DArTseq data of Musa splendida and Musa viridis

This project consists of high-throughput sequencing data (DArTseq) of Musa splendida and Musa viridis individuals originating from northern Viet Nam. A modified cetyltrimethylammonium bromide (CTAB) protocol from Doyle & Doyle (1987) was used to extract DNA from 15 mg of silica-dried leaf material per individual. Next, 20 µl of DNA was shipped to Diversity Arrays Technology (DArT, University of Canberra, Bruce, Australia) for an enzyme-based genomic complexity reduction approach with the restriction enzymes PstI and MseI (DArTseq) following Killian et al. (2012). All DArTseq libraries were subsequently 150 base pairs (bp) single-end sequenced on an Illumina NovaSeq 6000 instrument. Demultiplexed raw reads retrieved from DArT were trimmed to remove barcodes and the PstI restriction site remnant at the 5'-end and the MseI restriction site remnant and adapter sequence at the 3'-end with Cutadapt v3.5 (Martin, 2011) in GBprocesS v4.0.0 (Schaumont, 2020). Reads with a barcode shorter than the maximum barcode were 3' trimmed with Cutadapt to compensate for variation in barcode lengths. In addition, reads shorter than 20 bp were deleted. Afterwards, all reads were filtered for maximum five ambiguous nucleotide calls (Ns) and an average base quality score of 25 using the MaxNFilter and AverageQualityFilter in GBprocesS. Reads with internal intact PstI or MseI restriction sites were discarded as well with the RemovePatternFilter in GBprocesS.