Plant Genomics - Christopher A. Cullis

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Résumé :

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 (?) 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 Annotati...

Biographie:

Christopher A. Cullis is the Francis Hobart Herrick Professor of Biology at Case Western Reserve University, an AAAS Fellow, and a Life Fellow of the Ohio Academy of Sciences. In addition to directing an MS in Biotechnology Entrepreneurship program from 2002 to 2023, he was instrumental in setting up the Society for International Bioenterprise Education and Research (SIBER) and incorporating it as a 503C3. He has published on the genomics of more than 20 plant species....

Sommaire:

Introduction to the range of molecular techniques to investigate unique facets of plant growth, development, and responses to the environment

Plant Genomics introduces the complex relationship between the genome, microbiome, genes, and epigenetics of plants, as well as the range of molecular techniques applicable to investigating the unique facets of plant growth, development, and response to the environment. State-of-the-art science in the field is discussed, as well as future outlooks on what the next decade is likely to bring.

This book includes new techniques for modifying the plant genome and their impact on modifying plants to combat the impact of biotic and abiotic stresses, including those associated with climate change, new technologies including long and short read sequencing and proximity ligation and the combination of these technologies for assembling sequence data into chromosomes, a new chapter on the sequences of the chloroplast and mitochondrial genomes, and a dedicated chapter to epigenetics and the importance in gene regulation.

Written by a highly qualified author with significant published research contributions to the field, Plant Genomics includes information on:

• Structure and information content of the chloroplast and mitochondrial genomes and their use in phylogeny
• Use of transcriptomes from various tissues to identify expressed sequences and their identification as genes
• Function of small regulatory RNAs and long non-coding RNAs and involvement of small RNAs in the control of gene expression
• Epigenetic silencing of transposable elements and their release by stress and cross-generational contribution of epigenetic variation
• Use of the pan-genome to assemble a comprehensive germplasm for a particular crop species

Plant Genomics is an ideal textbook for undergraduate courses on plant biology, particularly those focusing on molecular descriptions, and a helpful auxiliary text to plant biology laboratory courses. It will also be of interest to students in plant molecular biology, agricultural and food sciences, and plant, food, and crop bioengineering....