A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

Abstract

Bilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi‐C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker‐trait association between these two species, as the loci involved in key characters are orthologous.

Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry

“…PyMYB114 and PybHLH3 can regulate anthocyanin synthesis in peaches ( Yao et al, 2017 ). In bilberry ( Vaccinium myrtillus L.), Wu C. et al (2021) describe the complex MYBA locus and identify the key regulating MYB genes that determine anthocyanin production. In American cranberry ( Vaccinium macrocarpon Ait.…”

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

“…Recently, a draft genome assembly of bilberry ( V. myrtillus ) has also been made publicly available [ 49 ]. Long-read sequencing was completed on V. myrtillus (isolate NK2018) producing a 524 Mb genome assembly in 1418 scaffolds.…”

“…Accordingly, genetic engineering tools could provide a powerful approach for introducing and/or targetting desirable horticultural traits, which would not be possible by traditional breeding [ 174 , 176 ]. Recent advances in Vaccinium genomics and gene editing technologies are stimulating the application of genetic transformation for specific manipulation of the genomes of Vaccinium species [ 44 – 49 , 177 ]. Genetic engineering relies on the presence of suitable target genes and new biotechnological tools such as efficient transformation protocols and effective gene manipulation [ 176 ].…”

Fertile Intersectional Hybrids of 4x Andean Blueberry (Vaccinium meridionale) and 2x Lingonberry (V. vitis-idaea)

“…Furthermore, recent findings of high levels of synteny among Vaccinium spp. genomes suggest little differentiation in general among Vaccinium genomes (although V. vitis-idaea is not among those published genomes) (Qi et al, 2021, Wu et al, 2021. High levels of synteny suggest that ongoing recombination and fertility may be possible.…”