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Nat Genet. 2019 Mar;51(3):541-547. doi: 10.1038/s41588-019-0356-4. Epub 2019 Feb 25.

Origin and evolution of the octoploid strawberry genome.

Author information

1
Department of Horticulture, Michigan State University, East Lansing, MI, USA. edgerpat@msu.edu.
2
Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA. edgerpat@msu.edu.
3
Department of Plant Sciences, University of California-Davis, Davis, California, USA.
4
Department of Horticulture, Michigan State University, East Lansing, MI, USA.
5
Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.
6
Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
7
Department of Biology, College of William and Mary, Williamsburg, VA, USA.
8
School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
9
Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA.
10
NRGene, Ness Ziona, Israel.
11
Dovetail Genomics, Santa Cruz, CA, USA.
12
Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
13
Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
14
Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, USA.
15
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
16
Department of Plant Sciences, University of California-Davis, Davis, California, USA. sjknapp@ucdavis.edu.

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.

PMID:
30804557
DOI:
10.1038/s41588-019-0356-4
[Indexed for MEDLINE]

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