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SECTION II: Biochemistry, Molecular Biology, and Evolution of Plant Volatiles

The Role of Transcriptome Analysis in Shaping the Discovery of Plant Volatile Genes Past, Present, and Future

Darren C. J. Wong, Rod Peakall, and Eran Pichersky

CONTENTS

  • 6.1 Introduction...........................................................................................................................100
  • 6.1.1 The Diversity of Plant Volatiles................................................................................100
  • 6.1.2 The Spatial and Temporal Modulation of Volatile Biosynthesis and Emissions......100
  • 6.1.3 The Landscape of Plant Volatile Gene Discovery: From Functional Genomics

to Systems Biology...................................................................................................102

  • 6.2 Spearheading Plant Volatile Gene Discoveries with RNA-Seq Transcriptomes...................103
  • 6.2.1 Annotation of Functional Domains/Gene Families..................................................103
  • 6.2.2 Transcriptome Differential Expression Analyses.....................................................103
  • 6.2.3 Gene Co-expression Analyses and Omics Data Integration.....................................104
  • 6.2.4 New Opportunities for High-Resolution Sequence Variation Analysis with

RNA-Seq......................... 104

6.3 Lessons from Success Stories in the Discovery of Plant Volatile-Related Genes: From

Targeted Studies to Large-Scale Multi-omics Efforts...........................................................104

6.3.1 Leveraging Genome Sequence Data with Transcriptome, Targeted Genes, and

Metabolite Profiling: Lessons from Studies of Terpenes..........................................104

6.3.2 Integrating Transcriptome Analysis with Targeted Gene and Metabolite Profiling of Select Tissues/Organs and Developmental Stages: Lessons from

the Garden Petunia....................................................................................................105

6.3.3 Integrating Transcriptome Analysis with Targeted Gene and Metabolite Profiling

of Specialized Tissue/Cell Types: Lessons from Sweet Basil....................................106

6.3.4 Comparative Transcriptomics Analysis and Targeted Gene and Metabolite

Profiling: Harnessing Within- and Between-Species Genetic Variation in Floricultural and Agricultural Crop Plants...............................................................106

6.3.5 Integrating Proteomics Techniques with Transcriptome and Targeted Gene and

Metabolite Profiling..................................................................................................107

6.3.6 The Utility of Gene Co-Expression Analysis in Model and Nonmodel

Plant Systems............................................................................................................108

6.3.7 Integrating Population Genomics and Multi-omics Datasets for Large-Scale

Plant Volatile Gene Discovery..................................................................................109

  • 6.4 Future Directions..................................................................................................................109
  • 6.4.1 Harnessing TF Overexpression or Knockdown Coupled with Transcriptome
  • (or Multi-omics) Analysis.........................................................................................110
  • 6.4.2 Harnessing Single-Cell or Single-Cell Type Isolation Methods with

Next-Generation Transcriptome (or Multi-omics) Analysis.....................................110

  • 6.4.3 Harnessing the Physical Proximity of Genes with Gene Co-expression Analysis.......111
  • 6.4.4 Harnessing Expression Quantitative Trait Loci (eQTL) for Candidate

Prioritization.............................................................................................................111

6.4.5 Harnessing State-of-the-Art Machine Learning Algorithms: Putting All the

Pieces Together?.......................................................................................................Ill

  • 6.4.6 Maximizing the Success of Plant Volatile Gene Discovery......................................112
  • 6.5 Conclusion............................................................................................................................113

Acknowledgments..........................................................................................................................113

References......................................................................................................................................114

 
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