Reference genome (ONT) and annotation of Brassica fruticulosa, population sequencing of natural individuals from Catalonia, and transcriptome data

We first generated a Brassica fruticulosa reference genome of a particularly salinity-tolerant accession, TOS (from Tossa de Mar, Catalonia, Spain), using long-read Oxford Nanopore Technology (ONT). Gene models were predicted by an evidence-guided annotation approach incorporating RNA-Seq data and cross-species protein alignments in BRAKER2. we then sampled 18 populations for genome sequencing across the reported range of B. fruticulosa. We Illumina sequenced a total of 90 individuals, selecting 5 individuals from each of the 18 populations. One sample, Bla5, was excluded, due to suspicion of sample contamination. We chose the most sharply contrasting populations from the hydroponic salinity challenge experiment and then subjected them to salinity challenge (0 mM or 150 mM NaCl) for 10 days. Leaves and roots of 6 plants per population (48 samples total: 24 plants from 2 salt-tolerant and 2 salt-sensitive populations, 12 plants under control and 12 plants under salt stress conditions) were Illumina sequenced for transcriptome analysis.