Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

Abstract

The American cranberry ( Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum . More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry- V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.