DOI: 10.5061/dryad.44j0zpcnq
title: Striking variation in chromosome structure within Musa acuminata and its diploid cultivars

description: 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 showing a correlation with banana
 speciation. Chromosome painting of F1 hybrids was complemented by Illumina
 resequencing, which enabled to identify the contribution of parental
 subgenomes to the diploid hybrid clones. Balanced presence of both
 parental genomes was revealed in all F1 hybrids with the exception of one
 clone, which contained only Mchare specific SNPs, and thus most probably
 originated from an unreduced diploid gamete of Mchare.
description: 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 <em>M. acuminata</em> ssp.
 <em>malaccensis</em> ‘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 (&lt;6-fold coverage for the minor allele were converted
 to missing data) (https://github.com/SouthGreenPlatform/vcfHunter).
 Finally, proportion of parental genomes in the F1 hybrid clones along the
 individual chromosomes of the reference genome sequence was called using
 biallelic SNPs (SNPs specific to Mchare cultivars and <em>M.
 acuminata </em>spp. <em>burmannicoides</em> ‘Calcutta
 4’) in CDS genome regions using vcf2allPropAndCov.py and
 vcf2allPropAndCovByChr.py python scripts
 (https://github.com/SouthGreenPlatform/vcfHunter) according to Baurens et
 al. (2019).
description: # 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/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](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 (&lt;6-fold coverage for the minor allele were converted to missing data) ([https://github.com/SouthGreenPlatform/vcfHunter](https://github.com/SouthGreenPlatform/vcfHunter). Finally, proportion of parental genomes in the F1 hybrid clones along the individual chromosomes of the reference genome sequence was called using biallelic SNPs (SNPs specific to Mchare cultivars and M. acuminata spp. burmannicoides  ‘Calcutta 4’) in CDS genome regions using vcf2allPropAndCov.py and vcf2allPropAndCovByChr.py python scripts ([https://github.com/SouthGreenPlatform/vcfHunter](https://github.com/SouthGreenPlatform/vcfHunter) according to Baurens et al. (2019). ## Description of the data and file structure Genome proportion of eight F1 hybrid clones was analyzed: | **Accession name of F1 hybrid** | **Male parent** | **Female parent (Mchare clone)** | | :------------------------------ | :-------------------------- | :------------------------------- | | ‘NM275\_4’ | Musa acuminata ‘Calcutta 4’ | ‘Mchare Laini’ | | ‘NM258\_3’ | Musa acuminata ‘Calcutta 4’ | ‘Mchare Laini’ | | ‘NM209\_3’ | Musa acuminata ‘Calcutta 4’ | ‘Mchare Laini’ | | ‘NM237\_8’ | Musa acuminata ‘Calcutta 4’ | ‘Ijihu Inkudu’ | | ‘T2269\_1’ | Musa acuminata ‘Calcutta 4’ | ‘Huti White’ | | ‘T2274\_6’ | Musa acuminata ‘Calcutta 4’ | ‘Huti White’ | | ‘T2274\_9’ | Musa acuminata ‘Calcutta 4’ | ‘Huti White’ | | ‘T2619\_15’ | Musa acuminata ‘Calcutta 4’ | ‘Mchare Mlelembo’ | The vcf files contain biallelic SNPs specific to male (M. acuminata 'Calcutta4'; 2n = 2x = 22 ) and female (Mchare cultivars; 2n = 2x = 22) parents,whcih were used to analyze contribution of parental genomes in F1hybrids. Analysis was done using vcfHunter pipeline ([https://github.com/SouthGreenPlatform/vcfHunter](https://github.com/SouthGreenPlatform/vcfHunter) according to Baurens et al. (2019). ## Sharing/Access information This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any. Data was derived from the following sources: * Raw Illumina sequences of the parents and F1 hybrid clones are stored in the NCBI sequence Read Archive (SRA): SRA experiments: SRX22339926 - SRX22339938.