Genome assembly ofMusa beccariishows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes

Abstract

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.

Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana

“…Within the three haploid assemblies, 256.48 Mb (53.76%), 258.29 Mb (54.14%), and 258.84 Mb (55.13%) of repetitive regions were identified ( Table S3 , see online supplementary material), similar to those in other banana genomes (e.g. M. acuminata : 52.62% [ 7 ]; M. beccarii : 55.99% [ 12 ]). Among them, the most abundant repetitive sequences were long terminal repeats (LTRs), which accounted for 36.36%, 35.44%, and 33.53% of the BXJ1, BXJ2, and BXJ3 assemblies, respectively ( Table S3 , see online supplementary material).…”

“…Since then, the DH-Pahang genome has been improved twice [ 6 , 7 ]. Moreover, other Musa genomes, for instance M. balbisiana , Musa itinerans , M. schizocarpa , Musa troglodytarum , and Musa beccarii , have already been reported during the past decade [ 2 , 8 – 12 ]. These high-quality banana genomes have provided necessary and valuable resources for further research on evolution of Musa genus, as well as domestication and breeding of banana.…”

Draft genome and transcriptome of Nepenthes mirabilis, a carnivorous plant in China

“…In particular, it is currently a challenge to obtain an accurate genome size with only short whole genome sequencing reads [42,43], which is also true for N. mirabilis in this study. Although both KmerGenie and GenomeScope estimated comparable genome sizes at a k-mer of 99 with 791,766,648 bp and 774,029,535 bp, respectively, we observed that the estimated genome size was affected by increasing k-mer from 17 to 71 in GenomeScope [26].…”

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family

“…JAPMAH000000000.1. All additional supporting data are available in the GigaScience repository, GigaDB [ 73 ].…”