The Moso Bamboo Genome

Description

This book is the first comprehensive compilation describing the botanical traits, genetic resources, whole genome sequencing, Mitochondrial genome, transcriptomes of different organs with developmental stages, transcription factors, delineating gene evolution of gene family in Bambusoideae, alternative splicing (AS) and polyadenylation, case studies for economically important traits such as internode length, shoot fast growing, flowering, ageing and stress-resistant genes and small RNAs-mediated gene regulation of moso bamboo flowering and other developmental stages. Applications of transcriptome and genome approaches in moso bamboo in general and the prospects of transgenic breeding and genome editing technologies in bamboo are also discussed. Altogether, the book comprises eleven chapters covered over 200 pages authored by the researchers involved in genomic science, molecular biology, and breeding. This book appeals to graduate students, post-graduate students, research scholars, researchers, and industry players in the field of plantation bamboo in general, bamboo processing and bamboo garden owner and fans of bamboo culture in particular. Preface to the Series Preface Acknowledgements Contents Contributors Abbreviations 1 Economic Value and Research Significance of Moso Bamboo Abstract 1.1 Distribution of Moso Bamboo 1.1.1 Global Distribution of Moso Bamboo 1.1.2 Distribution in China 1.1.3 Quality of Moso Bamboo Forests 1.1.4 Biomass and Carbon Stock of Moso Bamboo Forests 1.1.5 Resource Distribution and Changes 1.2 Uses and Economic Value 1.2.1 Uses 1.2.1.1 Used as an Alternative to Timber 1.2.1.2 Used as Food 1.2.1.3 Medicinal Uses 1.2.1.4 Ornamental Uses 1.2.1.5 Used in Papermaking 1.2.1.6 Used as Fodder 1.2.1.7 Used for Soil Conservation and Wind Blocking 1.2.1.8 Other Uses 1.2.2 Economic Value 1.3 Status of Moso Bamboo Research 1.3.1 Ecological Management of Moso Bamboo Forests 1.3.1.1 Studies on Management Model of Moso Bamboo Forest 1.3.1.2 Management Model of Moso Bamboo Mixed Forests 1.3.2 Study on Moso Bamboo Materials Properties 1.3.2.1 Study on Moso bamboo’s Properties 1.3.3 Processing and Utilization of Moso Bamboo Materials 1.3.3.1 Bamboo-Based Panels 1.3.3.2 Bamboo Charcoal 1.3.3.3 Bamboo Vinegar 1.3.3.4 Bamboo Fibre 1.3.4 Moso Bamboo Genome References 2 Intraspecific Variation of Moso Bamboo Abstract 2.1 Introduction 2.2 Intraspecific Variation of Moso Bamboo 2.2.1 Phyllostachys edulis f. edulis 2.2.2 Phyllostachys edulis f. abbreviata 2.2.3 Phyllostachys edulis f. anjiensis 2.2.4 Phyllostachys edulis f. aureovariegata 2.2.5 Phyllostachys edulis f. bicolor 2.2.6 Phyllostachys edulis f. curviculmis 2.2.7 Phyllostachys edulis f. epruinosa 2.2.8 Phyllostachys edulis f. exaurita 2.2.9 Phyllostachys edulis f. gracilis 2.2.10 Phyllostachys edulis f. heterocycla 2.2.11 Phyllostachys edulis f. holochrysa 2.2.12 Phyllostachys edulis f. huamozhu 2.2.13 Phyllostachys edulis f. luteosulcata 2.2.14 Phyllostachys edulis f. mira 2.2.15 Phyllostachys edulis f. nabeshimana 2.2.16 Phyllostachys edulis f. obliquinoda 2.2.17 Phyllostachys edulis f. obtusangula 2.2.18 Phyllostachys edulis f. pachyloen 2.2.19 Phyllostachys edulis f. porphyrosticta 2.2.20 Phyllostachys edulis f. purpureoculmis 2.2.21 Phyllostachys edulis f. purpureosulcata 2.2.22 Phyllostachys edulis f. quadrangulata 2.2.23 Phyllostachys edulis f. tubaeformis 2.2.24 Phyllostachys edulis f. tumescens 2.2.25 Phyllostachys edulis f. ventricosa 2.2.26 Phyllostachys edulis f. venusta 2.2.27 Phyllostachys edulis ‘Anderson’ 2.2.28 Phyllostachys edulis ‘Bicanna’ 2.2.29 Phyllostachys edulis ‘Jinsilonglinzhu’ 2.2.30 Phyllostachys edulis ‘Moonbeam’ 2.2.31 Phyllostachys Edulis ‘Oboro’ 2.2.32 Phyllostachys edulis ‘Okina’ References 3 Biological Traits of Moso Bamboo Abstract 3.1 Introduction 3.2 Rhizome Characteristics of Moso Bamboo 3.3 Shoot Growth Characteristics 3.3.1 Daily Growth of Moso Bamboo Shoot 3.3.2 Dynamic Anatomical Variation in Shoot Tip Growth Stages 3.4 Culm Growth Characteristics 3.5 Characteristics of Leaves 3.6 Characteristics of Flowers 3.7 Characteristics of Moso Bamboo Seeds 3.8 Bamboo Maturation and Growth Characteristics of Bamboo Stands References 4 Moso Bamboo Genome Abstract 4.1 Introduction 4.2 Moso Bamboo Genome Size 4.3 Moso Bamboo Draft Genome 4.4 The Genome Database of Bamboos 4.5 The Draft Genome of Other Bamboos 4.6 The Genome Polyploidy of Woody Bamboos 4.7 The Genome Clue to the Unique Biological Traits of Bamboos References 5 Moso Bamboo Transposon Abstract 5.1 Introduction 5.2 Long Terminal Repeat Retroelements (LTR Retroelements) from Moso Bamboo 5.3 MITEs from Moso Bamboo 5.4 Transposable Mariner-Like Elements (MLE) in Moso Bamboo 5.5 Transposable Elements and Moso Bamboo Flowering 5.6 Transposable Elements and Moso Bamboo Variants References 6 Transcriptome of Moso Bamboo Abstract 6.1 Global Transcriptome Analysis in the Growth of Moso Bamboo Shoots 6.1.1 Introduction 6.1.2 Overview of Gene Expression in Each Shoot Growth Stage 6.1.3 Functional Analysis on DGEs 6.1.4 Importance of Cell Division and Elongation to Shoot Elongation 6.1.5 Spatio-Temporal Dynamic Changes in Moso Bamboo Shoots 6.1.6 Conclusion 6.2 Global Transcriptome Analysis in Moso Bamboo Flower Development 6.2.1 Quality Control and Filtering of Sequence Data 6.2.2 Reads Mapped to the Reference Genome Dataset 6.2.3 Putative Moso Bamboo Floral Development Transcription Factors 6.2.4 Detection of Putative Genes Associated with Flowering Time Control and Flower Development 6.2.5 Change of Gene Expression Profile in Varying Flower Developmental Stages 6.2.6 Expression Level of Putative Genes During Flower Development 6.2.7 Gene Validation and Expression Analysis 6.2.8 Conclusions 6.3 Global Transcriptome Analysis in Germinating Moso Bamboo Seeds 6.3.1 Global Transcriptome Analysis 6.3.2 Germination Respiration Pathway References 7 Alternative Splicing and Alternative Polyadenylation in Moso Bamboo Abstract 7.1 Introduction 7.1.1 AS and APA in Plant 7.1.2 The Tissue-Specific AS and APA Pattern in Moso Bamboo 7.2 The Database of AS and APA in Moso Bamboo 7.3 Methods for Identification of AS and APA 7.3.1 Experiment and Sequencing 7.3.2 Bioinformatics Analysis 7.4 The Potential Functions of AS and APA 7.4.1 Alteration in Protein Domain by AS and APA 7.4.2 Nonsense-Mediated mRNA Decay (NMD) Regulation by AS and APA 7.4.3 Alteration of miRNA Target Sites by AS and APA 7.4.4 Diverse Back-Splicing Landscape: Insights into Circular RNAs in Moso Bamboo 7.5 Future Prospects References 8 Characterizations and Functions of Transcription Factor Gene Families Abstract 8.1 Resistance Gene Candidates 8.1.1 MYB Transcription Factor 8.1.2 BHLH Transcription Factors 8.1.3 bZIP Transcription Factors 8.1.4 GRF Transcription Factor 8.1.5 HD-Zip Transcription Factors 8.1.6 PHD Transcription Factors 8.1.7 SPL Transcription Factors 8.1.8 TCP Transcription Factors 8.1.9 Trihelix Transcription Factors 8.1.10 WRKY Family of Transcription Factors (TFs) 8.2 Flowering and Stamen Development Gene Candidates 8.2.1 Dof Transcription Factor 8.2.2 MADS Transcription Factor 8.2.3 CONSTANS-Like Gene Family 8.3 Endogenous Hormones Regulation in Shoot Fast Growth 8.3.1 SAUR Family Members 8.3.2 WUSCHEL-Related Homeobox (WOX) Protein Family 8.4 Ageing 8.4.1 NAC Transcription Factor References 9 MicroRNAs of Moso Bamboo Abstract 9.1 Introduction 9.2 miRNAs Could Regulate Reproductive Growth of Moso Bamboo 9.3 miRNAs Could Regulate Vegetative Growth of Moso Bamboo 9.4 Functions of Moso Bamboo miRNAs in Abiotic Stress Responses References 10 Mitochondrial Genome of Bambusicolous Fungus- Shiraia bambusicola Abstract 10.1 Introduction 10.2 Mitogenome Summary 10.2.1 General Description of Dothideomycetes 10.2.1.1 Fast Development of Mitogenomes 10.3 Definition of S. bambusicola and Its Distribution 10.3.1 Variational Definition of S. bambusicola 10.3.2 Expansive Distribution of S. bambusicola 10.4 Fascinating Properties of S. bambusicola 10.4.1 Exceptional Bambusicolous Fungus and Its Special Host 10.4.2 Amazing Function of Natural Products 10.5 Mitogenome Structure of S. bambusicola 10.5.1 Small Mitogenome Size 10.5.2 Explicit Sequence Structure 10.6 Interesting Genes from Mitogenome 10.6.1 Special Gene Order 10.6.2 Introns and the ORFs in Introns 10.6.3 Unknown ORFs and Conserved ORFs Within Intergenic Regions 10.6.4 Additional Obvious Characteristics 10.7 Evolutionary Status of S. bambusicola 10.8 Conclusions and Future Prospects References 11 Breeding Status and Strategies of Moso Bamboo Abstract 11.1 Main Propagation Methods and Techniques of Moso Bamboo 11.1.1 Transplanting of Mother Bamboo 11.1.2 Seedling of Moso Bamboo 11.1.3 Propagation by Burying Rhizomes 11.2 Main Breeding Methods and Techniques of Moso Bamboo 11.2.1 Hybrid Breeding Technology 11.2.2 Radiation Mutation Breeding 11.2.3 Molecular Marker Assisted Breeding 11.3 Molecular Breeding 11.3.1 Tissue Culture of Sympodial Bamboo Species 11.3.2 Moso Bamboo Tissue Culture 11.3.3 Genetic Transformation 11.4 Gene Editing 11.5 Prospect of Future of Moso Bamboo Breeding 11.5.1 Main Problems in Moso Bamboo Breeding 11.5.2 Proposal of Moso Bamboo Breeding 11.5.3 The Main Goal and Direction of Breeding Research References