Plant Genomics

About the Author xiii Preface xv Acknowledgments xvii About the Companion Website xix Introduction xxi 1 The Structure of Plant Genomes 1 Introduction, 1 DNA Variation— Quantity, 1 Chromosome Variation, 4 Chromosome Structures, 7 Telomeres, 7 Centromeres, 8 The Nucleolus Organizer Region, 9 Heterochromatin, 9 Origin of DNA Variation, 10 Organization and Representation of the Various Classes of Sequences, 10 Low- Copy Sequences, 11 Dispersed Repetitive Sequences, 12 Tandemly Repeated Sequences, 15 Summary of the Organization of the Maize Genome, 17 Processes that Affect Genome Size, 17 Consequences of Multiple Genomes, 20 Pangenome Concept, 23 Extrachromosomal Circular DNA, 25 Intraspecific Genome Size Variation, 25 Summary, 26 References, 27 2 Basic Toolbox 31 The Fundamental Basis of Most Genomic Technologies, 31 Genome Fractionation, 32 Sequencing Genomes, 33 Next- Generation Sequencing (NGS) Technologies, 34 Third- Generation Sequencing (Long- Read Sequencing) - Single- Molecule Sequencing, 36 Two of the Third- Generation Sequencing Technologies, 36 Simultaneous Identification of Sequence and Methylation— Epigenetics, 38 Alternative Methylation Profiling, 38 Oxford Nanopore Technologies, 39 Assembling Telomere- to- Telomere Genome Assemblies, 39 Proximity- Based Ligation, 39 Optical Mapping, 40 Summary of Genomic Sequencing, 40 The Transcriptome, 40 RNA Library Preparation, 42 Single- Cell Sequencing, 43 Whole Transcriptome Sequencing (Total RNA- seq), 43 Poly(A) Selection RNA- seq, 43 Ribosome Profiling (Ribo- seq), 43 Strand- Specific RNA- seq, 44 Small RNA- seq, 44 Spatial Transcriptomics, 44 Pseudouridine (Ψ) Sequencing, 44 Quantitative PCR, 44 Digital Droplet PCR (ddPCR), 45 Microarrays, 45 Proteomics, 46 Extraction of the Proteome, 47 Protein Separation, 48 References, 51 3 Sequencing and Assembly Strategies for Large Complex Genomes 53 Assembling Genomes in the Cloning and Sanger Sequencing Era, 54 Steps for Genome Assembly from High- Throughput DNA Sequence Data, 54 Integration of Short Reads from Shotgun Sequencing, 56 Third- Generation Sequencing Technologies, 56 Hybrid Assemblies, 56 Stitching Scaffolds Together, 56 Advanced Bioinformatics Tools, 57 A Genome Assembly for a Polyploid Plant of Genome Size ~1 Gb as a Tetraploid with a Total Chromosome Count of 44 Using PacBio HiFi Reads, 58 DNA Isolation, 58 Data Assembly and Analysis, 58 Estimation of Genome Size and Heterozygosity, 59 De Novo Genome Assembly and Evaluation, 59 Comparison of the Genome Assemblies with a Close Relative, 59 Telomere- to- Telomere Assembly, 67 RNA Assembly, 67 Summary, 73 References, 73 4 The Organelle Genomes 75 Chloroplasts, 75 Chloroplast Genome Size and Structure, 76 Sequencing the Chloroplast Genome, 76 Chloroplast Genes, 76 Variation in the Chloroplast Genomes Within and Between Species, 76 Use in Phylogenetics, 84 Mitochondrial Genome Size and Structure, 84 Variation in the Mitogenome, 86 Transfer of DNA Between the Nucleus, Chloroplast, and Mitochondrion, 88 Heteroplasmy, 90 Anterograde and Retrograde Signaling, 92 Retrograde Signaling and RNA Metabolism in Plants, 94 References, 96 5 Gene Discovery Paradigms 99 Introduction, 99 Genome Annotation, 101 Identification of Genes by Mutagenesis, 107 Insertional Mutagenesis with T- DNA, 109 Targeting- Induced Local Lesions in Genomes (Tilling), 110 Gene Editing, 111 Summary, 112 References, 112 6 Control of Gene Expression 115 Introduction, 115 Specific Promoter Sequences Are Required for Regulated Gene Expression, 117 The Effect of Enhancer Elements on Gene Expression, 119 Posttranscriptional Effects of mRNA Signals, 120 Role of 5′ Sequences in Gene Expression, 122 Role of 3′ Sequences in Gene Expression, 122 Role of Introns in Gene Expression, 122 Conserved Sequences in Eukaryotic Promoters, 124 Trans- Acting Factors Control Gene Expression, 125 mRNA Stability, 125 Chemically/Physically Regulated Gene Expression in Plants, 127 Effects of Chromatin Structure, 128 Translational Control, 133 Summary, 137 References, 140 7 Epigenetics 145 Introduction, 145 DNA Methylation, 147 Histone Modifications, 148 Epigenetic Silencing of Transposable Elements, 149 Unstable Inheritance of Epialleles, 150 Summary, 151 References, 153 8 Functional Genomics 155 Introduction, 155 Transcriptome Profile, 157 Protein– Protein Interactions, 157 Yeast Two- Hybrid Systems, 158 Protein Tags and Transgenics, 158 Metabolomics, 161 Single- Cell – Omics, 163 Conclusions, 164 References, 164 9 The Microbiome 167 Introduction, 167 The Rhizosphere, 168 Bacterial Communities, 169 What Influences the Composition of the Bacterial Microbiome in the Rhizosphere?, 170 Phyllosphere, 170 Endosphere, 174 Plant Growth- Promoting Rhizobacteria, 175 Rhizobia and Mycorrhizae, 176 Importance and Use of the Microbiome, 179 References, 182 10 Interactions with the External Environment 185 Introduction, 185 Abiotic Stresses, 186 Biotic Interactions, 190 Disease Resistance, 191 Pest Resistance, 198 Biotechnological Opportunities, 198 References, 199 11 Complex Character Manipulation— Plant Breeding 201 Introduction, 201 Conventional Breeding Methods, 202 Marker- Assisted Selection, 204 Quantitative Trait Loci, 208 Genomic Selection, 214 High- Throughput Phenotyping, 215 Speed Breeding, 215 Pangenomics as a Source of Useful Alleles, 215 Concluding Integration, 218 References, 220 12 Genetic Manipulation of the Plant Genome 223 Introduction, 223 Agrobacterium-Mediated Plant Transformation: Biology and Applications, 225 Bypassing the Bottleneck of Tissue Culture, 228 Transformation Through Direct Delivery of DNA, 228 Biolistic Transformation, 228 Electroporation, 229 Nanotechnology Strategies, 229 Carbon Nanotubes, 229 Magnetofection, 229 DNA Origami, 232 Gene Editing, 233 Summary and Outlook, 235 References, 237 13 Bioethical Concerns and the Future of Plant Genomics 239 Development of Biotechnologically Modified Plants, 240 The Global Landscape for Regulation of GM Plants, 241 The Regulatory Environment in the United States, 247 European Union (EU) Responses to Genetically Modified (GM) Plants, 248 Case Studies, 250 BT Brinjal, 250 Golden Rice, 251 References, 253 Index 255