Abstract：
The 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.
摘要：
Phyllanthaceae家族包括各种各样的植物，具有药用，可食用,和观赏价值，在全世界广泛种植。多倍体物种通常发生在余香科。由于相当复杂的基因组和进化史，它们的形态形成过程一直缺乏研究。在这项研究中,我们在Phyllanthaceae家族中生成了两个八倍体物种（余甘子和sauropusspatulifolius）的染色体尺度单倍型解析基因组。结合我们先前报道的同一家族的一种四倍体（Sauropusandrogynus）和一种二倍体物种（Phyllanthuscochinensis），我们探索了它们的物种形成历史。三个多倍体物种都被鉴定为具有亚基因组A/B的异源多倍体。他们来自不同物种的两个不同的亚基因组组中的每一个都被发现独立地共享一个共同的二倍体祖先（祖先-AA和祖先-BB）。通过不同的进化路线，包括各种分叉发散的场景，异源多倍化（杂种多倍化），和自多倍化，它们最终进化成了目前的四倍体雌雄虫，和八倍体S.spatulifolius和P.emblica，分别。我们进一步讨论了等位基因拷贝数的变化以及两个八倍体中的潜在影响。此外,我们还研究了具有医学价值的代谢物的波动，并确定了其在八倍体物种中生物合成过程中的关键因素。我们的研究重建了这些毛竹科物种的进化史，强调多倍体化和杂交在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的进化和功能基因组学研究提供了宝贵的基因组资源。
