Striking variation in chromosome structure within Musa acuminata and its diploid cultivars

The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, Musa acuminata and Musa balbisiana. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility of edible clones and differences in the chromosome structure among M. acuminata subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo painting we investigated large chromosomal rearrangements in a set of wild M. acuminata subspecies and cultivars that originated by natural crosses. Additionally, we analyzed chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and wild M. acuminata ‘Calcutta 4’ genotype. Analysis of chromosome structure within M. acuminata revealed the presence of a large number of chromosomal rearrangements s..., Analysis of proportion of individual parental subgenomes in the F1 hybrid clones was done using vcfHunter pipeline (https://github.com/SouthGreenPlatform/vcfHunter) according to Baurens et al. (2019). Briefly, trimmed reads were aligned to reference genome sequence of M. acuminata ssp. malaccensis ‘DH Pahang’ v4 (Belser et al., 2021) by BWA-MEM v0.7.15 (Li 2013), followed by removing redundant reads using MarkDuplicate from Picard Tools v2.7.0, and locally realigned around indels using the IndelRealigner tool of GATK v3.3 package (McKenna et al., 2010). Bases with a mapping quality ≥10 were counted using the process_reseq_1.0.py python script (https://github.com/SouthGreenPlatform/vcfHunter). Variant calling and SNP filtering steps were performed according to Baurens et al. (2019) using the VcfPreFilter.1.0 python script (alleles supported by at least three reads and with a frequency 0.25 were kept as variant) and vcfFilter.1.0.py python script (<6-fold coverage for the minor allele ..., , # SNP datasets (vcf files) used for in silico painting of Mchare x M. acuminata 'Calcutta 4' F1 hybrid clones

[https://doi.org/10.5061/dryad.44j0zpcnq](https://doi.org/10.5061/dryad.44j0zpcnq)

Genomic DNA was isolated with the NucleoSpin PlantII kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations and further sheared by Bioruptor Plus (Diagenode, Liege, Belgium) to achieve an insert size of about 500 bp. Libraries for sequencing were prepared from 2 μg of fragmented DNA using TruSeq® DNA PCR-free kit (Illumina) and sequenced on a NovaSeq 6000 (Illumina), producing 2 × 150-bp paired-end reads to achieve a minimal sequence depth of 25 ×. Raw data were trimmed for low-quality bases and adapter sequences and to the same length using fastp v.0.20.1 (Chen et al., 2018).

Analysis of proportion of individual parental subgenomes in the F1 hybrid clones  was done using vcfHunter pipeline ([https://github.com/SouthGreenPlatform/vcfHunter](https://github.com/South...