The draft genome of sweet orange (Citrus sinensis) - PubMed (original) (raw)

doi: 10.1038/ng.2472. Epub 2012 Nov 25.

Ling-Ling Chen, Xiaoan Ruan, Dijun Chen, Andan Zhu, Chunli Chen, Denis Bertrand, Wen-Biao Jiao, Bao-Hai Hao, Matthew P Lyon, Jiongjiong Chen, Song Gao, Feng Xing, Hong Lan, Ji-Wei Chang, Xianhong Ge, Yang Lei, Qun Hu, Yin Miao, Lun Wang, Shixin Xiao, Manosh Kumar Biswas, Wenfang Zeng, Fei Guo, Hongbo Cao, Xiaoming Yang, Xi-Wen Xu, Yun-Jiang Cheng, Juan Xu, Ji-Hong Liu, Oscar Junhong Luo, Zhonghui Tang, Wen-Wu Guo, Hanhui Kuang, Hong-Yu Zhang, Mikeal L Roose, Niranjan Nagarajan, Xiu-Xin Deng, Yijun Ruan

Affiliations

• PMID: 23179022
• DOI: 10.1038/ng.2472

The draft genome of sweet orange (Citrus sinensis)

Qiang Xu et al. Nat Genet. 2013 Jan.

Abstract

Oranges are an important nutritional source for human health and have immense economic value. Here we present a comprehensive analysis of the draft genome of sweet orange (Citrus sinensis). The assembled sequence covers 87.3% of the estimated orange genome, which is relatively compact, as 20% is composed of repetitive elements. We predicted 29,445 protein-coding genes, half of which are in the heterozygous state. With additional sequencing of two more citrus species and comparative analyses of seven citrus genomes, we present evidence to suggest that sweet orange originated from a backcross hybrid between pummelo and mandarin. Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future.

PubMed Disclaimer

Comment in

• Genomics and fruit crop selection.
  Wincker P. Wincker P. Nat Genet. 2013 Jan;45(1):9-10. doi: 10.1038/ng.2498. Nat Genet. 2013. PMID: 23268131 No abstract available.

Similar articles

• Genome-wide analysis of the R2R3-MYB transcription factor gene family in sweet orange (Citrus sinensis).
  Liu C, Wang X, Xu Y, Deng X, Xu Q. Liu C, et al. Mol Biol Rep. 2014 Oct;41(10):6769-85. doi: 10.1007/s11033-014-3563-1. Epub 2014 Jul 10. Mol Biol Rep. 2014. PMID: 25008995
• Genome-Wide Characterization and Expression Analysis of the SBP -Box Gene Family in Sweet Orange (Citrus sinensis).
  Song N, Cheng Y, Peng W, Peng E, Zhao Z, Liu T, Yi T, Dai L, Wang B, Hong Y. Song N, et al. Int J Mol Sci. 2021 Aug 18;22(16):8918. doi: 10.3390/ijms22168918. Int J Mol Sci. 2021. PMID: 34445624 Free PMC article.
• Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).
  Biswas MK, Xu Q, Mayer C, Deng X. Biswas MK, et al. PLoS One. 2014 Aug 22;9(8):e104182. doi: 10.1371/journal.pone.0104182. eCollection 2014. PLoS One. 2014. PMID: 25148383 Free PMC article.
• The State of the Art in Biosynthesis of Anthocyanins and Its Regulation in Pigmented Sweet Oranges [(Citrus sinensis) L. Osbeck].
  Lo Piero AR. Lo Piero AR. J Agric Food Chem. 2015 Apr 29;63(16):4031-41. doi: 10.1021/acs.jafc.5b01123. Epub 2015 Apr 20. J Agric Food Chem. 2015. PMID: 25871434 Review.
• Rationale for reconsidering current regulations restricting use of hybrids in orange juice.
  Stover E, Gmitter FG Jr, Grosser J, Baldwin E, Wu GA, Bai J, Wang Y, Chaires P, Motamayor JC. Stover E, et al. Hortic Res. 2020 Mar 7;7:38. doi: 10.1038/s41438-020-0277-5. eCollection 2020. Hortic Res. 2020. PMID: 32194974 Free PMC article. Review.

Cited by

• Genome-wide investigation of glycoside hydrolase 9 (GH9) gene family unveils implications in orchestrating the mastication trait of Citrus sinensis fruits.
  Deng C, Guo Y, Zhang J, Feng G. Deng C, et al. BMC Genomics. 2024 Sep 30;25(1):905. doi: 10.1186/s12864-024-10826-w. BMC Genomics. 2024. PMID: 39350029 Free PMC article.
• An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus.
  Sagawa CHD, Thomson G, Mermaz B, Vernon C, Liu S, Jacob Y, Irish VF. Sagawa CHD, et al. Plant Methods. 2024 Sep 28;20(1):148. doi: 10.1186/s13007-024-01274-4. Plant Methods. 2024. PMID: 39342225 Free PMC article.
• The genomes of Australian wild limes.
  Nakandala U, Furtado A, Masouleh AK, Smith MW, Mason P, Williams DC, Henry RJ. Nakandala U, et al. Plant Mol Biol. 2024 Sep 24;114(5):102. doi: 10.1007/s11103-024-01502-4. Plant Mol Biol. 2024. PMID: 39316221 Free PMC article.
• Comparative Analysis of Transposable Elements in the Genomes of Citrus and _Citrus_-Related Genera.
  Wu Y, Wang F, Lyu K, Liu R. Wu Y, et al. Plants (Basel). 2024 Sep 3;13(17):2462. doi: 10.3390/plants13172462. Plants (Basel). 2024. PMID: 39273946 Free PMC article.
• Elucidation of mechanisms underlying active oxygen burst in Citrus sinensis after Diaporthe citri infection using transcriptome analysis.
  Liu T, Zhou Z, Luo C, Luo H, Tang J, Shi X, Li D, Zhang Q, Li J, Xia Y, Song N, Yi T. Liu T, et al. Front Microbiol. 2024 Aug 29;15:1425441. doi: 10.3389/fmicb.2024.1425441. eCollection 2024. Front Microbiol. 2024. PMID: 39268534 Free PMC article.

References

1. 1. Bioinformatics. 2004 Jun 12;20(9):1453-4 - PubMed
2. 1. Genome Biol. 2009;10(3):R25 - PubMed
3. 1. Bioinformatics. 2010 Mar 1;26(5):589-95 - PubMed
4. 1. BMC Genomics. 2004 Mar 02;5(1):18 - PubMed
5. 1. Nat Biotechnol. 2010 Sep;28(9):951-6 - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • The Lens - Patent Citations

• Molecular Biology Databases

  • SILVA