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

Qin Qiao, Patrick P. Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, Alan E. Yocca, Adrian E. Platts, Steven J. Knapp, et al.
(2021) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 118(45).
Author
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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.
Keywords
Multidisciplinary, strawberry (Fragaria spp.), pan genome, comparative genomics, genetic differentiation, MYB transcription factors, MULTIPLE SEQUENCE ALIGNMENT, READ ALIGNMENT, GENE, ROSACEAE, DIVERSIFICATION, IDENTIFICATION, PERFORMANCE, PREDICTION, ANCESTRY, INSIGHTS

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MLA
Qiao, Qin, et al. “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, 2021, doi:10.1073/pnas.2105431118.
APA
Qiao, Q., Edger, P. P., Xue, L., Qiong, L., Lu, J., Zhang, Y., … Zhang, T. (2021). Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(45). https://doi.org/10.1073/pnas.2105431118
Chicago author-date
Qiao, Qin, Patrick P. Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, 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 118 (45). https://doi.org/10.1073/pnas.2105431118.
Chicago author-date (all authors)
Qiao, Qin, Patrick P. Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, Alan E. Yocca, Adrian E. Platts, Steven J. Knapp, Marc Van Montagu, Yves Van de Peer, Jiajun Lei, and Ticao Zhang. 2021. “Evolutionary History and Pan-Genome Dynamics of Strawberry (Fragaria Spp.).” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 (45). doi:10.1073/pnas.2105431118.
Vancouver
1.
Qiao Q, Edger PP, Xue L, Qiong L, Lu J, Zhang Y, et al. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2021;118(45).
IEEE
[1]
Q. Qiao et al., “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, 2021.
@article{8725812,
  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.}},
  articleno    = {{e2105431118}},
  author       = {{Qiao, Qin and Edger, Patrick P. and Xue, Li and Qiong, La and Lu, Jie and Zhang, Yichen and Cao, Qiang and Yocca, Alan E. and Platts, Adrian E. and Knapp, Steven J. and Van Montagu, Marc and Van de Peer, Yves and Lei, Jiajun and Zhang, Ticao}},
  issn         = {{0027-8424}},
  journal      = {{PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}},
  keywords     = {{Multidisciplinary,strawberry (Fragaria spp.),pan genome,comparative genomics,genetic differentiation,MYB transcription factors,MULTIPLE SEQUENCE ALIGNMENT,READ ALIGNMENT,GENE,ROSACEAE,DIVERSIFICATION,IDENTIFICATION,PERFORMANCE,PREDICTION,ANCESTRY,INSIGHTS}},
  language     = {{eng}},
  number       = {{45}},
  pages        = {{11}},
  title        = {{Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)}},
  url          = {{http://doi.org/10.1073/pnas.2105431118}},
  volume       = {{118}},
  year         = {{2021}},
}
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