The Moso Bamboo Genome

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