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.

Features
This publication contains information about 48,190 features:
Feature NameUniquenameType
GBFL01000401GBFL01000401.1region
GBFL01000402GBFL01000402.1region
GBFL01000403GBFL01000403.1region
GBFL01000404GBFL01000404.1region
GBFL01000405GBFL01000405.1region
GBFL01000406GBFL01000406.1region
GBFL01000407GBFL01000407.1region
GBFL01000408GBFL01000408.1region
GBFL01000409GBFL01000409.1region
GBFL01000410GBFL01000410.1region
GBFL01000411GBFL01000411.1region
GBFL01000412GBFL01000412.1region
GBFL01000413GBFL01000413.1region
GBFL01000414GBFL01000414.1region
GBFL01000415GBFL01000415.1region
GBFL01000416GBFL01000416.1region
GBFL01000417GBFL01000417.1region
GBFL01000418GBFL01000418.1region
GBFL01000419GBFL01000419.1region
GBFL01000420GBFL01000420.1region
GBFL01000421GBFL01000421.1region
GBFL01000422GBFL01000422.1region
GBFL01000423GBFL01000423.1region
GBFL01000424GBFL01000424.1region
GBFL01000425GBFL01000425.1region

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
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:24927653