Journal
GENOME BIOLOGY AND EVOLUTION
Volume 6, Issue 12, Pages 3295-3313Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evu261
Keywords
Fragaria; polyploidy; phylogenetics; introgression; transposition; genome assembly
Categories
Funding
- National Science Foundation [DEB 1020523, DEB 1241006, DEB 1020271, DEB 1241217]
- United States Department of Agriculture
- University of Pittsburgh [USDA-CSREES 2005-00765]
- Direct For Biological Sciences
- Division Of Environmental Biology [1020523] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1020271, 1241217] Funding Source: National Science Foundation
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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 bemore 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.
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