A chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae
GigaScience(2021)
Abstract
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.
MoreTranslated text
AI Read Science
Must-Reading Tree
Example
![](https://originalfileserver.aminer.cn/sys/aminer/pubs/mrt_preview.jpeg)
Generate MRT to find the research sequence of this paper
Chat Paper
Summary is being generated by the instructions you defined