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. 2022 Sep 28:9:uhac221.
doi: 10.1093/hr/uhac221. eCollection 2022.

The banana genome hub: a community database for genomics in the Musaceae

Gaëtan Droc  1   2   3 , Guillaume Martin  1   2   3 , Valentin Guignon  3   4 , Marilyne Summo  1   2   3 , Guilhem Sempéré  3   5   6 , Eloi Durant  3   7   8 , Alexandre Soriano  1   2   3 , Franc-Christophe Baurens  1   2 , Alberto Cenci  3   4 , Catherine Breton  3   4 , Trushar Shah  9 , Jean-Marc Aury  10 , Xue-Jun Ge  11   12 , Pat Heslop Harrison  11   13 , Nabila Yahiaoui  1   2 , Angélique D'Hont  1   2 , Mathieu Rouard  3   4
Affiliations

The banana genome hub: a community database for genomics in the Musaceae

Gaëtan Droc et al. Hortic Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Screenshot of the Banana Genome Hub homepage showing a subset of available genome sequence and visualisation and analytical tools.
Figure 2
Figure 2
(A) Gene search interface enabling access results hits that can be visualized in (B) genome browser (JBrowse) with Liftoff tracks. Red arrows indicate region that are inconsistent between gene prediction and that might need curation and (C) in an orthogroup context with associated multiple alignments and phylogenetic tree
Figure 3
Figure 3
(A) Transcriptomic interface with a list of RGA2 genes from M. acuminata “DH Pahang” submitted to visualize their level of expression for a study on Fusarium wilt. (B) GO enrichment interface with a list of genes submitted. (C) First steps of the carotenoid pathways with Phytoene desaturase (PDS) identified by MusaCyc in the Musa acuminata genome.
Figure 4
Figure 4
Overview of the genetic variant interface powered by GIGWA (A) Main interface for the GWAS panel with discriminated variants between 2 groups (seeded vs non-seeded) (B) Statistics of SNPs along Chromosome 2. (C) SNP visualization in JBrowse from the GIGWA interface (D) Data export online for graphical previews of genotype data in Flapjack-bytes.
Figure 5
Figure 5
Overview of proposed web interfaces for comparative genomics within Musaceae. (A) Overview of the Musaceae Pangenome represented with the Panache interface. (B) Examples of genome ancestry mosaics. (C) Synteny between Ensete glaucum, Musa acuminata, Musa balbisiana and M. schizocarpa using Synvisio.
See this image and copyright information in PMC

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