The Duckweed Genomes (Compendium of Plant Genomes)

Preface to the Series
Preface
Contents
Contributors
1 Importance of Duckweeds in Basic Research and Their Industrial Applications
	Abstract
	1.1 Introduction
	1.2 Current State of Duckweed-Based Applications
		1.2.1 Historical
		1.2.2 Water Treatment
		1.2.3 Bioenergy
		1.2.4 Animal Feed
		1.2.5 Human Nutrition
	1.3 Future Prospects in Duckweed-Based Applications
	Acknowledgments
	References
2 Tiny Plants with Enormous Potential: Phylogeny and Evolution of Duckweeds
	Abstract
	2.1 Introduction
	2.2 Taxonomy
	2.3 Phylogenetic Relationships
	2.4 Morphological Evolution
	2.5 Biogeography
	2.6 Conclusions
	Acknowledgements
	References
3 Worldwide Genetic Resources of Duckweed: Stock Collections
	Abstract
	3.1 Introduction
	3.2 Duckweed: Genera and Species
	3.3 Duckweed Stock Collection: The Pioneer
	3.4 Requirements of a Duckweed Stock Collection
	3.5 Species Identification of the Clones
	3.6 Duckweed Stock Collections Around the Globe
	References
4 Cytogenetics, Epigenetics and Karyotype Evolution of Duckweeds
	Abstract
	4.1 Introduction
	4.2 Genome Size, Chromosome Number and Karyotype Evolution
		4.2.1 Genome Size Evolution
		4.2.2 Chromosome Number and Karyotype Evolution
	4.3 Genome Features, Organization and Adaptation
	4.4 Epigenetic and Epigenomic Aspects
	Acknowledgements
	References
5 Genetic Diversity and DNA Barcoding in the Duckweed Family
	Abstract
	5.1 Species Diversity and Distribution in the Duckweed Family
	5.2 Population and Genetic Diversity
	5.3 Species Identification of Duckweed Based on DNA Barcoding
	References
6 Strategies and Tools for Sequencing Duckweeds
	Abstract
	6.1 Strategies for Sequencing Duckweeds
		6.1.1 Illumina Paired-End Sequencing for Low Complexity Duckweed Genomes
		6.1.2 PacBio and Oxford Nanopore Sequencing Providing an Opportunity to Crack the Complex Duckweed Genomes
		6.1.3 Bionano, 10X Genomics, and Hi-C for Scaffolding Duckweed Genomes
	6.2 Tools for Assembling Duckweeds
		6.2.1 De Novo Assembling Tools for Illumina Paired-End Reads
		6.2.2 De Novo Assembling Tools for PacBio or Nanopore Long Reads
	6.3 Summary
	References
7 The Journey of Spirodela Whole-Genome Sequencing
	Abstract
	7.1 Introduction
	7.2 Fast-Growing, Forever-Young Plants as a Promising Biofuel
	7.3 A Valuable Plant for Biomanufacturing
	7.4 An Aquatic Plant in Wastewater Treatment
	7.5 Why Sequence Spirodela Genome
	7.6 History and Consortium
	7.7 Sequencing Overview
	7.8 Construction of Physical Map
	7.9 Spirodela Genes
	7.10 Resequencing of Spirodela Genome
	7.11 Going Back to the Native Ecotypes
	7.12 Data Availability
	7.13 Conclusions
	References
8 Repetitive Sequences: Impacts and Uses in the Spirodela Genome
	Abstract
	Acknowledgements
	References
9 Stranger than Fiction: Loss of MADS-Box Genes During Evolutionary Miniaturization of the Duckweed Body Plan
	Abstract
	9.1 Small Is Beautiful: Evolutionary Developmental Biology of the Duckweed Body Plan
	9.2 MADS About Development: MTF Phylogeny and the Ontogeny of Angiosperms
	9.3 When Less Is More: Loss of MADS-Box Genes During Evolution
	9.4 Previous Studies on the Loss of MADS-Box Genes in Alismatales
	9.5 Lost in Miniaturization: Setback of MADS-Box Genes in Duckweed Genomes
		9.5.1 Conserved Clades of MIKC-Type Genes in Alismatales
		9.5.2 Clades of MIKCC-Group Genes Missing Completely in Alismatales
		9.5.3 Clades of MIKCC-Group Genes Lost in the Lineage Leading to Duckweeds
		9.5.4 Link Between the Simplified Body Plan of Duckweeds and Loss of Clades of MIKCC-Group Genes
	Acknowledgements
	References
10 Duckweed Chloroplast Genome Sequencing and Annotation
	Abstract
	10.1 Introduction
	10.2 DNA Preparation
		10.2.1 Pure cpDNA Isolation
			10.2.1.1 Gradient Centrifuge
			10.2.1.2 Enzyme Digestion
			10.2.1.3 High Ionic Strength
		10.2.2 DNA Amplification
			10.2.2.1 Whole Genome Amplification
			10.2.2.2 Long PCR Amplification
		10.2.3 Computational Filtration
	10.3 Chloroplast Genome Sequencing and Annotation
		10.3.1 Chloroplast Genome of L. minor Sequenced by Sanger Technology
		10.3.2 Chloroplast Genomes of S. polyrhiza, W. lingulata and W. australiana Sequenced by NGS Technology
		10.3.3 Other Chloroplast Genomes Sequenced by TGS Technology
	10.4 Chloroplast Genome Applications
		10.4.1 Chloroplast Genome Sequences for Plant Barcode
		10.4.2 Engineering the Chloroplast Genomes for Biotechnology Applications
	References
11 Genotyping-by-Sequencing for Species Delimitation in Lemna Section Uninerves Hegelm. (Lemnaceae)
	Abstract
	11.1 Introduction
	11.2 Materials and Methods
		11.2.1 Plant Material
		11.2.2 Molecular Methods
		11.2.3 Data Analysis
	11.3 Results
	11.4 Discussion
	Acknowledgements
	References
12 The Transcriptome in Landoltia punctata
	Abstract
	12.1 Introduction
	12.2 Starch Production and Transcriptome Analysis
	12.3 Heavy Metal Accumulation and Transcriptome Analysis
	12.4 Flavonoids Accumulation and Transcriptome Analysis
	12.5 Other Transcriptomes Analysis
	12.6 Conclusion
	References
13 Transcriptome Responses of Spirodela polyrhiza
	Abstract
	References
14 Proteomics in Duckweeds
	Abstract
	14.1 Introduction
	14.2 Starch Production and Proteomics in Landoltia punctata
	14.3 Flavonoids, Anthocyanin, Lignin Biosynthesis, and Proteomics in Landoltia punctata
	14.4 Conclusion
	References
15 Transformation Development in Duckweeds
	Abstract
	15.1 Introduction
	15.2 Transformation Methods
		15.2.1 Stable Transformation of Duckweeds
		15.2.2 Transient Transformation of Duckweeds
		15.2.3 Agrobacterium Strains and Density
	15.3 Regeneration and Selection of Transformed Plants
	15.4 Applications of Genetic Transformation in Duckweeds
		15.4.1 Fundamental Researches
		15.4.2 Bioenergy and Wastewater Treatment
		15.4.3 Bioreactor
	15.5 Conclusion and Future Perspectives
	References
16 Small RNAs in Duckweeds
	Abstract
	Acknowledgements
	References
17 Editing the Genome of Wolffia australiana
	Abstract
	17.1 Introduction
	17.2 Culture and Transformation
	17.3 The Draft Genome of W. australiana
	17.4 Genome Editing 	of W. australiana
	17.5 Conclusions and Perspectives for the Biotechnological Use of W. australiana
	Acknowledgements
	References
18 Future Prospects of Duckweed Research and Applications
	Abstract
	18.1 Introduction
	18.2 Future Prospects in Duckweed Genome Research
	18.3 Future Prospects in Duckweed-Based Applications
	Acknowledgements
	References