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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Plant genome and transcriptome annotations: from misconceptions to simple solutions.

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Summary

This review provides plant scientists with essential tools and resources for functional genome and transcriptome annotation. It details a pipeline and reference chart for efficient annotation using public data.

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Area of Science:

  • Plant genomics and transcriptomics
  • Bioinformatics and computational biology

Background:

  • Next-generation sequencing has generated vast plant genomic and transcriptomic data.
  • Functional annotation tools and resources are not comprehensively enumerated, hindering research progress.

Purpose of the Study:

  • To provide a comprehensive review of resources and methods for plant genome and transcriptome functional annotation.
  • To present a practical guide for plant researchers to annotate their data efficiently.

Main Methods:

  • Review of typical ontologies for plant science.
  • Identification of useful databases and resources for functional annotation.
  • Development of an automated annotation pipeline.
  • Creation of a reference chart for annotation steps.

Main Results:

  • Enumeration of key ontologies, databases, and resources.
  • Description of expected outcomes for annotated plant genomes.
  • Presentation of an automated annotation pipeline.
  • A step-by-step guide for annotating plant genomes/transcriptomes.

Conclusions:

  • Efficient functional annotation is crucial for leveraging plant genomic and transcriptomic data.
  • This review offers a practical framework and resources to bridge the gap in plant functional genomics.
  • The provided pipeline and reference chart empower researchers to annotate their data effectively.