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.
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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.
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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.
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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
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DOI: https://doi.org/10.1038/s41467-023-37940-9
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