriptome of Mycorrhizal Interactions

1. Introduction

2. Microarrays Versus Deep Sequencing

3. Dual Transcriptomics of Plant–Fungus Interaction: Monitoring Both Partners at the Same Time

4. Combination of Transcriptomics and Microdissection

5. Bioinformatic Tools for RNA-Seq Data Analysis

5.1. Reads mapping onto reference sequences

5.2. Transcriptome reconstruction

5.3. Gene expression quantification

6. Mycorrhizal Transcriptomes in the Genome Era

6.1. Transcriptome of L. bicolor, a basidiomycete ectomycorrhizal fungus

6.2. Transcriptome of T. melanosporum, an ascomycete ectomycorrhizal fungus

6.3. Transcriptome of AM fungi

6.4. Transcriptome of Paxillus involutus

7. Outlook

Acknowledgements

Glossary

References

Chapter Three: Evolutionary and Adaptive Role of Transposable Elements in Fungal Genomes

1. Introduction

1.1. Fungal genomes

1.1.1. Fungal genomics

1.1.2. Fungal effectors

1.2. TEs: General facts

1.2.1. Classification

1.2.2. Retrotransposons

1.2.3. DNA transposons

1.2.4. TEs in eukaryote genomes

1.2.5. The main representative TE classes in genomes

1.2.6. Selfish DNA?

1.3. TEs: How genomes control proliferation

1.3.1. How can genomes control TE proliferation?

1.3.2. In fungi

1.4. TEs in fungal genomes

1.4.1. Main families found in fungal genomes

1.4.2. Repertoire of TEs and dating the invasion of fungal genomes

1.4.3. Incidence of TEs on genome architecture

2. TEs and Speciation in Fungi

2.1. The mesosynteny postulate

2.2. TEs at the origin of mesosynteny?

3. TEs and Adaptation to Host Plant and Plant Disease Resistance

3.1. TEs associated with effector genes in fungi

3.2. TEs and the generation/diversification of novel pathogenicity genes

3.3. TEs and adaptation to the host in gene-for-gene systems

4. Concluding Remarks

Acknowledgements

References

Chapter Four: The Genomics of Powdery Mildew Fungi: Past Achievements, Present Status and Future Prospects

1. General Introduction

2. Biology of Powdery Mildew Infection

2.1. Introduction

2.2. Phylogeny

2.3. Lifecycle and infection strategy

3. Genomic Insights into the Obligate Biotrophic Lifestyle

3.1. Introduction

3.2. Genome-size expansion

3.3. Transposable elements proliferation

3.4. Gene family contraction

3.5. Missing genes and pathways

4. Comparative Genomics of Powdery Mildew Isolates: Insights into Their Reproductive Mode and Their Evolutionary Origin

4.1. Introduction

4.2. Mosaic genome structure

4.3. Importance of clonal propagation

4.4. Evolutionary origin

5. Powdery Mildew Effector Research in the Genomic Area

5.1. Introduction

5.2. Prediction and variation of CSEP repertoires

5.3. Evolution of CSEPs

5.4. Structural features of CSEPs

5.5. Functional analysis of CSEPs

6. Transcriptomics of Powdery Mildew Fungi

6.1. Introduction

6.2. Haustorial transcriptome

6.3. Transcript profiling during host infection

7. Future Challenges in Powdery Mildew Research

Acknowledgements

References

Chapter Five: Functional Genomics of Smut Fungi: From Genome Sequencing to Protein Function

1. Introduction

2. The U. maydis Genome

2.1. Adaptation to a biotrophic lifestyle

2.2. Regulation of pathogenic development

3. Effector Clusters of U. maydis

4. Genome Comparison of Smut Fungi

4.1. Genome comparison to S. reilianum

4.2. Genome comparison to U. hordei

5. Organ Specificity in the U. maydis: Maize Interaction

6. Functional Effector Biology

7. Adaptation to the Host Environment

8. Summary and Future Perspectives

Acknowledgements

References

Chapter Six: Advancing Knowledge on Biology of Rust Fungi Through Genomics

1. Introduction

2. Rust Fungi in the Genomics Era

2.1. Genomics of plant-interacting fungi

2.2. Sequencing genomes of rust fungi

2.3. Major genomic features of rust fungi

2.4. NGS to assess genome-scale polymorphism in rust fungi

3. Rust Transcriptomics

3.1. Genome oligoarray-based transcriptomics

3.2. RNA-Seq-based transcriptomics

3.3. Comparison of transcriptome in different hosts

4. Rust Secretome, Effectors, and Avirulent Genes

5. Population Genomics: From Genomes to Landscapes

5.1. The rapidly evolving rust genomes

5.2. Host–pathogen adaptation in coevolved pathosystems

6. Coming Up Next in Rust Genomics

Acknowledgements

References

Chapter Seven: Truffle Phylogenomics: New Insights into Truffle Evolution and Truffle Life Cycle

1. Introduction

2. Truffle Diversity and Phylogeography

2.1. Tuber biodiversity

2.2. Phylogeography and origin of Tuber

3. Harnessing Genomes to Unravel the Black Périgord Truffle Life Cycle

3.1. Black Périgord truffle life cycle: An intimate relation between the fungi, plant, and climate

3.2. Intraspecific genetic diversity: From microsatellites to SNPs

3.3. Sexual reproduction: Where are both mating-type strains?

4. Comparative Genomic in Pezizomycetes

4.1. Sequencing the genome of Tuber spp.

4.2. Sequencing the genome of other Pezizomycetes

5. Concluding Remarks

Acknowledgements

References

Chapter Eight: The Natural Histories of Species and Their Genomes: Asymbiotic and Ectomycorrhizal Amanita Fungi

1. Introduction

2. The Fungi and Their Genomes

2.1. The out-group Volvariella volvacea, an edible mushroom and decomposer of agricultural waste

2.2. Amanita thiersii, a fungus of lawns undergoing a range expansion

2.3. Amanita inopinata, an Amanita known only from introduced ranges

2.4. Amanita muscaria, a species complex of ECM fungi with different ecologies

2.5. Amanita polypyramis, an ECM fungus

2.6. Amanita brunnescens, another ECM fungus about which relatively little is known

2.7. Genomics to date, and comparisons to L. bicolor and T. melanosporum

3. Ecological Genomics of Asymbiotic and ECM Amanita Species

3.1. Does symbiosis influence the pace of speciation in ECM Amanita?

3.2. Does symbiosis reshape the ECM genome?

3.3. Conclusions

4. Unanswered Questions: Range Expansions and Genomic Architectures

Acknowledgements

References

Chapter Nine: Genomics of Arbuscular Mycorrhizal Fungi: Out of the Shadows

1. Introduction

1.1. The evolutionary and ecological success of AM symbiosis

1.2. The biology of AM fungi

1.2.1. Phylogeny and taxonomy

1.2.2. Life cycle

2. Toward the Genome of Rhizophagus Irregularis DAOM197198

2.1. The first brick in the wall: Choosing a model organism

2.1.1. Rhizophagus irregularis as a useful organism in laboratory studies

2.1.2. Organization and size of AM fungal genomes

2.1.3. The genome of Rhizophagus Irregularis DAOM197198: A cold case

3. The Biology of Rhizophagus Irregularis from Its Gene Repertoire

3.1. Spore germination and early signal perception

3.2. Plant invasion

3.3. Fungal metabolism during symbiotic life

3.3.1. Phosphate transport and metabolism

3.3.2. Nitrogen transport and metabolism

3.3.3. Sugar transport and metabolism

3.3.4. Lipid metabolism

3.4. Sexual reproduction of AM fungi

4. Conclusion and Perspectives

Acknowledgements

References

Chapter Ten: Genomes of Plant-Associated Clavicipitaceae

1. Introduction

1.1. Biology of plant-associated Clavicipitaceae

1.1.1. Symbiosis and transmission strategies of plant-associated Clavicipitaceae

1.1.2. Vertically transmitted symbionts, including asexual Epichloë species

1.1.3. Biology and life history of ergot fungi

1.2. Phylogenetic relationships

1.2.1. Gene trees

1.2.2. Phylogenetic relationships of pathogenic and symbiotic life histories

2. Sequenced Genomes of the Clavicipitaceae

2.1. Repeat content

2.2. Telomeric regions

2.3. Mating-type loci

2.4. Mitochondrial genomes

2.5. Gene ontology categories

2.6. Variation of SM clusters

3. Alkaloid Gene Loci

3.1. Relationships between gene contents and alkaloid structures

3.1.1. Ergot alkaloids

3.1.2. Indole-diterpenes

3.1.3. Lolines and aminopyrrolizidines

3.1.4. Peramine

3.2. Variation in gene order

3.3. Variations in gene expression

4. Future Perspectives

Acknowledgments

References

Chapter Eleven: Genomics, Lifestyles and Future Prospects of Wood-Decay and Litter-Decomposing Basidiomycota

1. Introduction: Plant and Soil Organic Matter

1.1. Organic matter and Earth´s carbon cycle

1.2. Structure of plant biomass and lignocellulose

2. Wood and Litter Decay and Fungal Lifestyles

2.1. White rot

2.2. Brown rot

2.3. Soft rot

2.4. Blue stain

2.5. Litter decomposition

3. Fungal Enzymes in Degradation of Plant Lignocellulose Carbohydrates: Genomic View

3.1. Carbohydrate-active enzymes

3.2. Cellulose breakdown

3.3. Hemicellulose breakdown

3.4. Pectin breakdown

4. Lignin Breakdown and Lignin-Modifying Enzymes

4.1. Multicopper oxidases

4.2. Lignin-modifying class II peroxidases

4.3. Other lignin-modifying, fungal-secreted peroxidases

4.4. GMC superfamily oxidases and oxidoreductases

5. Phanerochaete chrysosporium and Wood Decay

5.1. Phanerochaete transcriptome and secretome on lignocellulose

5.2. White Rot fungal secretome and selective degradation of lignin

5.3. Brown rot versus white rot decay of wood

6. Conclusions and Outlook

References

Chapter Twelve: Heterobasidion annosum s.l. Genomics

1. Introduction

1.1. Relevance and impact

1.2. Overview of species complex

1.3. Evolutionary history

2. Intraspecific Interactions

2.1. Mating and sexual compatibility

2.2. Intersterility and interfertility

3. Hybridisation

3.1. Natural hybridisation in north America and Italy

3.2. Artificial hybrids

4. Genomics

4.1. Genome sequencing and linkage mapping

4.2. Mapping of quantitative trait loci

4.3. Intraspecific genome variation and association mapping in H. annosum s.s.

5. Genome Secrets

5.1. Gene environment

5.2. Signal pathways

5.3. Secondary metabolite clusters

6. Future Prospects

Acknowledgements

References

Chapter Thirteen: Speciation Genomics of Fungal Plant Pathogens

1. Fungal Speciation

2. The Genetics of Speciation: A Population Genetics Perspective

2.1. Isolation with migration

2.2. Genetic divergence

2.3. Genetic incompatibility and reproductive isolation

2.4. Hybridization

3. The Genomics of Speciation

3.1. Comparative genomics and the inference of species histories

3.2. Natural selection and genomic footprints

3.3. Chromosomal rearrangements and their role in speciation

4. Speciation in Plant Pathogenic Fungi: Examples from Genome Studies

4.1. Speciation and adaptive evolution of the rice blast genome: Repetitive elements and clonal divergence of Magnaporthe...

4.2. Insight from comparative population genomics and coalescence analyses: Ecological speciation of the wheat pathogen Z...

4.3. The happy rendezvous of old relatives: Hybrid speciation in pathogenic fungi

5. Experimental Evolution and the Identification of ``Dobzhansky-Muller Incompatibilities´´: Integrating Experimental, Ge...

6. Conclusions: Species and Species Dynamics of Fungal Plant Pathogens

7. Future Perspectives

Acknowledgements

References

Author Index

Subject Index

Color Plate