Origin and evolution of the triploid cultivated banana genome
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Date
Authors
Li, Xiuxiu
Yu, Sheng
Cheng, Zhihao
Chang, Xiaojun
Yun, Yingzi
Jiang, Mengwei
Chen, Xuequn
Wen, Xiaohui
Li, Hua
Zhu, Wenjun
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
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.
Description
DATA AVAILABILITY :
Genome assemblies of Cavendish, Gros Michel and Zebrina v2.0 have been deposited into NCBI under GenBank numbers JAVVNX000000000, JAVVNW000000000 and JAVVNV000000000 and in the National Genomics Data Center BioProject database (https://ngdc.cncb.ac.cn/bioproject/) under the accession number PRJCA019650. Genome assemblies with annotations and results of ChIP–seq and DNase-seq can be accessed at FigShare (https://figshare.com/projects/Origin_and_evolution_of_the_triploid_cultivated_banana_genome/178041). Raw data used for the assemblies, including PacBio, Illumina and Hi-C data, are available through the Sequence Read Archive of the National Centre for Biotechnology Information (NCBI) under the BioProject PRJNA1017453 with SRA accessions from SRR23425440 to SRR23425472 and from SRR23885547 to SRR23885549. Fifty-eight RNA-seq datasets were downloaded from NCBI BioProject accessions PRJNA381300, PRJNA394594 and PRJNA598018. DNA methylation data were downloaded from NCBI BioProject PRJNA381300.
Keywords
Genomics, Plant hybridization, Bananas, Cavendish, Gros Michel, Receptor-like protein (RLP), SDG-02: Zero hunger
Sustainable Development Goals
SDG-02:Zero Hunger
Citation
Li, X., Yu, S., Cheng, Z. et al. Origin and evolution of the triploid cultivated banana genome. Nature Genetics 56, 136–142 (2024). https://doi.org/10.1038/s41588-023-01589-3.