Origin and evolution of the triploid cultivated banana genome

Xiuxiu Li; Sheng Yu; Zhihao Cheng; Xiaojun Chang; Yingzi Yun; Mengwei Jiang; Xuequn Chen; Xiaohui Wen; Hua Li; Wenjun Zhu; Shiyao Xu; Yanbing Xu; Xianjun Wang; Chen Zhang; Qiong Wu; Jin Hu; Zhenguo Lin; Jean-Marc Aury; Yves Van de Peer; Zonghua Wang; Xiaofan Zhou; Jihua Wang; Peitao Lü; Liangsheng Zhang

doi:10.1038/s41588-023-01589-3

Origin and evolution of the triploid cultivated banana genome

Nat Genet. 2024 Jan;56(1):136-142. doi: 10.1038/s41588-023-01589-3. Epub 2023 Dec 11.

Authors

Xiuxiu Li^#¹, Sheng Yu^#², Zhihao Cheng^#³, Xiaojun Chang^#⁴, Yingzi Yun^#¹, Mengwei Jiang^#¹, Xuequn Chen¹, Xiaohui Wen^{5

6}, Hua Li¹, Wenjun Zhu¹, Shiyao Xu¹, Yanbing Xu¹, Xianjun Wang¹, Chen Zhang^{1

7}, Qiong Wu³, Jin Hu^{5

6}, Zhenguo Lin⁸, Jean-Marc Aury⁹, Yves Van de Peer^{10

11

12}, Zonghua Wang^{13

14}, Xiaofan Zhou¹⁵, Jihua Wang¹⁶, Peitao Lü¹⁷, Liangsheng Zhang^{18

19}

Affiliations

¹ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
² Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
³ Haikou Experimental Station, National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
⁴ Laboratory of Medicinal Plant Biotechnology, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China.
⁵ Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
⁶ Hainan Institute of Zhejiang University, Sanya, China.
⁷ Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China.
⁸ Department of Biology, Saint Louis University, St. Louis, MO, USA.
⁹ Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
¹⁰ Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium. yvpee@psb.vib-ugent.be.
¹¹ Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. yvpee@psb.vib-ugent.be.
¹² College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China. yvpee@psb.vib-ugent.be.
¹³ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China. wangzh@fafu.edu.cn.
¹⁴ Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China. wangzh@fafu.edu.cn.
¹⁵ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China. xiaofan_zhou@scau.edu.cn.
¹⁶ Yunnan Seed Laboratory, Kunming, China. wjh0505@gmail.com.
¹⁷ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Haixia Institute of Science and Technology, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China. ptlv@fafu.edu.cn.
¹⁸ Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China. zls83@zju.edu.cn.
¹⁹ Hainan Institute of Zhejiang University, Sanya, China. zls83@zju.edu.cn.

^# Contributed equally.

PMID: 38082204
DOI: 10.1038/s41588-023-01589-3

Abstract

Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.

MeSH terms

Fusarium* / genetics
Musa* / genetics
Plant Breeding
Plant Diseases / genetics
Transcription Factors / genetics
Triploidy

Substances

Transcription Factors

Grants and funding

833522/EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)