The draft genome of sweet orange (Citrus sinensis)

Abstract

Citrus is a large genus that includes several major cultivated species, including C. sinensis (sweet orange), Citrus reticulata (tangerine and mandarin), Citrus limon (lemon), Citrus grandis (pummelo) and Citrus paradisi (grapefruit). In 2009, the global citrus acreage was 9 million hectares and citrus production was 122.3 million tons (FAO statistics, see URLs), which is the top ranked among all the fruit crops. Among the 10.9 million tons (valued at $9.3 billion) of citrus products traded in 2009, sweet orange accounted for approximately 60% of citrus production for both fresh fruit and processed juice consumption (FAO statistics, see URLs). Moreover, citrus fruits and juice are the prime human source of vitamin C, an important component of human nutrition.Citrus fruits also have some unique botanical features, such as nucellar embryony (nucellus cells can develop into apomictic embryos that are genetically identical to mother plant). Consequently, somatic embryos grow much more vigorously than the zygotic embryos in seeds such that seedlings are essentially clones of the maternal parent. Such citrus-unique characteristics have hindered the study of citrus genetics and breeding improvement 1,2 . Complete genome sequences would provide valuable genetic resources for improving citrus crops.Citrus is believed to be native to southeast Asia 3-5 , and cultivation of fruit crops occurred at least 4,000 years ago 3,6 . The genetic origin of the sweet orange is not clear, although there are some speculations that sweet orange might be derived from interspecific hybridization of some primitive citrus species 7,8 . Citrus is also in the order Sapindales, a sister order to the Brassicales in the Malvidae, making it valuable for comparative genomics studies with the model plant Arabidopsis.We aimed to sequence the genome of Valencia sweet orange (C. sinensis cv. Valencia), one of the most important sweet orange varieties cultivated worldwide and grown primarily for orange juice production. Normal sweet oranges are diploids, with nine pairs of chromosomes and an estimated genome size of ~367 Mb 9 . To reduce the complexity of the sequenced genome, we obtained a doublehaploid (dihaploid) line derived from the anther culture of Valencia sweet orange 10 . We first generated whole-genome shotgun pairedend-tag sequence reads from the dihaploid genomic DNA and built a de novo assembly as the citrus reference genome; we then produced shotgun sequencing reads from the parental diploid DNA and mapped the sequences to the haploid reference genome to obtain the complete genome information for Valencia sweet orange. In addition, we conducted comprehensive transcriptome sequencing analyses for four representative tissues using shotgun RNA sequencing (RNA-Seq) to capture all transcribed sequences and paired-end-tag RNA sequencing (RNA-PET) to demarcate the 5′ and 3′ ends of all transcripts. On the basis of the DNA and RNA sequencing data, we characterized the orange genome for its gene content, heterozygosity and evolutionary features. ...

Changes in Anthocyanin Production during Domestication of Citrus

“…Sweet orange (C. sinensis) is considered a complex hybrid involving mandarin (providing the predominant genetic material) and pummelo (Garcia-Lor et al, 2013b;Xu et al, 2013;Wu et al, 2014), and the allelic composition of the Ruby locus (r TATA and r DEL2 ) confirmed this. We have been unable to detect any expression of Ruby in different tissues of common varieties of sweet orange (Butelli et al, 2012), consistent with the complete absence of anthocyanin pigmentation.…”

Genomics of the origin and evolution of Citrus

“…To investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations.…”

“…This suggests that Tachibana should be designated a subspecies of C. reticulata. By contrast, the wild Mangshan 'mandarin' (Citrus mangshanensis) 7 represents a distinct species, with comparable distances to C. reticulata, pummelo and citron 2 (Extended Data Table 1). …”

Lateral organ boundaries 1 is a disease susceptibility gene for citrus bacterial canker disease

“…Genomic resources exist for citrus species, including draft genome sequences of several species and extensive expression sequence tags (ESTs) of mRNAs from different developmental and disease states (5,6). A variety of transcription profiling studies of diseased hosts with citrus bacterial canker have been conducted, comparing susceptible and resistant host reactions (7,8).…”