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.

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

“…S5), confirming that the older event is the shared γ event. The more recent WGD coincided with the Vm-α duplication reported earlier in cranberry 15 , and is a shared event since the species diverged much more recently (Fig. 3D).…”

“…documented both morphologically and chemically 116,137,138 . However, genes associated with wax biosynthesis have not been well defined in the published genomes of Vaccinium 14,15 . Here, we identified all candidate cuticle biosynthesis genes in V. darrowii (Fig.…”

“…The northern highbush blueberry, V. corymbosum (2n = 4x = 48), is the only species in the Cyanococcus section with a chromosome-level genome assembly 14 . Species in other sections of Vaccinium, such as cranberry (V. macrocarpon), a species sharing similar geographical distribution with the V. corymbosum in the temperate region, and the boreal bilberry (V. mytillus) have recently been sequenced 15,16 . These genomes serve as valuable resources for genome-enabled breeding of northern Vaccinium species, while genome information for southern adapted blueberries is still lacking.…”

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

“…We previously published a draft reference genome for the V. macrocarpon cultivar Ben Lear (BL) that was very useful, yet still rather fragmented [19]. Recently, a genome for a second cultivar Stevens (ST) and a fragmented assembly for V. oxycoccos was published [20]. Here we report an updated chromosome scale assembly for the BL reference genome and an improved draft genome of diploid V. oxycoccos .…”

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

“…Hence, TEs can also be applied as molecular markers for the differentiation of accessions and to inform plant breeding programs [19][20][21][22][23]. Thus, the correct annotation and characterization of repetitive sequences, particularly TEs, are a prerequisite for an enriched genome assembly as well as for subsequent genome characterization and valorization [10][11][12]. Nevertheless, as many different TE classification hierarchies have been suggested [24][25][26][27][28][29], as an integration of tools, databases, and pipelines is still discussed [30], and as there is still no gold standard for TE identification and classification available, TE annotation and classification for non-model species is still a considerable undertaking.…”