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

Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete, the Musaceae, and more widely in the Zingiberales. Using a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, supported by bioinformatic analysis of raw reads and molecular cytogenetic fluorescent in situ hybridization, we report a high-quality 481.5Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The 5S and 45S rDNA were each present at one locus, on chromosomes 5 and 6 respectively. The 5S rDNA had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all nine centromeres, together with a few copies of a LINE retroelement found at higher frequency at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. Only one E. glaucum chromosome has the same gene content as M. acuminata although rearranged. Three E. glaucum chromosomes represent part of only one M. acuminata chromosome, while the remaining chromosomes involve multiple, complex but clearly defined evolutionary rearrangements in the change between x = 9 and x = 11. The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation (CNV), and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence and genomic location, critical to understanding its role in diversity and evolution.