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Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

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https://ir.library.oregonstate.edu/concern/articles/6w924d42w

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  • Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.
  • This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. The published article can be found at: http://gbe.oxfordjournals.org/.
  • Keywords: Polyploidy, Transposition, Genome assembly, Introgression, Fragaria, Phylogenetics
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  • Tennessen, J. A., Govindarajulu, R., Ashman, T. L., & Liston, A. (2014). Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biology and Evolution, 6(12), 3295-3313. doi:10.1093/gbe/evu261
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  • 6
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  • 12
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  • This work was supported by the National Science Foundation to T.L.A. (DEB 1020523 and DEB 1241006) and A.L. (DEB 1020271 and DEB 1241217), and by the United States Department of Agriculture to T.L.A. and the University of Pittsburgh (USDA-CSREES 2005-00765).
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