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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.

References

  1. New Phytol. 1994 Aug;127(4):617-633 [PMID: 33874382]
  2. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13 [PMID: 19706486]
  3. Front Plant Sci. 2016 Dec 02;7:1778 [PMID: 27994606]
  4. Stat Appl Genet Mol Biol. 2005;4:Article17 [PMID: 16646834]
  5. Genome Biol. 2015 Dec 01;16:259 [PMID: 26619908]
  6. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
  7. Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
  8. Science. 2009 Oct 9;326(5950):289-93 [PMID: 19815776]
  9. BMC Genomics. 2008 Jan 30;9:58 [PMID: 18234080]
  10. New Phytol. 2018 Oct;220(1):87-93 [PMID: 29882360]
  11. BMC Plant Biol. 2013 Mar 12;13:41 [PMID: 23497122]
  12. Nat Methods. 2009 Sep;6(9):677-81 [PMID: 19668202]
  13. BMC Genomics. 2017 Jan 5;18(1):38 [PMID: 28056785]
  14. Bioinformatics. 2011 Feb 15;27(4):578-9 [PMID: 21149342]
  15. Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80 [PMID: 20451164]
  16. J Mol Evol. 1985;22(2):160-74 [PMID: 3934395]
  17. Plant Physiol. 1999 Dec;121(4):1257-66 [PMID: 10594112]
  18. BMC Bioinformatics. 2003 Sep 11;4:41 [PMID: 12969510]
  19. Science. 2000 Nov 10;290(5494):1151-5 [PMID: 11073452]
  20. BMC Evol Biol. 2011 Apr 16;11:103 [PMID: 21496296]
  21. New Phytol. 2012 Dec;196(4):966-971 [PMID: 23033870]
  22. BMC Bioinformatics. 2013 Nov 12;14:321 [PMID: 24219505]
  23. Mol Biol Evol. 2019 Jan 1;36(1):97-111 [PMID: 30403808]
  24. J Exp Bot. 2014 Aug;65(16):4561-75 [PMID: 25028558]
  25. Nature. 2009 Jan 15;457(7227):327-31 [PMID: 19029881]
  26. Genome Res. 2010 Sep;20(9):1297-303 [PMID: 20644199]
  27. Proc Natl Acad Sci U S A. 1979 Jan;76(1):170-4 [PMID: 16592605]
  28. Brief Funct Genomics. 2014 Jul;13(4):296-307 [PMID: 24907366]
  29. Genetics. 1996 Apr;142(4):1349-55 [PMID: 8846910]
  30. Front Plant Sci. 2017 Apr 04;8:475 [PMID: 28421102]
  31. BMC Bioinformatics. 2003 Jun 23;4:25 [PMID: 12820902]
  32. Plant Physiol. 1990 Sep;94(1):201-8 [PMID: 16667688]
  33. Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
  34. Bioinformatics. 2001 Aug;17(8):754-5 [PMID: 11524383]
  35. Nat Genet. 2017 Nov;49(11):1633-1641 [PMID: 28991254]
  36. CSH Protoc. 2007 Jul 01;2007:pdb.top17 [PMID: 21357135]
  37. Am J Bot. 2018 Nov;105(11):1888-1910 [PMID: 30368769]
  38. Science. 2014 Jul 18;345(6194):1251788 [PMID: 25035500]
  39. BMC Genomics. 2016 Mar 16;17:243 [PMID: 26984673]
  40. Front Plant Sci. 2017 Mar 30;8:454 [PMID: 28424724]
  41. Bioinformatics. 2015 Oct 1;31(19):3210-2 [PMID: 26059717]
  42. Plant Biotechnol J. 2017 Apr;15(4):520-532 [PMID: 27734628]
  43. Nat Genet. 2016 Oct;48(10):1225-32 [PMID: 27595476]
  44. Plant Physiol. 2008 Apr;146(4):1878-91 [PMID: 18263778]
  45. Plant Cell. 1995 Jul;7(7):971-85 [PMID: 7640529]
  46. Genome Res. 2003 Nov;13(11):2498-504 [PMID: 14597658]
  47. Nucleic Acids Res. 2000 Jan 1;28(1):45-8 [PMID: 10592178]
  48. Genome Res. 2003 Sep;13(9):2178-89 [PMID: 12952885]
  49. Mol Biol Evol. 2014 Feb;31(2):448-54 [PMID: 24296661]
  50. Am J Bot. 2016 Jul;103(7):1187-96 [PMID: 27206460]
  51. Genome Res. 1997 Oct;7(10):986-95 [PMID: 9331369]
  52. Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-4.11.39 [PMID: 25501943]
  53. Plant Biotechnol J. 2018 Jan;16(1):151-164 [PMID: 28500777]
  54. Plant Cell. 2002 Sep;14(9):2191-213 [PMID: 12215515]
  55. Science. 2014 Aug 22;345(6199):950-3 [PMID: 25146293]
  56. New Phytol. 2014 May;202(3):986-1000 [PMID: 24716518]
  57. Nat Genet. 2009 Dec;41(12):1275-81 [PMID: 19881527]
  58. Nucleic Acids Res. 1999 Jan 1;27(1):29-34 [PMID: 9847135]
  59. New Phytol. 2016 Jun;210(4):1453-65 [PMID: 26832306]
  60. Nucleic Acids Res. 2009 Jan;37(1):1-13 [PMID: 19033363]
  61. Genes (Basel). 2017 Dec 28;9(1): [PMID: 29283420]
  62. Nat Methods. 2008 Jul;5(7):621-8 [PMID: 18516045]
  63. Nature. 2012 May 30;485(7400):635-41 [PMID: 22660326]
  64. Genome Res. 2002 Apr;12(4):656-64 [PMID: 11932250]
  65. BMC Bioinformatics. 2008 Dec 29;9:559 [PMID: 19114008]
  66. Nature. 2012 Aug 9;488(7410):213-7 [PMID: 22801500]
  67. Genetics. 2004 Feb;166(2):935-45 [PMID: 15020478]
  68. Nat Biotechnol. 2015 May;33(5):531-7 [PMID: 25893781]
  69. Bioinformatics. 2006 May 15;22(10):1269-71 [PMID: 16543274]
  70. Mol Plant. 2016 Dec 5;9(12):1667-1670 [PMID: 27717919]
  71. Nat Biotechnol. 2013 Dec;31(12):1119-25 [PMID: 24185095]
  72. Nucleic Acids Res. 2010 Jan;38(Database issue):D822-7 [PMID: 19858103]
  73. Brief Bioinform. 2009 Nov;10(6):619-30 [PMID: 19720678]
  74. Plant Cell Rep. 2003 Feb;21(6):511-6 [PMID: 12789424]
  75. Bioinformatics. 2009 Aug 15;25(16):2078-9 [PMID: 19505943]
  76. Nucleic Acids Res. 2014 Jan;42(Database issue):D1182-7 [PMID: 24174544]
  77. Nucleic Acids Res. 1980 Oct 10;8(19):4321-5 [PMID: 7433111]
  78. BMC Genomics. 2013 Oct 05;14:683 [PMID: 24094114]
  79. Science. 2008 Apr 25;320(5875):486-8 [PMID: 18436778]

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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