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Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

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Title Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes
 
Creator Wang, Zheng-Feng
Rouard, Mathieu
Droc, Gaëtan
Heslop-Harrison, Pat
Ge, Xue-Jun
 
Subject genome annotation
evolution
musa
wild plants
genomes
bioinformatics
data analysis
transcriptomics
 
Description Background

Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae.

Findings

The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes.

Conclusions

The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
 
Date 2022-12-28
2023-03-14T09:19:43Z
2023-03-14T09:19:43Z
 
Type Journal Article
 
Identifier Wang, Z-F.; Rouard, M.; Droc, G.; Heslop-Harrison, P. Ge, X-J. (2023) Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. GigaScience 12: giad005. ISSN: 2047-217X
2047-217X
https://hdl.handle.net/10568/129634
https://doi.org/10.1093/gigascience/giad005
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format giad005
application/pdf
 
Publisher Oxford University Press (OUP)
 
Source GigaScience