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08, 2019;5 (8): 810-821.

Musa balbisiana genome reveals subgenome evolution and functional divergence.

Zhuo Wang, Hongxia Miao, Juhua Liu, Biyu Xu, Xiaoming Yao, Chunyan Xu, Shancen Zhao, Xiaodong Fang, Caihong Jia, Jingyi Wang, Jianbin Zhang, Jingyang Li, Yi Xu, Jiashui Wang, Weihong Ma, Zhangyan Wu, Lili Yu, Yulan Yang, Chun Liu, Yu Guo, Silong Sun, Franc-Christophe Baurens, Guillaume Martin, Frederic Salmon, Olivier Garsmeur, Nabila Yahiaoui, Catherine Hervouet, Mathieu Rouard, Nathalie Laboureau, Remy Habas, Sebastien Ricci, Ming Peng, Anping Guo, Jianghui Xie, Yin Li, Zehong Ding, Yan Yan, Weiwei Tie, Angélique D'Hont, Wei Hu, Zhiqiang Jin
Author Information
  1. Zhuo Wang: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  2. Hongxia Miao: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  3. Juhua Liu: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  4. Biyu Xu: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  5. Xiaoming Yao: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  6. Chunyan Xu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  7. Shancen Zhao: BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, China.
  8. Xiaodong Fang: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  9. Caihong Jia: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  10. Jingyi Wang: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  11. Jianbin Zhang: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  12. Jingyang Li: Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
  13. Yi Xu: Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
  14. Jiashui Wang: Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
  15. Weihong Ma: Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, China.
  16. Zhangyan Wu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  17. Lili Yu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  18. Yulan Yang: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  19. Chun Liu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  20. Yu Guo: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  21. Silong Sun: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  22. Franc-Christophe Baurens: CIRAD, UMR AGAP, Montpellier, France.
  23. Guillaume Martin: CIRAD, UMR AGAP, Montpellier, France. ORCID
  24. Frederic Salmon: AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
  25. Olivier Garsmeur: CIRAD, UMR AGAP, Montpellier, France.
  26. Nabila Yahiaoui: CIRAD, UMR AGAP, Montpellier, France.
  27. Catherine Hervouet: CIRAD, UMR AGAP, Montpellier, France.
  28. Mathieu Rouard: Bioversity International, Montpellier, France. ORCID
  29. Nathalie Laboureau: CIRAD, UMR BGPI, Montpellier, France.
  30. Remy Habas: CIRAD, UMR BGPI, Montpellier, France.
  31. Sebastien Ricci: AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
  32. Ming Peng: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  33. Anping Guo: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  34. Jianghui Xie: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  35. Yin Li: Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. ORCID
  36. Zehong Ding: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  37. Yan Yan: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  38. Weiwei Tie: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
  39. Angélique D'Hont: CIRAD, UMR AGAP, Montpellier, France. dhont@cirad.fr. ORCID
  40. Wei Hu: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China. huwei2010916@126.com. ORCID
  41. Zhiqiang Jin: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China. 18689846976@163.com. ORCID
PMID: 31308504 DOI: 10.1038/s41477-019-0452-6

Abstract

Banana cultivars (Musa ssp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminata and Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisiana with 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata (A-genome) and M. balbisiana (B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACO genes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars.

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MeSH Term

Ethylenes
Evolution, Molecular
Genetic Variation
Genome, Plant
Molecular Sequence Annotation
Musa

Chemicals

Ethylenes
ethylene
Journal Article Research Support, Non-U.S. Gov't

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