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Revisiting the origin of octoploid strawberry

Matters Arising to this article was published on 16 December 2019

The Original Article was published on 25 February 2019

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Fig. 1: Phylogenomics of octoploid subgenomes.
Fig. 2: Phylogenetic positions of the four octoploid subgenomes in maximum-likelihood estimates of phylogeny in 2,191 windows of 100 kb across the seven base chromosomes.

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.

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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.).

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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

Correspondence to Aaron Liston.

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The authors declare no competing interests.

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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.

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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

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