SUMMARYThe Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome‐scale haplotype‐resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor‐AA and Ancestor‐BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high‐quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

中文翻译：

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叶下珠科八倍体物种的单倍型解析基因组揭示了多倍体化和杂交在物种形成中的关键作用

摘要 叶下珠科包含多种具有药用、食用和观赏价值的植物，在世界各地广泛种植。多倍体物种常见于叶下珠科。由于基因组和进化历史相当复杂，它们的物种形成过程仍然缺乏研究。在这项研究中，我们生成了两个八倍体物种的染色体规模单倍型解析基因组（余甘子和匙叶蜥）属于叶下珠科。结合我们之前报道的一种四倍体（雌雄蜥蜴）和一个二倍体物种（交趾叶下珠）来自同一个家族，我们探索了它们的物种形成历史。三个多倍体物种均被鉴定为亚基因组A/B的异源多倍体。研究发现，来自不同物种的两个不同的亚基因组群各自独立地共享一个共同的二倍体祖先（祖先-AA 和祖先-BB）。经过不同的进化路线，包括分叉分歧、异源多倍化（杂种多倍化）、同源多倍化等多种情况，最终进化成现在的四倍体雌雄同体链霉菌，和八倍体匙叶海棠和余甘子， 分别。我们进一步讨论等位基因拷贝数的变化以及两个八倍体内的潜在影响。此外，我们还研究了八倍体物种中具有药用价值的代谢物的波动，并确定了其生物合成过程的关键因素。我们的研究重建了这些叶下珠科物种的进化历史，强调了多倍体化和杂交在其物种形成过程中的关键作用。这两个八倍体物种的高质量基因组为进一步研究进化和功能基因组学提供了宝贵的基因组资源。