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

Description

Notes

Methods

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 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 M. acuminata spp. burmannicoides '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).