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Genome biology
11 04, 2021;22 (1): 304.

High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height.

Shouchuang Wang, Yong Xiao, Zhi-Wei Zhou, Jiaqing Yuan, Hao Guo, Zhuang Yang, Jun Yang, Pengchuan Sun, Lisong Sun, Yuan Deng, Wen-Zhao Xie, Jia-Ming Song, Muhammad Tahir Ul Qamar, Wei Xia, Rui Liu, Shufang Gong, Yong Wang, Fuyou Wang, Xianqing Liu, Alisdair R Fernie, Xiyin Wang, Haikuo Fan, Ling-Ling Chen, Jie Luo
Author Information
  1. Shouchuang Wang: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  2. Yong Xiao: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  3. Zhi-Wei Zhou: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
  4. Jiaqing Yuan: College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
  5. Hao Guo: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  6. Zhuang Yang: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  7. Jun Yang: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  8. Pengchuan Sun: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.
  9. Lisong Sun: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  10. Yuan Deng: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  11. Wen-Zhao Xie: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
  12. Jia-Ming Song: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
  13. Muhammad Tahir Ul Qamar: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
  14. Wei Xia: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  15. Rui Liu: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  16. Shufang Gong: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  17. Yong Wang: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  18. Fuyou Wang: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  19. Xianqing Liu: College of Tropical Crops, Hainan University, Haikou, 570228, China.
  20. Alisdair R Fernie: Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
  21. Xiyin Wang: Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China. wangxiyin@vip.sina.com.
  22. Haikuo Fan: Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China. venheco@163.com.
  23. Ling-Ling Chen: State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China. llchen@gxu.edu.cn.
  24. Jie Luo: College of Tropical Crops, Hainan University, Haikou, 570228, China. jie.luo@hainanu.edu.cn. ORCID
PMID: 34736486 DOI: 10.1186/s13059-021-02522-9

Abstract

BACKGROUND: Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation of ancient plants.
RESULTS: Here, we report the assembly and annotation of reference-grade genomes of Cn. tall and Cn. dwarf, whose genome sizes are 2.40 Gb and 2.39 Gb, respectively. The comparative analysis reveals that the two coconut subspecies diverge about 2-8 Mya while the conserved Arecaceae-specific whole-genome duplication (ω WGD) occurs approximately 47-53 Mya. It additionally allows us to reconstruct the ancestral karyotypes of the ten ancient monocot chromosomes and the evolutionary trajectories of the 16 modern coconut chromosomes. Fiber synthesis genes in Cn. tall, related to lignin and cellulose synthesis, are found at a higher copy number and expression level than dwarf coconuts. Integrated multi-omics analysis reveals that the difference in coconut plant height is the result of altered gibberellin metabolism, with both the GA20ox copy number and a single-nucleotide change in the promoter together leading to the difference in plant height between Cn. tall and Cn. dwarf.
CONCLUSION: We provide high-quality coconut genomes and reveal the genetic basis of trait differences between two coconuts through multi-omics analysis. We also reveal that the selection of plant height has been targeted for the same gene for millions of years, not only in natural selection of ancient plant as illustrated in coconut, but also for artificial selection in cultivated crops such as rice and maize.

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MeSH Term

Biosynthetic Pathways
Chromosomes, Plant
Cocos
Evolution, Molecular
Genome, Plant
Genomics
Karyotype
Journal Article Research Support, Non-U.S. Gov't

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