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

Abstract

Background 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 is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Findings Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb 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 single 5S ribosomal DNA locus 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 centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. Conclusions The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows 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.

Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (Boesenbergia rotunda)

“…The genome of the plant we sequenced, when in cultivation a largely vegetatively propagated species, shows an unusually high heterozygosity of 3.01%, suggesting that the cultivar may be of hybrid origin or may have undergone whole genome duplication events. This is also suggested based on the large number of unigenes in B. rotunda , notably more than twice that of Ensete glaucum 56 , and 46,765 duplication events (65.8% of the B. rotunda genome, with at least 50% support). As noted in Citrus limon 64 , high levels of heterozygosity complicate the assembly process.…”

“…Larger plant genomes have now been sequenced including those of important monocot species such as wheat ∼ 17 Gb (International Wheat Genome Sequencing Consortium), Aegilops tauschii ∼ 4.3 Gb 49 , oil palm ∼ 1.8 Gb 50 and maize ∼ 2.6 Gb 51 , in addition to species known for their unique metabolites such as tea (Camellia sinensis) ∼ 2.98 Gb 52, 53 and ginseng ( Panax ginseng ) ∼ 3.2 Gb 54 . However, even with the recent advances in long sequence technology, large plant genomes can be challenging to assemble due to high repeat content and high levels of heterozygosity 55, 56 .…”

Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera

“…Data from different organisms indicate that sex chromosome-autosome fusions can enhance the role of sex chromosomes in speciation and initiate rapid divergence between populations and incipient species (Kitano & Peichel, 2012; Bracewell et al, 2017; Wang et al, 2022). At least three different mechanisms of this process have been described.…”

“…The situation has changed quite recently due to the use of chromosome-level genome assemblies for karyotype analysis (Huang et al, 2022; Wang et al, 2022). This led to the first attempts to analyze rapid karyotypic evolution in different groups (Mudd et al, 2020; Yin et al, 2021), including Lepidoptera (Hill et al, 2019; Cicconardi et al, 2021; Mackintosh et al, 2021).…”

Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

“…Structural genomic studies have been undertaken in other Zingiberales including turmeric (Curcuma longa; genome size of 1.24 Gb) [47] and for several Musaceae species and cultivars, which have genome sizes ranging from 462 Mb to 598 Mb (Banana Genome Hub https://banana-genome-hub.southgreen.fr/ accessed on 28 May 2022) [48], while the Pan-genome of Musa Ensete has a genome size of 951.6 Mb [49]. Larger plant genomes have now been sequenced including those of important monocot species such as wheat ~17 Gb (International Wheat Genome Sequencing Consortium), Aegilops tauschii ~4.3 Gb [50], oil palm ~1.8 Gb [51] and maize ~2.6 Gb [52], in addition to species known for their unique metabolites such as tea (Camellia sinensis) ~2.98 Gb [53,54] and ginseng (Panax ginseng) ~3.2 Gb [55]; however, even with the recent advances in long sequence technology, large plant genomes can be challenging to assemble due to a high repeat content and high levels of heterozygosity [56,57].…”