The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources—planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr

17 Background and Aims 18 Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing 19 countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral 20 origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB, or 21 ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, 22respectively. Previous studies suggested that inter-genome recombinations were relatively 23 common in banana cultivars and that triploids were more likely to have passed through an 24 intermediate hybrid. In this study, we investigated the chromosome structure within the ABB 25 group, composed of starchy cooking bananas that play an important role in food security. 26 Methods 27Using SNP markers called from RAD-Seq data, we studied the chromosome structure of 36 ABB 28 genotypes spanning defined taxonomic subgroups. To complement our understanding, we search 29 for similar events within nine AB hybrid genotypes. 30 Key Results 31Recurrent Homoeologous Exchanges (HEs), i.e. chromatin exchanges between A and B 32 subgenomes were unraveled with at least 9 founding events at the origin of the ABB bananas 33 prior to the clonal diversification. The discovery of this nine founding events allows discussing 34 the possible routes that led to the creation of the different subgroups and formulate new 35 hypotheses. Based on our observations, we suggest different routes that gave rise to the current 36 diversity in the ABB cultivars. Routes involving primary AB hybrids, routes leading to shared 37 HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and 38 M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploid 39 originated and where cultivated M. balbisiana are abundant. 40 Conclusions 41The result of this study clarifies the classification of ABB cultivars and leading possibly to the 42 revision of the classification of this subgroup. This is an important step to unravel the origin of 43 polyploid bananas, and contributes to possible scenarios on the origin. ABB bananas are 44 hypothesized to be more drought tolerant. Knowing the origin of our current cultivars and so 45 their potential parents will help breeders to make the right choices for future crosses. The M. 46 balbisiana genome is a good source to create new cultivars able to answer the numerous 47 49