The monocot family Melanthiaceae with varying genome sizes in a range of 230-fold is an ideal model to study the genome size fluctuation in plants. Its family member Paris genus demonstrates an evolutionary trend of bearing huge genomes characterized by an average c-value of 49.22 pg. Here, we report a 70.18 Gb genome assembly out of the 82.55 Gb genome of Paris polyphylla var. yunnanensis (PPY), which represents the biggest sequenced genome to date. We annotate 69.53% repetitive sequences in this genome and 62.50% of which are long-terminal repeat (LTR) transposable elements. Further evolution analysis indicates that the giant genome likely results from the joint effect of common and species-specific expansion of different LTR superfamilies, which might contribute to the environment adaptation after speciation. Moreover, we identify the candidate pathway genes for the biogenesis of polyphyllins, the PPY-specific medicinal saponins, by complementary approaches including genome mining, comprehensive analysis of 31 next-generation RNA-seq data and 55.23 Gb single-molecule circular consensus sequencing (CCS) RNA-seq reads, and correlation of the transcriptome and phytochemical data of five different tissues at four growth stages. This study not only provides significant insights into plant genome size evolution, but also paves the way for the following polyphyllin synthetic biology.

中文翻译：

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巨大的巴黎多叶植物基因组揭示了基因组大小演变和多叶植物的生物发生

基因组大小在230倍范围内变化的单子叶植物Melanthiaceae是研究植物基因组大小波动的理想模型。它的家族成员巴黎属（Paris genus）表现出具有庞大基因组的进化趋势，其特征是平均c值为49.22 pg。在这里，我们报道了巴黎七叶树的82.55 Gb基因组中的70.18 Gb基因组组装。云南（PPY），代表迄今为止最大的测序基因组。我们在此基因组中注释了69.53％的重复序列，其中62.50％是长末端重复（LTR）可转座元件。进一步的进化分析表明，巨大的基因组可能是由于不同LTR超家族的共同扩展和物种特异性扩展的共同作用导致的，这可能有助于物种形成后的环境适应。此外，我们通过互补方法（包括基因组挖掘，对31个下一代RNA-seq数据的综合分析和55.23 Gb单分子环形共有序列（CCS）RNA），确定了多叶素生物合成的候选途径基因，即PPY特异的药用皂苷。 -seq读数，以及四个生长阶段的五个不同组织的转录组和植物化学数据的相关性。这项研究不仅提供了对植物基因组大小演变的重要见解，而且还为随后的多叶素合成生物学铺平了道路。四个生长阶段的五个不同组织的转录组和植物化学数据的相关性 这项研究不仅为植物基因组大小的演变提供了重要的见识，而且为随后的多叶素合成生物学铺平了道路。四个生长阶段的五个不同组织的转录组和植物化学数据的相关性和相关性 这项研究不仅提供了对植物基因组大小演变的重要见解，而且还为随后的多叶素合成生物学铺平了道路。