Origin and evolution of the octoploid strawberry genome

Patrick P. Edger, Thomas J. Poorten, Robert VanBuren, Michael A. Hardigan, Marivi Colle, Michael R. McKain, Ronald D. Smith, Scott J. Teresi, Andrew D.L. Nelson, Ching Man Wai, Elizabeth I. Alger, Kevin A. Bird, Alan E. Yocca, Nathan Pumplin, Shujun Ou, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily ShiueCharlotte B. Acharya, Glenn S. Cole, Jeffrey P. Mower, Kevin L. Childs, Ning Jiang, Eric H Lyons, Michael Freeling, Joshua R. Puzey, Steven J. Knapp

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.

Original languageEnglish (US)
JournalNature Genetics
DOIs
StatePublished - Jan 1 2019

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Fragaria
Genome
Diploidy
Chromosomes
DNA Shuffling
Disease Resistance
Metabolomics
Gene Expression
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M. A., Colle, M., McKain, M. R., ... Knapp, S. J. (2019). Origin and evolution of the octoploid strawberry genome. Nature Genetics. https://doi.org/10.1038/s41588-019-0356-4

Origin and evolution of the octoploid strawberry genome. / Edger, Patrick P.; Poorten, Thomas J.; VanBuren, Robert; Hardigan, Michael A.; Colle, Marivi; McKain, Michael R.; Smith, Ronald D.; Teresi, Scott J.; Nelson, Andrew D.L.; Wai, Ching Man; Alger, Elizabeth I.; Bird, Kevin A.; Yocca, Alan E.; Pumplin, Nathan; Ou, Shujun; Ben-Zvi, Gil; Brodt, Avital; Baruch, Kobi; Swale, Thomas; Shiue, Lily; Acharya, Charlotte B.; Cole, Glenn S.; Mower, Jeffrey P.; Childs, Kevin L.; Jiang, Ning; Lyons, Eric H; Freeling, Michael; Puzey, Joshua R.; Knapp, Steven J.

In: Nature Genetics, 01.01.2019.

Research output: Contribution to journalArticle

Edger, PP, Poorten, TJ, VanBuren, R, Hardigan, MA, Colle, M, McKain, MR, Smith, RD, Teresi, SJ, Nelson, ADL, Wai, CM, Alger, EI, Bird, KA, Yocca, AE, Pumplin, N, Ou, S, Ben-Zvi, G, Brodt, A, Baruch, K, Swale, T, Shiue, L, Acharya, CB, Cole, GS, Mower, JP, Childs, KL, Jiang, N, Lyons, EH, Freeling, M, Puzey, JR & Knapp, SJ 2019, 'Origin and evolution of the octoploid strawberry genome', Nature Genetics. https://doi.org/10.1038/s41588-019-0356-4
Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR et al. Origin and evolution of the octoploid strawberry genome. Nature Genetics. 2019 Jan 1. https://doi.org/10.1038/s41588-019-0356-4
Edger, Patrick P. ; Poorten, Thomas J. ; VanBuren, Robert ; Hardigan, Michael A. ; Colle, Marivi ; McKain, Michael R. ; Smith, Ronald D. ; Teresi, Scott J. ; Nelson, Andrew D.L. ; Wai, Ching Man ; Alger, Elizabeth I. ; Bird, Kevin A. ; Yocca, Alan E. ; Pumplin, Nathan ; Ou, Shujun ; Ben-Zvi, Gil ; Brodt, Avital ; Baruch, Kobi ; Swale, Thomas ; Shiue, Lily ; Acharya, Charlotte B. ; Cole, Glenn S. ; Mower, Jeffrey P. ; Childs, Kevin L. ; Jiang, Ning ; Lyons, Eric H ; Freeling, Michael ; Puzey, Joshua R. ; Knapp, Steven J. / Origin and evolution of the octoploid strawberry genome. In: Nature Genetics. 2019.
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