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DNA Res. 2014;21(2):169-81. doi: 10.1093/dnares/dst049. Epub 2013 Nov 26.

Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species.

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1
1 Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan.

Abstract

Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.

KEYWORDS:

Fragariax ananassa; comparative analysis; genome sequence assembly; polyploidy; wild Fragaria species

PMID:
24282021
PMCID:
PMC3989489
DOI:
10.1093/dnares/dst049
[Indexed for MEDLINE]
Free PMC Article
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