College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206,China.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad079. Epub 2023 Sep 30.
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.
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 Isoetestaiwanensis 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 provide insights into environmental adaption of lycophytes.
The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic and environmental studies of not only I. sinensis but also other lycophytes.
石松类植物是现存与早期维管植物最相似的类群，而早期维管植物曾在地球上大量存在。然而，它们的分布范围大大缩小了。到目前为止，缺乏染色体水平组装的石松类基因组阻碍了我们对石松类进化和环境适应的理解。
我们呈现了四倍体水生卷柏（Isoetes sinensis）的参考基因组，这是一种石松类植物。这个基因组代表了第一个染色体水平组装的四倍体无种子植物基因组。对 I. sinensis 和 Isoetestaiwanensis 基因组的比较揭示了二倍体和多倍体石松类植物之间保守和不同的基因组特征。将 I. sinensis 基因组与代表绿色植物进化谱系的其他物种的基因组进行比较，揭示了 I. sinensis 中转录调控和大多数植物激素的遗传工具。与发育和应激反应相关的关键基因的存在和缺失为石松类植物的环境适应提供了深入的了解。
本研究中提供的高质量参考基因组和基因组分析不仅对 I. sinensis ，而且对其他石松类植物的未来遗传和环境研究都至关重要。
