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

Publication Overview
TitleThe American cranberry: first insights into the whole genome of a species adapted to bog habitat
AuthorsPolashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N
TypeJournal Article
Journal NameBMC plant biology
Volume14
Year2014
Page(s)165
CitationPolashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC plant biology. 2014; 14:165.

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.

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Pages

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN1471-2229
eISSN1471-2229
Publication Date2014
Journal AbbreviationBMC Plant Biol.
DOI10.1186/1471-2229-14-165
Elocation10.1186/1471-2229-14-165
Publication TypeJournal Article
Journal CountryEngland
LanguageEnglish
Language Abbreng
Publication TypeResearch Support, U.S. Gov't, Non-P.H.S.
Cross References
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DatabaseAccession
PMID: PMID:24927653