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Title: The American cranberry: first insights into the whole genome of a species adapted to bog habitat

Author
item Polashock, James
item ZELZION, UDI - Rutgers University
item Fajardo, Diego
item Zalapa, Juan
item GEORGI, LAURA - Rutgers University
item BHATTACHARYA, DEBASHISH - Rutgers University
item VORSA, NICHOLI - Rutgers University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2014
Publication Date: 6/13/2014
Publication URL: http://handle.nal.usda.gov/10113/61457
Citation: Polashock, J.J., Zelzion, U., Fajardo, D.A., Zalapa, J.E., Georgi, L., Bhattacharya, D., Vorsa, N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. Biomed Central (BMC) Plant Biology. 14:165.

Interpretive Summary: The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America. Considerable variation present within cranberry populations presents valuable opportunities for crop improvement. In order to better exploit genetic variation in cranberry to develop varieties with improved dietary health benefits and disease resistance, better knowledge of the cranberry genome is needed for identifying valuable genes that control these atttributes. We developed experimental cranberry plants suitable for genome sequencing and determined the cranberry DNA sequence. We analyzed the sequence and identified genes involved in production of health related comounds and plant defense for resistance to pathogens. The genes identified are valuable for studying important biochemical pathways and cellular processes as well as for genetic markers that are useful in breeding improved cultivars.

Technical Abstract: 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.) such as Vitis labrusca L. 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. The karyotype is composed of 12 submetacentric to metacentric chromosomes. To minimize heterozygosity, we sequenced the genome of a fifth-generation inbred accession derived from five self-pollination cycles of the cultivar Ben Lear. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50 = 4237 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%). Shotgun sequencing, with high coverage, of the cranberry genome allowed efficient assembly and gene calling. The candidate genes we identified represent a useful collection to further study important biochemical pathways and cellular processes as well as for marker development for breeding and the study of horticultural characteristics, such as disease resistance.