OpenLB
Open Library of Bioscience
Advanced Search
Horticulture research
Dec 01, 2021;8 (1): 255.

The Cymbidium genome reveals the evolution of unique morphological traits.

Ye Ai, Zhen Li, Wei-Hong Sun, Juan Chen, Diyang Zhang, Liang Ma, Qing-Hua Zhang, Ming-Kun Chen, Qing-Dong Zheng, Jiang-Feng Liu, Yu-Ting Jiang, Bai-Jun Li, Xuedie Liu, Xin-Yu Xu, Xia Yu, Yu Zheng, Xing-Yu Liao, Zhuang Zhou, Jie-Yu Wang, Zhi-Wen Wang, Tai-Xiang Xie, Shan-Hu Ma, Jie Zhou, Yu-Jie Ke, Yu-Zhen Zhou, Hsiang-Chia Lu, Ke-Wei Liu, Feng-Xi Yang, Gen-Fa Zhu, Laiqiang Huang, Dong-Hui Peng, Shi-Pin Chen, Siren Lan, Yves Van de Peer, Zhong-Jian Liu
Author Information
  1. Ye Ai: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  2. Zhen Li: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
  3. Wei-Hong Sun: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  4. Juan 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, China.
  5. 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, China.
  6. Liang Ma: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  7. Qing-Hua Zhang: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  8. Ming-Kun 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, China.
  9. Qing-Dong Zheng: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  10. Jiang-Feng Liu: Management Office of Yushan Scenic Area, Fuzhou, China.
  11. Yu-Ting Jiang: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  12. Bai-Jun Li: College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China. ORCID
  13. Xuedie Liu: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  14. Xin-Yu Xu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  15. Xia Yu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  16. Yu Zheng: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  17. Xing-Yu Liao: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  18. Zhuang Zhou: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  19. Jie-Yu Wang: Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. ORCID
  20. Zhi-Wen Wang: PubBio-Tech, Wuhan, China.
  21. Tai-Xiang 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, China.
  22. Shan-Hu Ma: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  23. Jie Zhou: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  24. Yu-Jie Ke: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  25. Yu-Zhen Zhou: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  26. Hsiang-Chia Lu: Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
  27. Ke-Wei Liu: Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
  28. Feng-Xi Yang: Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
  29. Gen-Fa Zhu: Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
  30. Laiqiang Huang: Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine and Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
  31. Dong-Hui 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, China.
  32. Shi-Pin Chen: College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
  33. 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, China.
  34. Yves Van de Peer: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium. yves.vandepeer@psb.vib-ugent.be.
  35. 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, China. zjliu@fafu.edu.cn.
PMID: 34848682 DOI: 10.1038/s41438-021-00683-z

Abstract

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

References

Science. 1986 Jun 27;232(4758):1625-7 [PMID: 17812141]
Mol Plant. 2020 Aug 3;13(8):1194-1202 [PMID: 32585190]
Nat Rev Genet. 2017 Jul;18(7):411-424 [PMID: 28502977]
Plant Physiol. 2012 May;159(1):433-49 [PMID: 22419827]
Nat Methods. 2020 Feb;17(2):155-158 [PMID: 31819265]
Plant Cell Physiol. 2011 Mar;52(3):563-77 [PMID: 21278368]
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9 [PMID: 16845043]
Bioinformatics. 2017 Jul 15;33(14):2202-2204 [PMID: 28369201]
Plant Cell. 2013 May;25(5):1641-56 [PMID: 23673982]
Science. 2017 Apr 7;356(6333):92-95 [PMID: 28336562]
BMC Plant Biol. 2006 Jul 13;6:14 [PMID: 16836766]
Cell Syst. 2016 Jul;3(1):95-8 [PMID: 27467249]
Nucleic Acids Res. 2015 Jan;43(Database issue):D222-6 [PMID: 25414356]
Ann Bot. 2009 Aug;104(3):583-94 [PMID: 19141602]
BMC Plant Biol. 2019 Aug 2;19(1):337 [PMID: 31375064]
BMC Bioinformatics. 2011 Dec 22;12:491 [PMID: 22192575]
Cytogenet Genome Res. 2005;110(1-4):462-7 [PMID: 16093699]
Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5 [PMID: 18940856]
Nat Protoc. 2012 Mar 01;7(3):562-78 [PMID: 22383036]
Nucleic Acids Res. 1997 Mar 1;25(5):955-64 [PMID: 9023104]
Plant Cell Physiol. 2011 Sep;52(9):1515-31 [PMID: 21757456]
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8 [PMID: 15961478]
Nature. 2020 Jan;577(7788):79-84 [PMID: 31853069]
Mol Biol Evol. 2006 Jan;23(1):212-26 [PMID: 16177230]
Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
Plant Physiol. 2008 Mar;146(3):1182-92 [PMID: 18203871]
Plant Cell Physiol. 2004 Jul;45(7):831-44 [PMID: 15295066]
Nucleic Acids Res. 1999 Jan 15;27(2):573-80 [PMID: 9862982]
Hortic Res. 2018 Nov 20;5:72 [PMID: 30479779]
Mol Biol Evol. 2011 Oct;28(10):2731-9 [PMID: 21546353]
Mitochondrial DNA B Resour. 2019 Jul 11;4(2):2236-2237 [PMID: 33365490]
Bioinformatics. 2020 Apr 1;36(7):2253-2255 [PMID: 31778144]
Trends Plant Sci. 2001 Aug;6(8):349-58 [PMID: 11495787]
Nature. 2017 Sep 21;549(7672):379-383 [PMID: 28902843]
Methods Mol Biol. 2019;1962:227-245 [PMID: 31020564]
Nucleic Acids Res. 2000 Jan 1;28(1):45-8 [PMID: 10592178]
Bioinformatics. 2009 May 1;25(9):1105-11 [PMID: 19289445]
Genome Res. 2003 Sep;13(9):2178-89 [PMID: 12952885]
Gigascience. 2018 Jan 1;7(1):1-6 [PMID: 29220494]
PLoS Comput Biol. 2011 Oct;7(10):e1002195 [PMID: 22039361]
BMC Genomics. 2007 Jul 18;8:242 [PMID: 17640358]
Nucleic Acids Res. 1999 Jan 1;27(1):29-34 [PMID: 9847135]
Plant Cell Physiol. 2008 May;49(5):814-24 [PMID: 18390881]
Comput Appl Biosci. 1997 Oct;13(5):555-6 [PMID: 9367129]
Nat Methods. 2015 Jan;12(1):59-60 [PMID: 25402007]
Plant Cell. 2011 Mar;23(3):865-72 [PMID: 21378131]
J Mol Biol. 1997 Apr 25;268(1):78-94 [PMID: 9149143]
Nature. 1991 Sep 5;353(6339):31-7 [PMID: 1715520]
Nat Commun. 2018 Apr 24;9(1):1615 [PMID: 29691383]
Plant Cell. 2002;14 Suppl:S153-64 [PMID: 12045275]
Plant Cell. 2003 Jul;15(7):1538-51 [PMID: 12837945]
J Chem Ecol. 2006 Apr;32(4):725-43 [PMID: 16718568]
Nat Genet. 2015 Jan;47(1):65-72 [PMID: 25420146]
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
Genome Biol. 2008 Jan 11;9(1):R7 [PMID: 18190707]
Mol Biol Evol. 2013 Aug;30(8):1987-97 [PMID: 23709260]
Bioinformatics. 2009 Aug 15;25(16):2078-9 [PMID: 19505943]
Sci Rep. 2016 Jan 12;6:19029 [PMID: 26754549]
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4 [PMID: 15608160]
Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
Plant Biotechnol J. 2018 Dec;16(12):2027-2041 [PMID: 29704444]
Trends Plant Sci. 2008 Feb;13(2):51-9 [PMID: 18262819]
Nucleic Acids Res. 2015 Jan;43(Database issue):D257-60 [PMID: 25300481]
Mol Phylogenet Evol. 2003 Dec;29(3):464-89 [PMID: 14615187]
Nat Genet. 2015 Dec;47(12):1435-42 [PMID: 26523774]
Journal Article

Links to CNCB-NGDC Resources

GWH: GWHBCII00000000 (Cymbidium ensifolium)

Word Cloud

Similar Articles

Cited By