Genomic hitchhiking with moisture adaptation patterns stem prickleless in rose

"Rose with prickles" is a symbol of adversity and sacrifice but the molecular bases patterning prickle remains poorly explored. Here we generated a high-quality reference genome assembly for prickleless Rosa wichuraiana Basyes Thornless (BT), and identified genetic elements relating to stem prickle patterning. BT genome harbors a significant high proportion of Copia-type LTR (62.74% of LTRs) and diverges remarkably from that of R. chinensis Old Blush, a founder genotype for rose domestication. Three negatively selected and fixed QTL were identified underlying BT prickleless. Differentially expressed genes in QTL were enriched for water-use-related genes, suggesting that prickleless might hitchhike the adaptation to moisture environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, expression variation of key candidate genes associated well with prickle-patterning divergence in roses. Our efforts provide fundamental resources and insights for Rosaceae genome evolution and molecular basis of key traits, thus should benefit rose improvement.