Genome Sequencing of American Cranberry

Fruit of the American cranberry (Vaccinium macrocarpon Ait.) is known to produce a variety of bioactive polyphenolic compounds. The best known of which are the A-type proanthocyanidins that help prevent urinary tract infections.  In addition, from a taxonomic standpoint, V. macrocarpon is a species in the core Ericales, a group for which genome sequence data are currently lacking. Whereas sequence data are relatively easy to obtain, accurate assembly remains an obstacle in higher plants that are highly heterozygous, particularly where reference genomes are not available. Cranberry offers the advantage of being a self-fertile diploid species. The genome size of V. macrocarpon is estimated to be 570 Mbp, based on flow cytometry. To minimize heterozygosity and thereby facilitate assembly, we selected a fifth-generation selfing-lineage (F > 0.97) individual derived from the cultivar Ben Lear. Genomic DNA was isolated and sequenced on the Illumina platform and the resulting sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20x average genome coverage. Over 43,000 predicted genes were identified, representing about 19% of the assembled genome. Almost 70% of the predicted genes were assigned to candidate genes based on sequence similarity and the genes supported by transcriptome data totaled about 77%.  Thus, shotgun sequencing of an inbred cranberry accession allowed efficient assembly and gene calling. These data will be used as a basis to further study important biochemical pathways and the genes associated with those pathways as well as for marker development for breeding and selection