This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Data availability
The sequence alignments and phylogenetic trees are available on Dryad: https://doi.org/10.5061/dryad.ncjsxksqj. The raw sequence data are available in the Sequence Read Archive under NCBI BioProject nos. PRJNA577462 and PRJNA576199. Biological samples are available from the authors on request.
Code availability
Custom perl and R scripts used to summarize and display the phylogenomic results are available at https://github.com/jacobtennessen/FragariaGenome.
References
Edger, P. P. et al. Origin and evolution of the octoploid strawberry genome. Nat. Genet. 51, 541–547 (2019).
Tennessen, J. A., Govindarajulu, R., Ashman, T.-L. & Liston, A. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol. Evol. 6, 3295–3313 (2014).
Kamneva, O. K., Syring, J., Liston, A. & Rosenberg, N. A. Evaluating allopolyploid origins in strawberries (Fragaria) using haplotypes generated from target capture sequencing. BMC Evol. Biol. 17, 180 (2017).
Yang, Y. & Davis, T. M. A new perspective on polyploid Fragaria (strawberry) genome composition based on large-scale, multi-locus phylogenetic analysis. Genome Biol. Evol. 9, 3433–3448 (2017).
Liston, A., Cronn, R. & Ashman, T.-L. Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. Am. J. Bot. 101, 1686–1699 (2014).
Njuguna, W., Liston, A., Cronn, R., Ashman, T.-L. & Bassil, N. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Mol. Phylogenet. Evol. 66, 17–29 (2012).
Rousseau-Gueutin, M. et al. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol. Phylogenet. Evol. 51, 515–530 (2009).
Wei, N., Tennessen, J. A., Liston, A. & Ashman, T.-L. Present-day sympatry belies the evolutionary origin of a high-order polyploid. New Phytol. 216, 279–290 (2017).
Edger, P. P. et al. Reply to: Revisiting the origin of octoploid strawberry. Nat. Genet. https://doi.org/10.1038/s41588-019-0544-2 (2019).
Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017).
Wei, N., Cronn, R., Liston, A. & Ashman, T.-L. Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments. New Phytol. 221, 2286–2297 (2019).
Buti, M. et al. The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). Gigascience 7, giy010 (2018).
Edger, P. P. et al. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 7, gix124 (2018).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Acknowledgements
The authors thank L. Longway and R. Cronn for laboratory assistance, K. Weitemier and T. Jennings for assistance with targeted sequence capture and K. Schuller, E. Jiang, A. Freundlich and the University of Pittsburgh glasshouse staff for plant cultivation. The OSU Center for Genome Research and Biocomputing conducted Illumina sequencing and provided computational support. This work was funded by the US National Science Foundation (no. DEB 1241217 to A.L. and no. DEB 1241006 to T.-L.A.) and the National Natural Science Foundation of China (no. 31261120580 to M.D. and J.L.).
Author information
Authors and Affiliations
Contributions
Fragaria moschata linkage mapping was conducted by N.W. and T.-L.A. Phylogenetic analyses were performed by A.L., N.W. and J.T. Figures were prepared by J.T. and N.W. Sample collection and DNA sequencing in China was led by J.L. and M.D. All authors contributed to the writing and reviewing of the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Maximum likelihood estimate of phylogeny for base chromosomes 2-7.
Bootstrap values for all nodes are 100%, unless indicated.
Extended Data Fig. 2 Maximum-likelihood phylogenies of base chromosomes 1–7 involving the maternal linkage groups (LGs) of the hexaploid Fragaria moschata.
These LGs are named after species (‘Fmos’), chromosome (I–VII), maternal map (m) and LG number (1–3). Some chromosomes (e.g. 1, 5 and 6) have incomplete F. moschata LG numbers. Numbers associated with branches are ML bootstrap support values from 100 replicates.
Extended Data Fig. 3 Maximum-likelihood phylogenies of base chromosomes 1–7 involving the paternal linkage groups (LGs) of the hexaploid Fragaria moschata.
These LGs are named after species (‘Fmos’), chromosome (I–VII), paternal map (p) and LG number (1–3). Chromosome 1 has incomplete F. moschata LG numbers. Numbers associated with branches are ML bootstrap support values from 100 replicates.
Supplementary information
Supplementary Information
Supplementary Note and Tables 1–4
Rights and permissions
About this article
Cite this article
Liston, A., Wei, N., Tennessen, J.A. et al. Revisiting the origin of octoploid strawberry. Nat Genet 52, 2–4 (2020). https://doi.org/10.1038/s41588-019-0543-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41588-019-0543-3
This article is cited by
-
Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Nature Communications (2024)
-
On the origin of strawberries
Nature Plants (2023)
-
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Nature Plants (2023)
-
Transposon signatures of allopolyploid genome evolution
Nature Communications (2023)
-
Characterization of expansin genes and their transcriptional regulation by histone modifications in strawberry
Planta (2021)