Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome

Abstract

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/.

Genome-wide Identification, Classification and Expression Analysis of the Mildew Resistance Locus O ( MLO ) Gene Family in Sweet Orange ( Citrus sinensis )

“…The subcellular location was predicted with the WoLF PSORT programs (http://www.genscript.com/wolf-psort.html) and CELLO v.2.5 (http://cello.life.nctu.edu.tw) [ 43 ]. To identify the locations of MLO genes on sweet orange chromosomes, the positions of these genes were retrieved from the sweet orange genome data downloaded from the CAP database (http://citrus.hzau.edu.cn/orange/) [ 44 ]. The 14 sweet orange MLO genes were mapped to the chromosomes using MapChart [ 45 ].…”

“…To investigate the expression profiles of all CisMLOs in four distinct tissues, i.e., callus, flower, leaf and fruit, the normalized RNA-Seq RPKM (reads per kilobase exon model per million mapped reads) values of all CisMLOs were downloaded from the online database of the CAP [ 44 ], and imagined by the heat maps with transformed log 2 values using MultiExperiment Viewer (MeV) Version 4.9.0 software (http://www.tm4.org/mev.html) [ 52 ]. RESULTS…”

“…To verify all potential genes of the MLO family in the sweet orange genome, we used BLASTP and the keywords "MLO" to search the CAP (http://citrus.hzau.edu.cn/orange/) [ 44 ] with the 15 A. thaliana and 12 rice MLO proteins as a retrieve. Adopt this method, 14 potential MLO genes, named CisMLO1 to CisMLO14, were identified.…”

“…It has been documented that proteins rich in leucine residues responsible for the mechanisms of defense response [ 53,54 ]. The genomic locations of CisMLOs were illuminated on chromosomes of sweet orange available at CAP [ 44 ]. CisMLOs were widely scattered among all the chromosomes except chromosomes 4, 6, and 9.…”

“…To predict the function of CisMLOs, RNA-seq data were downloaded from C. sinensis genome database [ 36,44 ] and the expression patterns of CisMLOs in various tissues (callus, leaf, flower, and fruit) were analyzed and demonstrated in Fig. 5.…”