Origin and evolution of the octoploid strawberry genome.,Nature Genetics

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Origin and evolution of the octoploid strawberry genome.
Nature Genetics ( IF 31.7 ) Pub Date : 2019-02-25 , DOI: 10.1038/s41588-019-0356-4
Patrick P Edger _{1,

2} , Thomas J Poorten ₃ , Robert VanBuren _{1,

4} , Michael A Hardigan ₃ , Marivi Colle ₁ , Michael R McKain ₅ , Ronald D Smith ₆ , Scott J Teresi ₆ , Andrew D L Nelson ₇ , Ching Man Wai ₁ , Elizabeth I Alger ₁ , Kevin A Bird _{1,

2} , Alan E Yocca ₁ , Nathan Pumplin ₃ , Shujun Ou _{1,

2} , Gil Ben-Zvi ₈ , Avital Brodt ₈ , Kobi Baruch ₈ , Thomas Swale ₉ , Lily Shiue ₉ , Charlotte B Acharya ₃ , Glenn S Cole ₃ , Jeffrey P Mower ₁₀ , Kevin L Childs _{11,

12} , Ning Jiang _{1,

2} , Eric Lyons ₇ , Michael Freeling ₁₃ , Joshua R Puzey ₆ , Steven J Knapp ₃

Affiliation

Department of Horticulture, Michigan State University, East Lansing, MI, USA.
Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA.
Department of Plant Sciences, University of California-Davis, Davis, California, USA.
Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.
Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
Department of Biology, College of William and Mary, Williamsburg, VA, USA.
School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
NRGene, Ness Ziona, Israel.
Dovetail Genomics, Santa Cruz, CA, USA.
Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA.
Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.

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.

中文翻译：

章鱼体草莓基因组的起源和进化。

栽培草莓是两种野生章鱼物种杂交而成的，都是 100 多万年前四种二倍体祖先物种合并成一个细胞核的后代。在这里，我们报道了培养的八倍体草莓（Fragaria × ananassa）的近乎完整的染色体规模组装，并揭示了塑造这种复杂同种异体多倍体的起源和进化过程。我们鉴定了每个二倍体祖先物种的现存亲戚，并为章鱼草莓的北美起源提供支持。我们检查了章鱼体草莓中四个亚基因组之间的动态，并发现存在一个显性亚基因组，与其他亚基因组相比，该亚基因组的基因含量、基因表达丰度和同源染色体之间的偏向交换明显更高。通路分析表明，某些代谢组学和抗病性状在很大程度上受优势亚基因组控制。这些发现和参考基因组应该成为未来进化研究的有力平台，并使草莓的分子育种成为可能。

更新日期：2019-02-26

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