Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)
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Date
Authors
Qiao, Qin
Edger, Patrick P.
Xue, Li
Qiong, La
Lu, Jie
Zhang, Yichen
Cao, Qiang
Yocca, Alan E.
Platts, Adrian E.
Knapp, Steven J.
Journal Title
Journal ISSN
Volume Title
Publisher
National Academy of Sciences
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.
Description
DATA AVAILABILITY: The raw genomic reads generated in this study have been deposited in the NCBI Sequence Read Archive (BioProject nos. PRJNA743176 and PRJNA757203). The genome assembly and annotation files are available at the Genome Database for Rosaceae (F. daltoniana: https://www.rosaceae.org/Analysis/11885161; F. pentaphylla: https://www.rosaceae.org/Analysis/12137892; F. mandschurica: https://www.rosaceae.org/Analysis/12137893; F. nilgerrensis: https://www.rosaceae.org/Analysis/12137894; F. viridis: https://www.rosaceae.org/Analysis/12137895).
Keywords
Strawberry (Fragaria spp.), Pan-genome, Comparative genomics, Genetic differentiation, MYB transcription factors
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Citation
Qiao, Q., Edger, P.P., Xue, L. et al. 2021, 'Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)', Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 45, art. e2105431118, pp. 1-11, doi : 10.1073/pnas.2105431118.