Dissecting the subtropical adaptation traits and cuticle synthesis pathways via the genome of the subtropical blueberry Vaccinium darrowii

Vaccinium darrowii is a subtropical wild blueberry species, which was used to breed economically important southern highbush cultivars. The adaptation traits of V. darrowii to subtropical climate would provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochoromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and predicted 41 815 genes using RNAseq evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and V. corymbosum. This conserved genome structure may explain the high fertilization during crossbreeding between V. darrowii and other blueberry cultivars. Gene expansion and tandem duplication analysis indicated possible roles of defense and flowering associated genes in adaptation of V. darrowii to the subtropics. The possible SOC1 genes in V. darrowii were identified with phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA-sequencing, the cuticle biosynthesis pathways of Vaccinium species were delineated here in V. darrowii. This result could serve as a reference for breeding berries with customer-desired colors. The V. darrowii reference genome, together with the unique traits of this species, including diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.