What can hornworts teach us?

Abstract

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

“…Several reference genome of ferns have been assembled in recent years, including Azolla filiculoides (0.75 Gb, n = 22), Salvinia cucullata (0.26 Gb, n = 9) (Li et al, 2018), Alsophila spinulosa (6.27 Gb, n = 69) (Huang et al, 2022), Adiantum capillus-veneris (4.83 Gb, n = 30) (Fang et al, 2022), Ceratopteris richardii (7.46 Gb, n = 39) (Marchant et al, 2022), and Marsilea vestita (1.0 Gb, n = 20) (Rahmatpour et al, 2023) (Table 1). These high-quality genome sequences enable future research into the functional genomics and applications of ferns (Chen, 2022; Kinosian and Wolf, 2022; Frangedakis et al, 2023). In the available transformation methods, particle bombardment and Agrobacterium -mediated stable transformation have been successfully applied to C. richardii (Plackett et al, 2014; Bui et al, 2015) and Pteris vittata (Muthukumar et al, 2013).…”

“…While the genetic transformation of fern gametophytes as the explant usually has a low success rate, it should be noted that the majority of these methods were developed and optimized according to the well-established protocols targeting to angiosperm flowers, immature embryos, and calli (Bui et al, 2015; Bui et al, 2017). Efficient gene editing protocol for fern species has not been developed, but an efficient and fast verification system in C. richardii will facilitate the analysis of gene function in ferns (Frangedakis et al, 2023).…”

Performance of localization prediction algorithms decreases rapidly with the evolutionary distance to the training set increasing

“…1b), as well as indirectly, as integral component of widely used software packages and databases. These databases contain genomes from hundreds of diverse species, including taxa with ecological and academic relevance [80][81][82][83][84][85][86] such as on streptophyte algae and bryophytes. Proteins from these newly accumulating genomes, however, continue to receive their intracellular localisation annotation from the same set of algorithms and, on an average, 70-80% of these predicted annotations might be unreliable.…”

“…1b) or indirectly through being part of software packages and databases. Databases contain genomes from hundreds of diverse species, including for instance bryophyte and algae taxa of ecological and academic relevance [80][81][82][83][84][85][86] . Their genome annotations, however, receive localisation predictions from the same set of algorithms, but on an average 70-80% of them are likely wrong (Fig.…”

The ancestral chromatin landscape of land plants

“…Hornworts form a monophyletic group that diverged before the divergence of liverworts and mosses and thus the traits common to hornworts and mosses or liverworts are hypothetically representative of the ancestral traits of bryophytes (Puttick et al, 2018;Harris et al, 2022). To reconstruct the ancestral chromatin landscape of bryophytes, we investigated DNA methylation and a set of five histone H3 PTMs in the model hornwort Anthoceros agrestis (Frangedakis et al, 2023) and compared it with P. patens and M. polymorpha. We conclude that the chromatin organization of bryophytes is distinct from that described in other groups of eukaryotes.…”