The genome sequence of star fruit ().

Shasha Wu, Wei Sun, Zhichao Xu, Junwen Zhai, Xiaoping Li, Chengru Li, Diyang Zhang, Xiaoqian Wu, Liming Shen, Junhao Chen, Hui Ren, Xiaoyu Dai, Zhongwu Dai, Yamei Zhao, Lei Chen, Mengxia Cao, Xinyu Xie, Xuedie Liu, Donghui Peng, Jianwen Dong, Yu-Yun Hsiao, Shi-Lin Chen, Wen-Chieh Tsai, Siren Lan, Zhong-Jian Liu
Author Information
  1. Shasha Wu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  2. Wei Sun: Institute of Chinese Materia Medica, Chinese Academy of China Medical Sciences, Beijing, 100700 China.
  3. Zhichao Xu: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 China.
  4. Junwen Zhai: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  5. Xiaoping Li: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  6. Chengru Li: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  7. Diyang Zhang: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China. ORCID
  8. Xiaoqian Wu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  9. Liming Shen: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  10. Junhao Chen: State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300 China.
  11. Hui Ren: Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China.
  12. Xiaoyu Dai: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  13. Zhongwu Dai: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  14. Yamei Zhao: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  15. Lei Chen: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  16. Mengxia Cao: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  17. Xinyu Xie: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  18. Xuedie Liu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  19. Donghui Peng: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  20. Jianwen Dong: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  21. Yu-Yun Hsiao: Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 China. ORCID
  22. Shi-Lin Chen: Institute of Chinese Materia Medica, Chinese Academy of China Medical Sciences, Beijing, 100700 China.
  23. Wen-Chieh Tsai: Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 China.
  24. Siren Lan: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.
  25. Zhong-Jian Liu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China.

Abstract

Oxalidaceae is one of the most important plant families in horticulture, and its key commercially relevant genus, , has diverse growth habits and fruit types. Here, we describe the assembly of a high-quality chromosome-scale genome sequence for (star fruit). distribution analysis showed that underwent a whole-genome triplication event, i.e., the gamma event shared by most eudicots. Comparisons between and other angiosperms also permitted the generation of Oxalidaceae gene annotations. We identified unique gene families and analyzed gene family expansion and contraction. This analysis revealed significant changes in MADS-box gene family content, which might be related to the cauliflory of . In addition, we identified and analyzed a total of 204 nucleotide-binding site, leucine-rich repeat receptor (NLR) genes and 58 WRKY genes in the genome, which may be related to the defense response. Our results provide insights into the origin, evolution and diversification of star fruit.

Keywords

References

  1. Neurochem Int. 2005 Jun;46(7):523-31 [PMID: 15843046]
  2. Nat Genet. 2000 Dec;26(4):403-10 [PMID: 11101835]
  3. Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
  4. Dev Cell. 2008 Jul;15(1):110-20 [PMID: 18606145]
  5. Genome Res. 2000 Apr;10(4):516-22 [PMID: 10779491]
  6. Nephrol Dial Transplant. 2003 Jan;18(1):120-5 [PMID: 12480969]
  7. Bioinformatics. 2001 Sep;17(9):847-8 [PMID: 11590104]
  8. Front Plant Sci. 2016 Jun 03;7:760 [PMID: 27375634]
  9. Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
  10. Development. 2011 Feb;138(4):677-85 [PMID: 21228003]
  11. Genetica. 2011 Aug;139(8):973-83 [PMID: 21805321]
  12. Plant Physiol. 2016 Apr;170(4):2095-109 [PMID: 26839128]
  13. Phytochemistry. 2003 May;63(2):131-7 [PMID: 12711133]
  14. Cytogenet Genome Res. 2005;110(1-4):462-7 [PMID: 16093699]
  15. Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5 [PMID: 18940856]
  16. Bioinformatics. 2014 May 1;30(9):1312-3 [PMID: 24451623]
  17. Nat Protoc. 2012 Mar 01;7(3):562-78 [PMID: 22383036]
  18. Nucleic Acids Res. 1997 Mar 1;25(5):955-64 [PMID: 9023104]
  19. Genome Res. 2015 Feb;25(2):246-56 [PMID: 25367294]
  20. Genome Res. 2004 May;14(5):988-95 [PMID: 15123596]
  21. Nature. 2020 Jan;577(7788):79-84 [PMID: 31853069]
  22. Nat Ecol Evol. 2017 Feb 06;1(3):59 [PMID: 28812732]
  23. Nat Genet. 2011 Feb;43(2):101-8 [PMID: 21186351]
  24. Plant Cell. 2004 Jul;16(7):1667-78 [PMID: 15208399]
  25. Nature. 2017 Sep 21;549(7672):379-383 [PMID: 28902843]
  26. Bioinformatics. 2009 May 1;25(9):1105-11 [PMID: 19289445]
  27. Genome Res. 2003 Sep;13(9):2178-89 [PMID: 12952885]
  28. BMC Bioinformatics. 2006 Feb 09;7:62 [PMID: 16469098]
  29. Genome Res. 2006 Jun;16(6):738-49 [PMID: 16702410]
  30. Nucleic Acids Res. 1999 Jan 1;27(1):29-34 [PMID: 9847135]
  31. Comput Appl Biosci. 1997 Oct;13(5):555-6 [PMID: 9367129]
  32. Plant Cell. 2003 Jul;15(7):1538-51 [PMID: 12837945]
  33. Nat Genet. 2015 Jan;47(1):65-72 [PMID: 25420146]
  34. Plant Cell. 2017 Oct;29(10):2336-2348 [PMID: 29025960]
  35. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
  36. Nat Rev Genet. 2009 Oct;10(10):725-32 [PMID: 19652647]
  37. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4 [PMID: 15608160]
  38. Syst Biol. 2012 Oct;61(5):823-34 [PMID: 22357726]
  39. BMC Genomics. 2017 Sep 15;18(1):730 [PMID: 28915793]
  40. Plant J. 2009 Nov;60(4):626-37 [PMID: 19656343]
  41. Nucleic Acids Res. 2015 Jan;43(Database issue):D257-60 [PMID: 25300481]

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