Introduction to this Project

    Citrus is one of the most important and widely grown fruit crop in the world, with global production of 122.3 million tons and total acreage of 8.9 million hectares in 2009 (FAOSTAT data, 2011), both ranking firstly among all the fruit crops. Citrus is a large genus with more than 10 major species. Among them, sweet orange is responsible for about 60% of Citrus production used both as fresh fruit and processed juice.
    Most sweet oranges are diploids, with the haploid chromosome number x=9. It has a relatively small genome about 367 Mb (Arumuganathan and Earle, 1991). By employing a whole-genome shotgun approach combined with DNA-PET technology, we sequenced the genome of a doubled-haploid callus line of sweet orange. The genome was assembled using SOAPdenovo, resulting in 4,811 scaffolds with N50=1.7 Mb. The total contig length (320.5 Mb) covers about 87.3% of the sweet orange genome. The scaffolds were aligned and oriented to the Citrus linkage map and about 80% of the assembled genome was anchored and organized as nine pseudo-chromosomes.
    The Citrus sinensis Annotation Project (CAP) was constructed in 2012 upon the completion of the sweet orange genome sequencing with the aim of providing the scientific community with an accurate annotation of the sweet orange genome sequence. One of the major goals is to facilitate a comprehensive analysis of the genome structure and function of sweet orange on the basis of the annotation. In addition, the predicted metabolic network (based on KEGG pathways) and protein-protein interaction network are also provided in this project.

1. Qiang Xu#, Ling-Ling Chen#, Xiaoan Ruan#, Di-Jun Chen, Andan Zhu, Chunli Chen, Denis Bertrand, Wen-Biao Jiao, Bao-Hai Hao, Matthew P. Lyon, et al. The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013 Jan;45(1):59-66. doi: 10.1038/ng.2472. Epub 2012 Nov 25.
2. Wen-Biao Jiao, Ding Huang, Feng Xing, Yibo Hu, Xiu-Xin Deng, Qiang Xu, Ling-Ling Chen. Genome-wide characterization and expression analysis of genetic variants in sweet orange. Plant J. 2013 Sep;75(6):954-64. doi: 10.1111/tpj.12254. Epub 2013 Jul 19.
3. Jia Wang#, Di-Jun Chen#, Yang Lei#, Ji-Wei Chang, Bao-Hai Hao, Feng Xing, Sen Li, Qiang Xu, Xiu-Xin Deng, Ling-Ling Chen. Citrus sinensis Annotation Project (CAP): a comprehensive database for sweet orange genome. PLOS ONE, 2014, 9(1): e87723. doi: 10.1371/journal.pone.0087723.
4. Yu-Duan Ding#, Ji-Wei Chang#, Jing Guo, Di-Jun Chen, Sen Li, Qiang Xu, Xiu-Xin Deng, Yun-Jiang Cheng, Ling-Ling Chen. Prediction and functional analysis of sweet orange protein-protein interaction network. BMC Plant Biol. 2014, 14(1): 213. doi: 10.1186/s12870-014-0213-7.