replying to R.-G. Zhang et al. Nature Communications https://doi.org/10.1038/s41467-023-37939-2 (2023)
We assembled genomes of three Papaver species, P. somniferum, P. rhoeas and P. setigerum, and revealed two-round whole genome duplication (WGD) events and the punctuated patchwork evolution of morphinan and noscapine biosynthesis pathway based on comparative genomic analyses of collinearity, phylogenetic tree, and synonymous substitution rate (Ks) at species level1. Recently, Zhang et al. reanalyzed our three Papaver genomes based on the subgenome-phasing analysis by their newly published tool SubPhaser2. They confirmed the two WGDs we previously detected, but provide strong evidence that the WGDs were likely allopolyploidy events. We consider the subgenome-phasing analysis from Zhang et al. to be an important research development building on our original study1, promoting the illuminating the evolutionary history of Papaver species.
Although alternative model proposed by Zhang et al. based on subgenome-phasing analysis further the complicated evolutionary history of Papaver species, the actual types of WGDs and the true evolution history of Papaver species are still open questions for further investigation. Both novel computational methods and high-quality genomes of more species, especially those closely related species for the subgenomes A, B, C, and D, are required and welcome to further advance our interpretation of the evolutionary model of Papaver species, key gene clusters and key genes, like STORR.
Reporting Summary
Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.
Data availability
Data sharing not applicable to this article as no new datasets were generated during the current study.
References
Yang, X. et al. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nat. Commun 12, 6030 (2021).
Jia, K. H. et al. SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers. New Phytol 235, 801–809 (2022).
Acknowledgements
We thank Yuannian Jiao for helpful discussions. K. Y. and X.Y. are supported by the National Science Foundation of China (32125009, 62172325, 32070663), the Key Construction Program of the National ‘985’ Project, and the Fundamental Research Funds for the Central Universities.
Author information
Authors and Affiliations
Contributions
K. Y. conceived the study; X. Y., S. G., T. X., B. W., and J. Y. analyzed data; K. Y., X. Y., S. G., and T. X. wrote the paper.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Yang, X., Gao, S., Xu, T. et al. Reply to “Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes”. Nat Commun 14, 2203 (2023). https://doi.org/10.1038/s41467-023-37940-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41467-023-37940-9
Comments
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.
