A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae

Background Ensete glaucum (2 n = 2 x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana ( Musa ). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete , the Musaceae, and more widely in the Zingiberales. Findings Using a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, we report a high-quality assembly of the 481.5Mb genome with 9 pseudochromosomes and 36,836 genes (BUSCO 94.7%). A total of 55% of the genome is composed of repetitive sequences with LTR-retroelements (37%) and DNA transposons (7%) predominant. The 5S and 45S rDNA were each present at one locus, and the 5S rDNA had an exceptionally long monomer length of c.1,056 bp, contrasting with the c. 450 bp monomer at multiple loci in Musa . A tandemly repeated c. 134 bp satellite, 1.1% of the genome (with no similar sequence in Musa ), was present around all nine centromeres, with a LINE retroelement also found at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between the x = 9 species and x = 11 species of Musa . Only one chromosome has the same gene content as M. acuminata (ma). Three ma chromosomes represent part of only one E. glaucum (eg) chromosome, while the remaining seven ma chromosomes are fusions of parts of two, three, or four eg chromosomes, demonstrating complex and multiple evolutionary rearrangements in the change between x = 9 and x = 11. Conclusions The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show how chromosome number evolves, and features of the rapid evolution of repetitive sequences. ### Competing Interest Statement The authors have declared no competing interest. * BLAST : Basic Local Alignment Search Tool bp : base pairs BUSCO : Benchmarking Universal Single-Copy Orthologs BWA : Burrows-Wheeler Aligner FISH : fluorescence in situ hybridization GeMoMa : Gene Model Mapper Gb : gigabase pairs GC : guanine-cytosine GO : gene ontogeny CTAB : cetyl trimethylammonium bromide GWAS : Genome Wide Association Studies Hi-C : High-throughput chromosome conformation capture ITS : internal transcribed spacer of rDNA kb : kilobase pairs KEGG : Kyoto Encyclopedia of Genes and Genomes GeMoMa : Gene Model Mapper LACHESIS : Ligating Adjacent Chromatin Enables Scaffolding In Situ LINE : long interspersed nucleotide elements LTR : long terminal repeat Mb : megabase pairs ML : maximum likelihood miRNA : microRNA Mya : million years ago NCBI : National Center for Biotechnology Information NR : RefSeq non-redundant proteins NOR : Nucleolar Organizing Region NTS : non transcribed spacer of rDNA ONT : Oxford Nanopore Technologies PAML : Phylogenetic Analysis by Maximum Likelihood PacBio : Pacific Biosciences PASA : Program to Assemble Spliced Alignments RAxML : Randomized Accelerated Maximum Likelihood RNA-seq : RNA sequencing rDNA : ribosomal DNA SRA : Sequence Read Archive SSR : Simple sequence repeat TE : transposable element TF : Transcription Factor tRNA : transfer RNA WGD : whole genome duplication.