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

• Published in: PloS one Vol. 9; no. 1; p. e87723
• Main Authors: Wang, Jia, Chen, Dijun, Lei, Yang, Chang, Ji-Wei, Hao, Bao-Hai, Xing, Feng, Li, Sen, Xu, Qiang, Deng, Xiu-Xin, Chen, Ling-Ling
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.01.2014; Public Library of Science (PLoS)
• Subjects: Agricultural production; Agriculture; Annotations; Anopheles; Bioinformatics; Biology; Citrus; Citrus fruits; Citrus sinensis; Citrus sinensis - genetics; Computer Science; Crops; Databases, Genetic; Fruit crops; Fruits; Gene expression; Genes; Genome, Plant; Genomes; Genomics; Horticulture; Internet; Laboratories; Life sciences; Metabolic Networks and Pathways; Metabolic pathways; Metabolism; Molecular Sequence Annotation; Molecular Sequence Data; Ontology; Plant biology; Predictions; Protein interaction; Protein Interaction Maps; Protein-protein interactions; Proteins; Rankings; Ribonucleic acid; RNA; Woody plants
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0087723

Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.