Flight Craft 27: The Boeing B-17

Volume Preface to the Third Edition
Series Preface
	The Mycota Series: 2022
Contents
About the Editors and Contributors
About the Series Editors
About the Volume Editors
Contributors
Part 1: Genome Sequences and Beyond
	1: Starship Discovery: A Collaborative Approach to Uncover Massive Transposable Elements
		1.1	 Introduction
		1.2	 ToxhAT
		1.3	 Enterprise
		1.4	 Hephaestus
		1.5	 Voyager
		1.6	 Starships and Perspectives
		References
	2: The Three-Dimensional Chromatin Architecture in Fungi
		2.1	 Introduction
		2.2	 General Features of the 3D Genome Organization in the Nucleus
		2.3	 Centromere Clustering and its Role in Nuclear Architecture
		2.4	 Fungi
		2.5	 Features of the Genome Organization in Different Organisms
			2.5.1	 S. cerevisiae and S. pombe
			2.5.2	 Other Fungal Model Organisms
		2.6	 The Dynamic Architecture of Chromatin: How Chromatin Is Modulated to Suit Cell Division
		2.7	 Cohesins and Condensins: Molecular Rings that Organize Chromosomes
			2.7.1	 Cohesins
			2.7.2	 Condensins
		2.8	 Cell Cycle-Associated Changes in Chromatin Architecture
			2.8.1	 S. cerevisiae
			2.8.2	 S. pombe
		2.9	 Functional Role of the 3D Genome Organization and Nuclear Architecture
			2.9.1	 Genome Organization and DNA Replication Timing
			2.9.2	 Nuclear Architecture and DNA Replication Timing
		2.10	 Conclusions
		References
	3: Fungi from Extreme Environments: Genome Sequences and Beyond
		3.1	 Extremophilic and Extremotolerant Fungi
		3.2	 From Genotype to Phenotype
		3.3	 From One Genome to Many
		3.4	 Perspectives
		References
Part 2: Cell and Developmental Biology
	4: Recent Advances in High-Throughput Genetics in Fungi
		4.1	 Introduction
		4.2	 Classic Mutant Collections
		4.3	 Insertional Mutagenesis
		4.4	 TN-SEQ
		4.5	 CRISPR
		4.6	 Other Applications of High-Throughput Genetics
			4.6.1	 Knockout Sudoku
			4.6.2	 RH-seq
		4.7	 Conclusions
		References
	5: Genome-Wide A-to-I RNA Editing During Sexual Reproduction in Filamentous Ascomycetes
		5.1	 Introduction
		5.2	 Stage-Specific A-to-I RNA Editing During Sexual Reproduction in Fungi
			5.2.1	 Discovery of RNA Editing Events in PUK1
			5.2.2	 Genome-Wide RNA Editing During Sexual Reproduction
		5.3	 Distinct Features of Fungal A-to-I Editing
		5.4	 Importance of Fungal mRNA Editing
			5.4.1	 Editing of Stop Codons in Genes Important for Ascosporogenesis
			5.4.2	 Importance of Nonsynonymous Editing
		5.5	 Mechanisms of Stage-Specific RNA Editing
		5.6	 Conclusions and Perspectives
		References
	6: A Symphony of Roles for Codon Usage in Fungal Genomics
		6.1	 Introduction
			6.1.1	 Measures of Codon Usage
			6.1.2	 Codon Usage Bias in Fungi
			6.1.3	 Forces Shaping Codon Bias Variation in Fungi
		6.2	 Functional Role of Codon Usage Bias Across the Central Dogma
			6.2.1	 Translation
				6.2.1.1	 Translation Initiation
				6.2.1.2	 Elongation Rate
				6.2.1.3	 Co-translational Protein Folding
				6.2.1.4	 Protein Modification and Transport
				6.2.1.5	 Translation Accuracy
				6.2.1.6	 Global Translational Dynamics
			6.2.2	 Codon Optimization Metrics
				6.2.2.1	 Frequency of Optimal Codons (Fop)
				6.2.2.2	 Codon Adaptation Index (CAI)
				6.2.2.3	 tRNA Adaptation Index (tAI)
				6.2.2.4	 Function Specific Codon Metrics
				6.2.2.5	 Complex Optimization Metrics
				6.2.2.6	 Measuring the Degree of Codon Optimization
			6.2.3	 Transcription
				6.2.3.1	 mRNA Stability
				6.2.3.2	 Translation Independent Effects on Transcription
				6.2.3.3	 Other Effects of Codon Usage on mRNAs
		6.3	 Codon Usage in Regulation
			6.3.1	 Codon Usage during Stress Response
			6.3.2	 Codon Usage Across the Cell Cycle
			6.3.3	 A Role for Non-optimal Codon Usage
			6.3.4	 Other Regulatory Processes
		6.4	 Codon Usage in Organelles and Viruses
			6.4.1	 Mitochondrial Codon Usage
			6.4.2	 Viral Codon Usage
		6.5	 Applications of Codon Usage in Fungal Genomics
			6.5.1	 Codon Usage in Phylogenetic Inference
			6.5.2	 Reverse Ecology
		6.6	 Conclusions
		References
	7: Epigenetic Regulation in Early-Diverging Fungi
		7.1	 Introduction
		7.2	 Epigenetic Modifications in EDF
			7.2.1	 DNA Methylation
			7.2.2	 Histone Modifications
			7.2.3	 Non-coding RNAs
		7.3	 Biological Processes Under Epigenetic Control in EDF
			7.3.1	 Genome Defense
			7.3.2	 Acquired Resistance to Antifungal Drugs
		7.4	 Conclusions
		References
Part 3: Biotechnology
	8: Fungal Diversity Related to Plant Biomass Degradation
		8.1	 Introduction
			8.1.1	 Plant Biomass Composition
			8.1.2	 Cellulose
			8.1.3	 Hemicelluloses
				8.1.3.1	 Xylan
				8.1.3.2	 Xyloglucan
				8.1.3.3	 Galactomannan
			8.1.4	 Pectin
				8.1.4.1	 Homogalacturonan and Xylogalacturonan
				8.1.4.2	 Rhamnogalacturonan I and II
			8.1.5	 Lignin
		8.2	 Plant Biomass Degrading Enzymes of Fungi
			8.2.1	 Novel Enzymes Activities and Families Involved in Plant Biomass Degradation
			8.2.2	 Lytic Polysaccharide Monooxygenases
			8.2.3	 Current Status of Fungal Genomes and Post-Genomics in Relation to Plant Biomass Degradation
		8.3	 Conclusions
		References
	9: Genomes and Genomics of the Genus Trichoderma
		9.1	 Introduction
		9.2	 Genome Research with Trichoderma
			9.2.1	 Aspects of Evolution
			9.2.2	 Horizontal Gene Transfer (HGT) in the Genus Trichoderma
			9.2.3	 Telomere-to-Telemere Sequences of Trichoderma Strains (Gold Standard Genomes)
			9.2.4	 Random Mutants Demystified: New Insights for Protein Production
		9.3	 Sexual Development and Recombination
			9.3.1	 Repeat Induced Point Mutation (RIP)
			9.3.2	 Segmental Aneuploidy in Trichoderma
		9.4	 Regulatory Non-Coding RNAs in Trichoderma
			9.4.1	 microRNA-like RNAs
			9.4.2	 Long Non-Coding RNAs (lncRNAs)
		9.5	 Mitochondrial Genomes
		9.6	 Mycoviruses in Trichoderma
		9.7	 Gene Regulation for Heterologous Protein Expression: New Promotors
		9.8	 Discoveries in Genome Wide Gene Regulation at the Transcript Level
		9.9	 Genomics for Discovery of Novel Enzymes
		9.10	 Genomics for Discovery of Novel Secondary Metabolite Clusters and Other Genes Contributing to Production of Bioactive Metabolites
		9.11	 Conclusions and Further Directions of Research
		References
Part 4: Interactions: Symbioses, Mutualisms, and Pathogens
	10: Genomic Innovation and Virulence Evolution in the Emerging Human Fungal Pathogen Candida auris
		10.1	 Introduction
			10.1.1	 Emergence Detection
			10.1.2	 Global Spread
			10.1.3	 Clinical Management
			10.1.4	 C. auris Pathogenicity
			10.1.5	 C. auris Virulence
		10.2	 Genomic Innovation Strategies
			10.2.1	 Structural Variation
			10.2.2	 Aneuploidy
			10.2.3	 Hypermutation
			10.2.4	 Polyploidy
			10.2.5	 Hybridisation
			10.2.6	 Gene Family Expansions
				10.2.6.1	 Hydrolases
				10.2.6.2	 Transporters
				10.2.6.3	 Adhesins
		10.3	 Discussion
			10.3.1	 Moving Fungal Genomic Inquiry Closer to the Patient
			10.3.2	 Escalate Environmental Fungal Pathogen Genomics Towards Global Priority
			10.3.3	 Interdisciplinary Genomics Towards Exhaustive Characterisation
		10.4	 Conclusions
		References
	11: General Trends of Genomic Signatures of the Ectomycorrhizal Symbiosis in Fungi: A Comparison Across Multiple Lineages
		11.1	 Introduction
		11.2	 Expansion of Genome Size as a Result of Proliferation of Transposable Elements
		11.3	 The Secretome of Ectomycorrhizal Fungi
		11.4	 Loss of Plant Cell Wall Degrading Enzymes in Ectomycorrhizal Fungi
		11.5	 ECM Genome Features Pre-Date the Evolution of the ECM Lifestyle
		11.6	 Host Specificity
		11.7	 Conclusions and Future Remarks
		References