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Nature genetics
05, 2022;54 (5): 715-724.

SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya.

Jingjing Yue, Robert VanBuren, Juan Liu, Jingping Fang, Xingtan Zhang, Zhenyang Liao, Ching Man Wai, Xiuming Xu, Shuai Chen, Shengchen Zhang, Xiaokai Ma, Yaying Ma, Hongying Yu, Jing Lin, Ping Zhou, Yongji Huang, Ban Deng, Fang Deng, Xiaobing Zhao, Hansong Yan, Mahpara Fatima, Dessireé Zerpa-Catanho, Xiaodan Zhang, Zhicong Lin, Mei Yang, Nancy J Chen, Eric Mora-Newcomer, Patricia Quesada-Rojas, Antonio Bogantes, Víctor M Jiménez, Haibao Tang, Jisen Zhang, Ming-Li Wang, Robert E Paull, Qingyi Yu, Ray Ming
Author Information
  1. Jingjing Yue: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  2. Robert VanBuren: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  3. Juan Liu: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  4. Jingping Fang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  5. Xingtan Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  6. Zhenyang Liao: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  7. Ching Man Wai: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. ORCID
  8. Xiuming Xu: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  9. Shuai Chen: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  10. Shengchen Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  11. Xiaokai Ma: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  12. Yaying Ma: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  13. Hongying Yu: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  14. Jing Lin: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  15. Ping Zhou: Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China. ORCID
  16. Yongji Huang: Institute of Oceanography, Minjiang University, Fuzhou, China. ORCID
  17. Ban Deng: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  18. Fang Deng: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  19. Xiaobing Zhao: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  20. Hansong Yan: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  21. Mahpara Fatima: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  22. Dessireé Zerpa-Catanho: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  23. Xiaodan Zhang: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  24. Zhicong Lin: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  25. Mei Yang: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
  26. Nancy J Chen: Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
  27. Eric Mora-Newcomer: Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, Alajuela, Costa Rica. ORCID
  28. Patricia Quesada-Rojas: Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, Alajuela, Costa Rica.
  29. Antonio Bogantes: Estación Experimental Los Diamantes, Instituto de Innovación y Transferencia de Tecnología Agropecuaria, Guápiles, Costa Rica.
  30. Víctor M Jiménez: CIGRAS, Universidad de Costa Rica, San Pedro, Costa Rica. ORCID
  31. Haibao Tang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  32. Jisen Zhang: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
  33. Ming-Li Wang: Hawaii Agriculture Research Center, Kunia, HI, USA.
  34. Robert E Paull: Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
  35. Qingyi Yu: Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA. ORCID
  36. Ray Ming: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu. ORCID
PMID: 35551309 DOI: 10.1038/s41588-022-01068-1

Abstract

Transgenic papaya is widely publicized for controlling papaya ringspot virus. However, the impact of particle bombardment on the genome remains unknown. The transgenic SunUp and its progenitor Sunset genomes were assembled into 351.5 and 350.3 Mb in nine chromosomes, respectively. We identified a 1.64 Mb insertion containing three transgenic insertions in SunUp chromosome 5, consisting of 52 nuclear-plastid, 21 nuclear-mitochondrial and 1 nuclear genomic fragments. A 591.9 kb fragment in chromosome 5 was translocated into the 1.64 Mb insertion. We assembled a gapless 9.8 Mb hermaphrodite-specific region of the Y chromosome and its 6.0 Mb X counterpart. Resequencing 86 genomes revealed three distinct groups, validating their geographic origin and breeding history. We identified 147 selective sweeps and defined the essential role of zeta-carotene desaturase in carotenoid accumulation during domestication. Our findings elucidated the impact of particle bombardment and improved our understanding of sex chromosomes and domestication to expedite papaya improvement.

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MeSH Term

Carica
Chromosomes, Plant
Domestication
Plant Breeding
Sex Chromosomes
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Links to CNCB-NGDC Resources

GWH: GWHBFSC00000000 (Carica papaya)
GWH: GWHBFSD00000000 (Carica papaya)

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