Note: Intro -- Preface to the Series -- Preface -- Contents -- Contributors -- 1 The Broomcorn Millet Genome -- Abstract -- 1.1 Introduction -- 1.2 Taxonomy of Broomcorn Millet -- 1.2.1 Botanical Characteristics -- 1.2.2 Geographic Distribution -- 1.2.3 Conserved Germplasms of Broomcorn Millet -- 1.2.4 The Underutilized Status of Broomcorn Millet -- 1.2.5 Qualities and Values of Broomcorn Millet -- 1.3 Genome Sequencing -- 1.3.1 Genome Assembly -- 1.3.2 Genetic Linkage Map -- 1.3.3 Genome Annotation -- 1.3.4 Evolutionary History of Broomcorn Millet -- 1.3.5 Comparative Genomics with Other Crops -- 1.3.6 Genes Involved in C4 Photosynthesis -- 1.4 Future Goals and Prospects -- Acknowledgements -- References -- 2 Buckwheat Genome and Genomics -- Abstract -- 2.1 Introduction -- 2.2 Buckwheat Genome -- 2.3 Buckwheat Genomics -- 2.4 Key Traits and Gene Function -- 2.5 Conclusion and Perspective -- Acknowledgements -- References -- 3 Tef [Eragrostis tef (Zucc.) Trotter] -- Abstract -- 3.1 Crop Background -- 3.1.1 Botanical Description -- 3.1.2 Geographical Distribution -- 3.1.3 Accessible in Seed Banks -- 3.1.4 Why It Is Underutilized? -- 3.1.5 Benefits of Tef -- 3.2 Genome Sequencing -- 3.2.1 First Sequencing: Tef Improvement Project 2010 -- 3.2.2 Chromosome-Level Sequencing: Tef Sequencing Consortium -- 3.2.3 Repetitive Element Content -- 3.2.4 Resequencing -- 3.2.5 Candidate Genes for Agronomic Traits -- 3.3 Conclusions -- References -- 4 The Apricot Genome -- Abstract -- 4.1 Introduction -- 4.1.1 Botanical Description -- 4.1.1.1 The Main Species of Apricot -- 4.1.1.2 Eco-geographical Groups of Common Apricot -- 4.2 Origin and Distribution -- 4.2.1 Geographic Distribution -- 4.2.1.1 The Seed Banks of Apricot -- 4.2.2 Economic and Ecological Value of Apricot -- 4.2.2.1 Nutritional Value -- 4.2.2.2 Ecological Value -- 4.3 Genome Sequencing -- 4.3.1 Strategy. , 4.3.1.1 Plant Materials -- 4.3.1.2 Sequencing Strategy -- 4.3.2 The Apricot Genome Assembly -- 4.3.3 Resequencing -- 4.3.4 Comparison to Other Crops -- 4.3.5 Gene Discovery -- 4.3.6 Candidate Genes for Agronomic Traits -- 4.3.6.1 Accumulation of β-Carotene in Apricot -- 4.3.6.2 Amygdalin Metabolism and the Sweet/Bitterness Kernel Forming -- 4.3.6.3 Plum Pox Virus (PPV) -- 4.4 Future Goals and Prospects -- 4.4.1 The Goal of Apricot Genomics Research -- 4.4.2 Prospects and Implications of Apricot Genomics -- References -- 5 Chinese Jujube: Crop Background and Genome Sequencing -- Abstract -- 5.1 Crop Background -- 5.1.1 Introduction -- 5.2 Botanical Description -- 5.2.1 Taxonomy -- 5.2.2 Geographic Distribution -- 5.2.3 Morphology -- 5.3 Nutrient, Utilization, and Propagation -- 5.4 Research Challenges and Opportunities -- 5.5 Genome Sequencing -- 5.6 Strategy for Jujube Genome Assembly and Annotation -- 5.7 Features of Jujube Genome -- 5.8 Comparison to Other Crops in Evolution -- 5.9 Candidate Genes for Agronomic Traits -- 5.9.1 Genes Related to Vitamin C Accumulation in Fruit -- 5.9.2 Genes Related to Sugar Accumulation in Fruit -- 5.9.3 Self-shoot-pruning Trait Related Genes -- 5.9.4 Abiotic/Biotic Stress-Related Genes -- 5.9.5 Genes Related to Flower Development -- 5.9.6 S-Locus Genes in Jujube -- 5.9.7 Gene Family-Related Research Based on the 'Dongzao' Genome -- 5.10 Resequencing in Jujube Research -- 5.11 Transcriptome-Related Research -- 5.12 Future Goals and Prospects -- References -- 6 The Longan (Dimocarpus longan) Genome -- Abstract -- 6.1 Background -- 6.2 Genome Sequencing -- 6.2.1 Strategy -- 6.2.2 Results-Genome Statistics -- 6.2.3 Resequencing -- 6.3 RNA Sequencing -- 6.3.1 Whole Transcriptome Sequencing -- 6.3.2 Single-Cell RNA Sequencing -- 6.3.3 microRNAs -- 6.3.4 Long Noncoding RNAs -- 6.3.5 Circular RNAs. , 6.4 DNA Methylation Sequencing -- 6.5 Proteomics -- 6.6 Genetic Transformation -- 6.7 Future Prospects -- References -- 7 The Mangosteen Genome -- Abstract -- 7.1 The Genus Garcinia L. -- 7.2 Botanical Description of Mangosteen -- 7.2.1 Mangosteen as an Apomictic Species -- 7.2.2 Genetic Variation of Mangosteen -- 7.3 Origin and Distribution of Mangosteen -- 7.3.1 Origin of Mangosteen -- 7.3.2 Closely Related Species of Mangosteen -- 7.3.2.1 G. celebica L. (Syn. G. hombroniana Pierre) -- 7.3.2.2 G. malaccensis Hook. F. -- 7.3.2.3 G. penangiana Pierre -- 7.3.2.4 G. opaca King -- 7.3.3 Geographic Distribution of Mangosteen -- 7.3.4 Mangosteen Export from Malaysia -- 7.4 Conservation of Mangosteen Germplasm -- 7.5 Why Mangosteen is Underutilised? -- 7.6 Benefits of Mangosteen -- 7.7 Genomics Study of Mangosteen -- 7.7.1 Genome Sequencing of Mangosteen -- 7.7.2 Genome Size of Mangosteen -- 7.7.3 Cytogenetics of Mangosteen -- 7.8 Conclusion -- Acknowledgements -- References -- 8 The Passion Fruit Genome -- Abstract -- 8.1 Introduction -- 8.1.1 Genetic Studies and Breeding Efforts -- 8.2 Sequencing and Assembly of Passiflora Genomes -- 8.2.1 Transposable Element Detection in Passiflora Genomes -- 8.2.2 Passiflora Cytogenomics -- 8.2.3 Functional Annotation of Passiflora Genomes -- 8.2.4 The Passiflora MADS-Box Gene Family and Phase Change Transitions -- 8.2.5 Passiflora Organellar Genomes -- 8.3 Conclusion -- References -- 9 The Soursop Genome (Annona muricata L., Annonaceae) -- Abstract -- 9.1 Introduction -- 9.1.1 Early Angiosperm Genome Evolution -- 9.1.2 The Custard Apple Family (Annonaceae) and Pomology -- 9.2 Research Scope and Methodological Approach -- 9.2.1 Genomic DNA Extraction, Illumina Sequencing, and Genome Size Estimation -- 9.2.2 Library Preparation and Sequencing for PacBio, 10X Genomics and BioNano. , 9.2.3 Denovo Genome Assembly, 10X and Optical Scaffolding -- 9.2.4 Hi-C Scaffolding -- 9.2.5 Repeat Sequence Detection -- 9.2.6 RNA Sequencing and Transcriptome Assembly -- 9.2.7 Annotation -- 9.2.8 Positive Selection -- 9.2.9 Detecting Historical Changes in Population Size -- 9.2.10 Hybridization Capture Data Mapping -- 9.2.11 Coalescent Phylogenomics -- 9.2.12 Gene Family Expansion -- 9.2.13 Identification of Whole Genome Duplication Events -- 9.2.14 Evolutionary Incongruence in Early Angiosperms -- 9.3 Genome Perspectives for Pomological and Early Angiosperm Research -- 9.3.1 A High-Quality Genome of the Soursop -- 9.3.2 Repeat Sequences in the Soursop Genome -- 9.3.3 Genes Involved in Soursop Defence and Disease Resistance -- 9.3.4 Historical Fluctuations in Population Size of Annona muricata -- 9.3.5 Mapping of Annona Genes from Hybridization Capture Analyzes -- 9.3.6 Coalescent Phylogenomics in Annonaceae and Early Angiosperms -- 9.3.7 Gene Family Expansion in Annona muricata -- 9.3.8 Evolutionary Incongruence and WGD during Early Angiosperm Divergence -- 9.4 Future Goals and Prospects -- Acknowledgements -- References -- 10 Underutilised Fruit Tree Genomes from Indonesia -- Abstract -- 10.1 Overview -- 10.2 Underutilised Fruits -- 10.2.1 Menteng -- Baccaurea motleyana Müll.Arg. -- 10.2.2 Nangkadak -- Artocarpus heterophyllus x Artocarpus integer -- 10.2.3 Rambutan -- Nephelium lappaceum L. -- 10.2.4 Sidempuan Snake Fruit -- Salacca sumatrana Becc. -- 10.2.5 Gandaria -- Bouea macrophylla Griffith -- 10.2.6 Lobi-Lobi -- Flacourtia inermis (Burm. f.) Merr. -- 10.2.7 Duku -- Lansium domesticum (Lansium parasiticum (Osbeck) Sahni and Bennet) -- 10.2.8 Matoa -- Pometia pinnata J.R.Forst. and G.Forst. -- 10.2.9 Kedondong -- Spondias dulcis L. -- 10.2.10 Jambu Air or Wax Apple -- Syzygium samarangense (Blume) Merr. and L.M.Perry. , 10.2.11 Sentul or Kecapi -- Sandoricum koetjape (Burm.f.) Merr -- 10.2.12 Kasturi or Kalimantan Mango -- Mangifera casturi Kosterm -- 10.2.13 Durian Kura-Kura -- Durio testudinarius Becc -- 10.3 Conclusions -- References -- 11 The Bambara Groundnut Genome -- Abstract -- 11.1 Introduction -- 11.1.1 Botanical Description and General Ecology -- 11.1.2 Geographical Distribution -- 11.1.3 Genetic Resources, Accessibility to/from Seed Banks -- 11.1.4 Bambara Groundnut-An Important but Underutilised Crop -- 11.1.5 Nutritional Composition -- 11.1.6 Underutilisation of Bambara Groundnut -- 11.2 Molecular Tools and Their Application in Bambara Groundnut -- 11.2.1 Molecular Markers-Development and Applications -- 11.2.2 Microarrays -- 11.2.2.1 RNAseq in Bambara Groundnut -- 11.2.3 Bambara Groundnut Genome-Current Achievements -- 11.3 Structure and Nomenclature of Traits in Linkage to Genome -- 11.4 Future Goals and Prospects -- 11.5 Conclusion -- References -- 12 Grasspea -- Abstract -- 12.1 Overview -- 12.2 Practical Needs and Objectives -- 12.2.1 Constraints -- 12.2.2 Breeding Targets -- 12.2.3 Breeding Resources -- 12.3 Ongoing and Projected Research -- 12.3.1 Genetics -- 12.3.2 Genetic Maps -- 12.3.2.1 An F2 Map -- 12.3.2.2 Recombinant Inbred Mapping Populations -- 12.3.2.3 Relationship Between Genetic Maps of Related Legumes -- 12.3.3 Transcriptomic Studies -- 12.3.4 Genomics -- 12.4 Conclusion and Perspectives -- Acknowledgements -- References -- 13 The Lablab Genome: Recent Advances and Future Perspectives -- Abstract -- 13.1 Introduction -- 13.2 Biology, Resources and Utilisation -- 13.2.1 Botanical Description -- 13.2.2 Geographical Distribution and General Ecology -- 13.2.3 Genetic Resources and Accessibility from Genebanks -- 13.2.4 Traits of Benefit and Reasons for Being Underutilised -- 13.2.5 Traditional and Improved Varieties. , 13.3 Molecular Tools and Their Application in Lablab.

Note: Intro -- Preface to the Series -- Contents -- 1 Introduction: The Importance of Eggplant -- Abstract -- 1.1 Overview -- 1.2 Economic Importance of Eggplant -- 1.3 Academic Importance of Eggplant -- 1.3.1 Eggplant as a Model for Parallel Evolution -- 1.3.2 Eggplant Wild Relatives for Crop Improvement -- 1.3.3 Transcriptomics in Eggplant -- 1.3.3.1 Eggplant and Its Relatives as a Model for Understanding Pathogen Infection -- 1.3.3.2 Eggplant as a Model to Understanding Anthocyanin Accumulation in Plants -- 1.3.3.3 Eggplant as a Model for Understanding the Wider Effects of Genetic Modification -- 1.4 Conclusions -- Literature Cited -- 2 Eggplant (Solanum melongena L.): Taxonomy and Relationships -- Abstract -- 2.1 Introduction -- 2.2 The Leptostemonum Clade -- 2.3 The Old World spiny solanums -- 2.4 The Eggplant Clade -- 2.5 Other Cultivated Eggplant Species -- 2.6 Conclusions and Prospects for Future Understanding -- Acknowledgements -- Literature Cited -- 3 The Genetics of Eggplant Nutrition -- Abstract -- 3.1 Introduction -- 3.2 Solanaceae Biodiversity Resources: Translating Trait Variation to Nutritional Value -- 3.2.1 Fruit Size, Antioxidants, and Shelf Life: An Entangled Relationship -- 3.2.2 Exploiting the Genetic Basis of Traits to Understand Artificial Selection -- 3.2.3 Introgression for Meeting Nutrition Needs -- 3.3 Phenotypic Similarity in Solanum Predicts Some Genetic Similarity -- 3.3.1 From Species Comparison to Clade Comparisons -- 3.4 Case Study: Gene Expression Predicts the Phenylpropanoid Pathway -- 3.4.1 Methods -- 3.4.2 Results and Discussion -- Literature Cited -- 4 Molecular Mapping and Synteny -- Abstract -- 4.1 Introduction -- 4.2 Genome-scale Macrosynteny in the Solanaceae -- 4.3 Microsynteny in the Solanaceae -- 4.4 Comparative Mapping Between Eggplant and Other Members of the Solanaceae -- References. , 5 Molecular Mapping, QTL Identification, and GWA Analysis -- Abstract -- 5.1 Linkage Map Construction -- 5.1.1 First-Generation Maps -- 5.1.2 Second-Generation Maps -- 5.2 QTL Mapping -- 5.3 Genome-Wide Association Mapping -- References -- 6 The Draft Genome of Eggplant -- Abstract -- 6.1 Introduction -- 6.2 Genome Assembly of Eggplant -- 6.2.1 Sequencing of the Eggplant Genome -- 6.2.2 Genome Assembly -- 6.2.3 Repetitive Sequences -- 6.2.4 Gene Prediction -- 6.2.5 Gene Annotation -- 6.3 Databases -- 6.3.1 The Eggplant Genome DataBase -- 6.3.2 The Plant Genome DataBase Japan (PGDBj) -- 6.4 Genome Sequencing Projects by Other Research Groups -- 6.4.1 Genome Sequencing of Eggplant -- 6.4.2 Complete Chloroplast Genome Sequence -- 6.5 Conclusion -- Literature Cited -- 7 Advances in Eggplant Genome Sequencing -- Abstract -- 7.1 Development of a New Eggplant Genome Sequence -- 7.1.1 Genome Sequencing and Assembly of the Eggplant Inbred Line 67/3 -- 7.1.2 Optical Mapping of the Line 67/3 -- 7.1.3 Eggplant Genome Anchoring -- 7.2 The Chloroplast Genome of Eggplant -- Literature Cited -- 8 Genome Annotation -- Abstract -- 8.1 Identification of Transposable Elements (TEs) -- 8.2 Gene Prediction and Annotation -- 8.3 Comparison Among Solanaceae Genome Sequences -- 8.4 Gene Families -- 8.5 Discovery of Solanum melongena Genome-Wide Microsatellite Markers -- Literature Cited -- 9 Resequencing -- Abstract -- 9.1 Introduction -- 9.2 Resequencing in Eggplant -- 9.3 High-Throughput Sequencing and Mapping -- 9.4 Variant Calling, Distribution and Annotation -- 9.5 Conclusions -- Acknowledgements -- References -- 10 Eggplants and Relatives: From Exploring Their Diversity and Phylogenetic Relationships to Conservation Challenges -- Abstract -- 10.1 Introduction -- 10.2 The Genus Solanum and Its Taxonomic Treatment. , 10.2.1 Classifications Based on Phenotypic Similarities Between Species -- 10.2.2 Classifications Based on Phylogenetic Relationships Between Species -- 10.2.3 Phylogenetic Relationships Within Subgenus Leptostemonum (spiny solanums) -- 10.2.3.1 New World spiny solanums -- 10.2.3.2 Old World spiny solanums -- 10.2.3.3 The Cultivated Eggplants and Their Closest Relatives: From Morphology to Genomics -- 10.2.4 Species Relationships: A Breeder's Look at the Crossroads Between Approaches and Criteria -- 10.2.4.1 DNA-Based Similarities Between Species -- 10.2.4.2 DNA-Based Phylogeny Combined to Other Criteria -- 10.2.4.3 Ploidy, Chromosomes and Meiotic Behaviour -- 10.3 Old World Subgenus Leptostemonum: Inventory and Conservation -- 10.3.1 Preliminary Inventory -- 10.3.2 From Nature to Genebanks: Opportunities and Threats -- 10.3.2.1 Ex Situ Collections of Cultivated and Wild Eggplants -- 10.3.2.2 Ex Situ Regeneration of Eggplants and Relatives Germplasm -- 10.4 Other "Eggplant" Species -- 10.4.1 Lasiocarpa Clade (Leptostemonum Clade) -- 10.4.2 Morelloid Clade (M Clade) -- 10.4.3 Archaesolanum Clade (M Clade) -- 10.4.4 Potato Clade -- 10.4.5 Cyphomandra Clade -- 10.5 Conclusion -- Appendix 1 -- Appendix 2 -- Appendix 3 -- Appendix 4 -- References -- 11 Crossability and Diversity of Eggplants and Their Wild Relatives -- Abstract -- 11.1 Introduction -- 11.2 Diversity of Cultivated and Wild Germplasm -- 11.2.1 Morphological and Genetic Diversity -- 11.2.1.1 Cultivated Germplasm -- 11.2.1.2 Wild Germplasm -- 11.2.2 Pest and Disease Resistances -- 11.2.2.1 Cultivated Germplasm -- 11.2.2.2 Wild Germplasm -- 11.2.3 Diversity for Other Traits -- 11.3 Crossability Between Eggplants and Relatives -- 11.3.1 Prezygotic and Post-zygotic Barriers -- 11.3.2 Cytogenetic Observations of Late Post-zygotic Barriers -- 11.3.3 Variation of Hybridisation Results. , 11.4 Overview of the Best Results Obtained When Crossing Spiny Solanums -- 11.4.1 Crosses Between Cultivated Eggplants -- 11.4.1.1 Solanum aethiopicum and S. macrocarpon -- 11.4.1.2 Solanum aethiopicum and S. melongena -- 11.4.1.3 Solanum macrocarpon and S. melongena -- 11.4.2 Crosses Between Cultivated Eggplants and Their Wild Progenitors -- 11.4.3 Crosses Between Cultivated Eggplants and (Non-progenitor) Wild Species -- 11.4.3.1 Reciprocal Crosses -- 11.4.3.2 Global Results for All Types of Crosses -- 11.4.4 Crosses Between Wild Species -- 11.5 Is Interspecific Crossability Predictable? -- 11.6 Overcoming Interspecific Hybrid Sterility via Tetraploidisation -- 11.7 Disharmonic Interaction Between Wild Cytoplasms and Eggplant Nucleus: An Opportunity for Breeders -- 11.7.1 Indehiscent Anthers-Non-release Type -- 11.7.2 No Formation of Pollen Grains -- 11.7.3 Towards Genetic Comparisons Between the Two CMS Types -- 11.8 Genetic Information Drawn from Interspecific Hybrid Phenotypes -- 11.8.1 Hybrids Between Cultivated Eggplants -- 11.8.1.1 Solanum aethiopicum and S. macrocarpon -- 11.8.1.2 Solanum aethiopicum and S. melongena -- 11.8.1.3 Solanum macrocarpon and S. melongena -- 11.8.2 Hybrids Between Cultivated Eggplants and Wild Species -- 11.8.3 Hybrids Between Wild Species -- 11.9 Somatic Interspecific Hybrids -- 11.9.1 Solanum Melongena + New World Spiny Solanums -- 11.9.2 Solanum Melongena + Old World Spiny Solanums -- 11.9.3 Other Somatic Hybridisations Involving Spiny Solanums -- 11.9.4 Solanum Melongena + Distantly Related Solanaceae Crops -- 11.10 Conclusions -- 11.10.1 Germplasm Characterisation -- 11.10.2 Sexual Crossability -- 11.10.3 Somatic Crossability -- 11.10.4 Hybrid Phenotypes and Genetics of Morphological Traits -- Literature Cited -- 12 Domestication of Eggplants: A Phenotypic and Genomic Insight -- Abstract. , 12.1 Domestication: An Overview -- 12.2 The Need to Understand Domestication -- 12.3 The Pathway(s) to Eggplant Domestication(s) -- 12.3.1 Solanum aethiopicum was Domesticated from S. anguivi -- 12.3.2 Solanum macrocarpon was Domesticated from Solanum dasyphyllum -- 12.3.3 Solanum melongena was Domesticated from Solanum insanum -- 12.3.4 Ongoing Questions About the Domestication Pathways -- 12.4 Domestication Genetics and Genomics of Eggplant -- References -- 13 Conclusions and Future Directions -- Abstract -- 13.1 Summary of Current Eggplant Work -- 13.2 Pathways for Future Research -- 13.2.1 Eggplant Improvement Through Introgression from Wild Species -- 13.2.2 Ecological and Evolutionary Research -- 13.3 Conclusions -- Literature Cited.