Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Citrus, particularly sweet orange (Citrus sinensis), is a globally significant fruit crop, vital for fresh consumption and juice production.
• Understanding the sweet orange genome is crucial for advancing citrus research and crop improvement.

Purpose of the Study:

• To sequence the draft genome of a double-haploid sweet orange (Citrus sinensis cv. Valencia).
• To construct the Citrus sinensis annotation project (CAP) for storing and visualizing genomic and transcriptome data.
• To provide a user-friendly platform for accessing predicted protein-protein interactions and metabolic pathways.

Main Methods:

• Genome sequencing of a double-haploid sweet orange cultivar.
• Construction of the Citrus sinensis annotation project (CAP) using GBrowse.
• Integration of gene prediction (ab initio), EST, RNA-seq, and RNA-paired end tag (RNA-PET) data for gene annotation.
• Development of a web interface for data visualization and analysis.

Main Results:

• Successful sequencing of the sweet orange draft genome.
• Establishment of the Citrus sinensis annotation project (CAP) with integrated genomic and transcriptome data.
• CAP offers GBrowse-based organization and evidence-based gene annotation.
• A user-friendly interface is available for exploring predicted protein-protein interactions and metabolic pathways.

Conclusions:

• The Citrus sinensis annotation project (CAP) provides a comprehensive resource for sweet orange research.
• CAP facilitates the visualization and analysis of genomic and transcriptome data.
• This resource is valuable for researchers studying sweet orange and other woody plants.
• The CAP database is freely accessible at http://citrus.hzau.edu.cn/.