Origin and evolution of the triploid cultivated banana genome

dc.contributor.authorLi, Xiuxiu
dc.contributor.authorYu, Sheng
dc.contributor.authorCheng, Zhihao
dc.contributor.authorChang, Xiaojun
dc.contributor.authorYun, Yingzi
dc.contributor.authorJiang, Mengwei
dc.contributor.authorChen, Xuequn
dc.contributor.authorWen, Xiaohui
dc.contributor.authorLi, Hua
dc.contributor.authorZhu, Wenjun
dc.contributor.authorXu, Shiyao
dc.contributor.authorXu, Yanbing
dc.contributor.authorWang, Xianjun
dc.contributor.authorZhang, Chen
dc.contributor.authorWu, Qiong
dc.contributor.authorHu, Jin
dc.contributor.authorLin, Zhenguo
dc.contributor.authorAury, Jean-Marc
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorWang, Zonghua
dc.contributor.authorZhou, Xiaofan
dc.contributor.authorWang, Jihua
dc.contributor.authorLue, Peitao
dc.contributor.authorZhang, Liangsheng
dc.date.accessioned2024-02-15T05:39:04Z
dc.date.issued2024-01
dc.descriptionDATA 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.en_US
dc.description.abstractMost 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.en_US
dc.description.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.embargo2024-06-11
dc.description.librarianhj2024en_US
dc.description.sdgSDG-02:Zero Hungeren_US
dc.description.sponsorshipThe National Natural Science Foundation of China, Construction of Plateau Discipline of Fujian Province, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program and from Ghent University (Methusalem funding).en_US
dc.description.urihttp://www.nature.com/ngen_US
dc.identifier.citationLi, 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.en_US
dc.identifier.issn1061-4036 (print)
dc.identifier.issn1546-1718 (online)
dc.identifier.other10.1038/s41588-023-01589-3
dc.identifier.urihttp://hdl.handle.net/2263/94630
dc.language.isoenen_US
dc.publisherNature Researchen_US
dc.rights© 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.en_US
dc.subjectGenomicsen_US
dc.subjectPlant hybridizationen_US
dc.subjectBananasen_US
dc.subjectCavendishen_US
dc.subjectGros Michelen_US
dc.subjectReceptor-like protein (RLP)en_US
dc.subjectSDG-02: Zero hungeren_US
dc.titleOrigin and evolution of the triploid cultivated banana genomeen_US
dc.typePostprint Articleen_US

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