Dissection of the octoploid strawberry genome by deep sequencing of the genomes of fragaria species

Hideki Hirakawa, Kenta Shirasawa, Shunichi Kosugi, Kosuke Tashiro, Shinobu Nakayama, Manabu Yamada, Mistuyo Kohara, Akiko Watanabe, Yoshie Kishida, Tsunakazu Fujishiro, Hisano Tsuruoka, Chiharu Minami, Shigemi Sasamoto, Midori Kato, Keiko Nanri, Akiko Komaki, Tomohiro Yanagi, Qin Guoxin, Fumi Maeda, Masami IshikawaSatoru Kuhara, Shusei Sato, Satoshi Tabata, Sachiko N. Isobe

Research output: Contribution to journalArticle

129 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)169-181
Number of pages13
JournalDNA Research
Volume21
Issue number2
DOIs
Publication statusPublished - Apr 2014

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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    Hirakawa, H., Shirasawa, K., Kosugi, S., Tashiro, K., Nakayama, S., Yamada, M., Kohara, M., Watanabe, A., Kishida, Y., Fujishiro, T., Tsuruoka, H., Minami, C., Sasamoto, S., Kato, M., Nanri, K., Komaki, A., Yanagi, T., Guoxin, Q., Maeda, F., ... Isobe, S. N. (2014). Dissection of the octoploid strawberry genome by deep sequencing of the genomes of fragaria species. DNA Research, 21(2), 169-181. https://doi.org/10.1093/dnares/dst049