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

Abstract

BackgroundEnsete 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 of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete, the Musaceae, and more widely in the Zingiberales.FindingsUsing 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.ConclusionsThe 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.

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

“…Centromeres of some species harbor arrays of tandemly repeated satellite sequences (e.g., Arabidopsis thaliana [74, 75], Beta vulgaris [76] and Ensete glaucum [26]), but we found no equivalent tandem repeat in ALO. However, often in genomes with centromeric satellite sequences, abundant families of retroelements are also found at the centromeres, such as the Nanica LINE of Musa acuminata [77] and E. glaucum [26], Arabidopsis retroelement domains [67] or the wheat Quinta and other elements [32, 78].…”

“…In contrast to Musa (D’Hont et al [53] their supplementary Fig. S12) and Ensete [26] that do not share the grass ρ WGD event, there is clear evidence for two rounds of WGD in Avena .…”

“…The overall chromosomal distribution of TEs was relatively uniform along chromosomes (Fig. 1, circles b, c, d, except for centromeric domains), with no notable depletion in terminal or gene-rich regions (contrasting with other species with both large and small genomes such as for example wheat [32] or Ensete [26]) where there are abundant transposons and few genes in broad centromeric regions. In ALO, retrotransposons (Class I TEs) and their fragments were the dominant and accounted for 94.71% of the TE content (79.76% of the ALO assembly), with LTR retroelements ( Gypsy and Copia ) occupying 51.65% and 26.15% of the ALO assembly, respectively (Fig.…”

“…1). In many species with smaller genomes (<3.96 Gbp of ALO), broad pericentromeric regions are reservoirs for the accumulation of a medley of (often lineage-specific) TEs [26, 68, 69], but in ALO, the overall TE density is relatively similar along the chromosomes. However, there is a high and localized abundance of an LTR retrotransposon (Fig.…”

“…high-throughput chromatin conformation capture, Hi-C), together with Illumina short-reads used for sequence correction and optical mapping, have improved the genome contiguity and repeat annotation integrity [24]. For example, hybrid ONT/Illumina study revealed the genomic landscape among diploid Brassica species in unprecedented detail [25] and allowed de novo genome assembly of Ensete glaucum , identification of repeats and chromosomal rearrangements to the related genus Musa [26]. High-continuity assembly of large genomes with a high proportion of repeats is becoming possible [27, 28] and enables comparison between crops and their wild relatives as well as definition of the pangenome.…”