Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes

Background The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome level assembled lycophyte genomes, has hindered our understanding of evolution and environmental adaption of lycophytes. Findings We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis, a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and the I. taiwanensis revealed conserved and different genomic features between diploid and polyploid lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provides insights into environmental adaption of lycophytes. Conclusions The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic research and the environmental studies of not only I. sinensis but also other lycophytes. Refer to individual Series

**背景** 石松类植物（Lycophyta）是现存与曾在地球广泛分布的早期维管植物最为相似的类群，但其分布范围已大幅缩减。截至目前，尚无染色体级别组装（chromosome-level assembled）的石松类植物基因组，这阻碍了学界对石松类植物演化与环境适应性的研究。

**研究结果** 本研究报道了四倍体（tetraploid）水生水韭——中华水韭（Isoetes sinensis）的参考基因组，该基因组是首个完成染色体级别组装的四倍体无种子植物基因组。通过比较中华水韭与台湾水韭的基因组，揭示了二倍体（diploid）与多倍体（polyploid）石松类植物间保守及差异的基因组特征。将中华水韭基因组与代表绿色植物不同进化谱系的其他物种基因组进行比对，发现中华水韭拥有源自祖先的转录调控（transcriptional regulation）遗传工具以及绝大多数植物激素（phytohormones）相关基因。与发育及胁迫响应（stress responses）相关的关键基因的存在与缺失情况，为阐明石松类植物的环境适应性提供了新的认知。

**结论** 本研究报道的高质量参考基因组及基因组分析，不仅对中华水韭的后续遗传研究与环境研究至关重要，也为其他石松类植物的相关研究提供了重要支撑。请参阅各系列数据集。