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Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.).


ABSTRACT: Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

SUBMITTER: Qiao Q 

PROVIDER: S-EPMC8609306 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Evolutionary history and pan-genome dynamics of strawberry (<i>Fragaria</i> spp.).

Qiao Qin Q   Edger Patrick P PP   Xue Li L   Qiong La   Lu Jie J   Zhang Yichen Y   Cao Qiang Q   Yocca Alan E AE   Platts Adrian E AE   Knapp Steven J SJ   Van Montagu Marc M   Van de Peer Yves Y   Lei Jiajun J   Zhang Ticao T  

Proceedings of the National Academy of Sciences of the United States of America 20211101 45


Strawberry (<i>Fragaria</i> spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key <i>Fragaria</i> spec  ...[more]

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