Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Abstract

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbonconcentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W

“…Phylogenetic analyses of plant H2A was carried out following recommendation in. 45 Plant H2A sequences were identified through BLASTP 46 searches of published genomes [12][13][14][15][46][47][48][49][50][51] as indicated in Data S1 using Arabidopsis thaliana H2A sequences. Full-length sequences were aligned with MAFFT v7.427 52 using the default settings.…”

“…We used recently published genomes to generate a new phylogenetic tree of H2A variants in streptophytes, which comprise land plants and algal representatives of their ancestors. [12][13][14][15] H2A.Z, replicative H2A, and H2A.X variants are the only representatives of the histone H2A family present in the aquatic ancestors of land plants ( Figures 1A and 1B). A distinct fifth type of H2A variant characterized by a longer tail enriched in lysine (K) residues was previously identified as H2A.M in early diverging land plant lineages.…”

“…A distinct fifth type of H2A variant characterized by a longer tail enriched in lysine (K) residues was previously identified as H2A.M in early diverging land plant lineages. 7 In light of recent land plant phylogenies that demonstrate the monophyly of bryophytes, 12,[16][17][18] we refined H2A.M and H2A.W as being restricted to bryophytes and vascular plants, respectively (Figures 1A-1C; Data S1). H2A.W is further distinguished from H2A.M by the presence of a KSPK motif in its C-terminal tail (Figures 1A-1C; Data S1).…”

Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts

“…Most unicellular eukaryotic photosynthetic organisms and some non-vascular land plants have evolved highly efficient CO 2 -concentrating mechanisms (CCMs) that condense Rubisco into a micro compartment within the chloroplast called the pyrenoid 4,15 . The CCM functions to enrich the pyrenoid with high concentrations of CO 2 to enhance the performance of Rubisco carboxylation and suppress oxygenation 16 .…”

Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)

“…Reconstructions of the relationships of extant land plant lineages are converging on a scenario wherein bryophytes compose a sister lineage to living vascular plants, with mosses and liverworts sharing a unique common ancestor that arose from a split from the ancestor giving rise to hornworts [31]. Following the recent release of the hornwort genomes [29,32], gene and gene family evolution among bryophytes can be assessed within a robust phylogenetic framework.…”