Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

• Published in: Plant communications Vol. 5; no. 2; p. 100766
• Main Authors: Xie, Wen-Zhao, Zheng, Yu-Yu, He, Weidi, Bi, Fangcheng, Li, Yaoyao, Dou, Tongxin, Zhou, Run, Guo, Yi-Xiong, Deng, Guiming, Zhang, Wenhui, Yuan, Min-Hui, Sanz-Jimenez, Pablo, Zhu, Xi-Tong, Xu, Xin-Dong, Zhou, Zu-Wen, Zhou, Zhi-Wei, Feng, Jia-Wu, Liu, Siwen, Li, Chunyu, Yang, Qiaosong, Hu, Chunhua, Gao, Huijun, Dong, Tao, Dang, Jiangbo, Guo, Qigao, Cai, Wenguo, Zhang, Jianwei, Yi, Ganjun, Song, Jia-Ming, Sheng, Ou, Chen, Ling-Ling
• Format: Journal Article
• Language: English
• Published: China Elsevier Inc 12.02.2024; Elsevier
• Subjects: asymmetric evolution; bananas; Fusarium wilt; homologous exchange; Plantain; Silk; Plantain; Silk; bananas; Fusarium wilt; asymmetric evolution; homologous exchange
• ISSN: 2590-3462; 2590-3462
• DOI: 10.1016/j.xplc.2023.100766

Bananas (Musa spp.) are one of the world’s most important fruit crops and play a vital role in food security for many developing countries. Most banana cultivars are triploids derived from inter- and intraspecific hybridizations between the wild diploid ancestor species Musa acuminate (AA) and M. balbisiana (BB). We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types, Plantain and Silk, and precisely characterize ancestral contributions by examining ancestry mosaics across the genome. Widespread asymmetric evolution is observed in their subgenomes, which can be linked to frequent homologous exchange events. We reveal the genetic makeup of triploid banana cultivars and verify that subgenome B is a rich source of disease resistance genes. Only 58.5% and 59.4% of Plantain and Silk genes, respectively, are present in all three haplotypes, with >50% of genes being differentially expressed alleles in different subgenomes. We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4 (Foc TR4), which confirms that Plantain can initiate defense responses faster than Silk. Additionally, we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk. Our study provides resources for better understanding the genomic architecture of cultivated bananas and has important implications for Musa genetics and breeding. This study reports two haplotype-resolved genome assemblies for AAB banana cultivars (Plantain and Silk) and the characterization of the ancestry mosaics across their genomes. Widespread asymmetric evolution in their subgenomes is linked to frequent homologous exchange events. Plantain can initiate defense responses more quickly than Silk following banana Foc TR4 infection.