Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes

作者：Rengang Zhang, Chaoxia Lu, Guangyuan Li, Jie Lv, Longxin Wang, Zhaoxuan Wang, Zhe Chen, Dan Liu, Ye Zhao, Tian‐Le Shi, Wei Zhang, Zhao-Hui Tang, Jian‐Feng Mao, Yongpeng Ma, Kai‐Hua Jia, Wei Zhao · 发表于：Nature Communications · 年份：2023 · DOI：10.1038/s41467-023-37939-2 · 被引用次数：27 · 研究领域：Cassava research and cyanide、Chromosomal and Genetic Variations、Plant Pathogenic Bacteria Studies

Hybridization and polyploidization are important driving forces in angiosperm evolution, resulting in novel phenotypes capable of prompting ecological diversification and invasion of new niches 1 . The genus Papaver (Papaveraceae) contains many taxa used in the pharmaceutical and culinary industries and as ornamental plants 2 . Yang et al. assembled de novo two chromosome-level genomes of P. rhoeas (common poppy, 2n = 14) and P. setigerum (Troy poppy, 2n = 44), and improved the P. somniferum genome assembly (opium poppy, 2n = 22) 3 . These high-quality, chromosome-scale genome assemblies represent a valuable resource for studying the early evolutionary history of eudicots and the evolution of morphinan biosynthesis. Based on synteny and phylogenomic analyses, the authors identified two rounds of whole-genome duplication (WGD), one in the ancestor to P. setigerum and P. somniferum (WGD-1) at ~7.2 million years ago (MYA), and one lineage-specific WGD-2 in P. setigerum at ~4.0 MYA. In the absence of effective subgenome-phasing techniques, they proposed complex models to explain the extensive genome reorganization and gene family evolution built upon the duplication of the genome itself (their Figs. 2–4 and Supplementary Figs 27 – 34 ). Leveraging the recent developments in subgenome-phasing method published by Jia et al. 4 , we propose an alternative model, i.e., reticulate allopolyploidization, to account for the evolution and the genomic diversity of these three Papaver specie...