title: The American cranberry: first insights into the whole genome of a species adapted to bog habitat.
abstract: BACKGROUND
  The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.
  
  
  RESULTS
  The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).
  
  
  CONCLUSIONS
  Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.
authors.affiliation: USDA, Agricultural Research Service, Genetic Improvement of Fruits and Vegetables Lab, 125A Lake Oswego Rd,, Chatsworth, New Jersey 08019, USA. James.Polashock@ars.usda.gov.
authors.forename: James
authors.initials: J
authors.lastname: Polashock
authors.forename: Ehud
authors.initials: E
authors.lastname: Zelzion
authors.forename: Diego
authors.initials: D
authors.lastname: Fajardo
authors.forename: Juan
authors.initials: J
authors.lastname: Zalapa
authors.forename: Laura
authors.initials: L
authors.lastname: Georgi
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.forename: Nicholi
authors.initials: N
authors.lastname: Vorsa
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D007178:Inbreeding; D018895:Microsatellite Repeats / Q000235:genetics; D008928:Mitochondria / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics; D029799:Vaccinium macrocarpon / Q000235:genetics*; D053833:Wetlands
chemical_list: D004251:DNA Transposable Elements; D005819:Genetic Markers