Department of Systematic and Evolutionary Botany, University of Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland.
Boyce Thompson Institute, Ithaca, NY, USA.
Nat Plants. 2021 May;7(5):554-565. doi: 10.1038/s41477-021-00888-z. Epub 2021 Apr 5.
During the past few years several high-quality genomes has been published from Charophyte algae, bryophytes, lycophytes and ferns. These genomes have not only elucidated the origin and evolution of early land plants, but have also provided important insights into the biology of the seed-free lineages. However, critical gaps across the phylogeny remain and many new questions have been raised through comparing seed-free and seed plant genomes. Here, we review the reference genomes available and identify those that are missing in the seed-free lineages. We compare patterns of various levels of genome and epigenomic organization found in seed-free plants to those of seed plants. Some genomic features appear to be fundamentally different. For instance, hornworts, Selaginella and most liverworts are devoid of whole-genome duplication, in stark contrast to other land plants. In addition, the distribution of genes and repeats appear to be less structured in seed-free genomes than in other plants, and the levels of gene body methylation appear to be much lower. Finally, we highlight the currently available (or needed) model systems, which are crucial to further our understanding about how changes in genes translate into evolutionary novelties.
在过去的几年中，已经有几个高质量的基因组从轮藻、苔藓植物、石松类植物和蕨类植物中被公布。这些基因组不仅阐明了早期陆地植物的起源和进化，还为无种子谱系的生物学提供了重要的见解。然而，系统发育中仍然存在关键的空白，通过比较无种子植物和种子植物的基因组，已经提出了许多新的问题。在这里，我们回顾了现有的参考基因组，并确定了无种子谱系中缺失的那些。我们比较了无种子植物和种子植物中发现的各种水平的基因组和表观基因组组织模式。一些基因组特征似乎存在根本差异。例如，角苔、卷柏和大多数苔类植物缺乏全基因组复制，这与其他陆地植物形成鲜明对比。此外，无种子基因组中基因和重复的分布似乎不如其他植物那样有组织，基因体甲基化的水平也低得多。最后，我们强调了目前可用（或需要）的模式系统，这对于进一步了解基因的变化如何转化为进化的新颖性至关重要。
