Schafran Peter, Hauser Duncan A, Nelson Jessica M, Xu Xia, Mueller Lukas A, Kulshrestha Samarth, Smalley Isabel, de Vries Sophie, Irisarri Iker, de Vries Jan, Davies Kevin, Villarreal Juan Carlos A, Li Fay-Wei
Boyce Thompson Institute, Ithaca, NY, USA.
Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Nat Plants. 2025 Jan;11(1):49-62. doi: 10.1038/s41477-024-01883-w. Epub 2025 Jan 3.
Hornworts, one of the three bryophyte phyla, show some of the deepest divergences in extant land plants, with some families separated by more than 300 million years. Previous hornwort genomes represented only one genus, limiting the ability to infer evolution within hornworts and their early land plant ancestors. Here we report ten new chromosome-scale genomes representing all hornwort families and most of the genera. We found that, despite the deep divergence, synteny was surprisingly conserved across all hornwort genomes, a pattern that might be related to the absence of whole-genome duplication. We further uncovered multiple accessory and putative sex chromosomes that are highly repetitive and CpG methylated. In contrast to autosomes, these chromosomes mostly lack syntenic relationships with one another and are evolutionarily labile. Notable gene retention and losses were identified, including those responsible for flavonoid biosynthesis, stomata patterning and phytohormone reception, which have implications in reconstructing the evolution of early land plants. Together, our pan-phylum genomes revealed an array of conserved and divergent genomic features in hornworts, highlighting the uniqueness of this deeply diverged lineage.
角苔纲是苔藓植物三个门之一，在现存陆地植物中展现出一些最古老的分化，有些科之间的分化时间超过3亿年。先前的角苔基因组仅代表一个属，限制了推断角苔纲及其早期陆地植物祖先内部进化的能力。在此，我们报告了代表所有角苔科和大多数属的十个新的染色体级基因组。我们发现，尽管分化时间久远，但所有角苔基因组的共线性却惊人地保守，这种模式可能与没有全基因组复制有关。我们进一步发现了多个高度重复且CpG甲基化的辅助染色体和假定的性染色体。与常染色体不同，这些染色体彼此之间大多缺乏共线性关系，并且在进化上不稳定。我们识别出了显著的基因保留和丢失情况，包括那些与类黄酮生物合成、气孔模式形成和植物激素受体相关的基因，这对重建早期陆地植物的进化具有重要意义。总之，我们的全纲基因组揭示了角苔纲中一系列保守和分化的基因组特征，凸显了这个深度分化谱系的独特性。
