Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.

BackgroundHydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters.ResultsPhylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite) and divergence time estimates (BEAST) resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma). Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges) probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states.ConclusionsOur study has shed light on the previously controversial generic phylogeny of Hydrocharitaceae. The study has resolved the historical biogeography of this family and supported dispersal as the most likely explanation for the intercontinental distribution. We have also provided valuable information for understanding the evolution of breeding system and leaf phenotype in aquatic monocots.

Lobelioideae comprise about 1200 species in 30 genera worldwide and include famous cases of parallel evolution in the “giant rosette” lobelias occurring in East Africa, Hawaii, and Bhutan. To date, no phylogeny has included the Himalayan giant lobelia, and its age and phylogenetic distance from the Hawaiian and African giant species (the latter in the same section as the Bhutan species) are therefore unknown. Asian Lobelioideae in general have received little attention, partly because of the difficult access to material. Here we use nuclear and plastid markers of Lobelioideae (with worldwide sampling) to test the monophyly of the section that includes most Asian lobelias, and we then use a reduced concatenated matrix to resolve the position of Lobelia nubigena from Bhutan and of the likewise cold‐adapted lowland species L. sessilifolia. Most sequences come from herbarium material. Lobelia nubigena diverged from its Asian lowland relatives 13.8 (12.6–15) million years ago (about the time of the Bhutan Himalaya orogeny), and in an unexpected twist, L. sessilifolia is the sister species to a huge clade (ca. 265 species) that comprises African, South American, Asian, and the entire Hawaiian Lobelioideae radiation. The African and Hawaiian high‐elevation lobelias in our sample are younger than L. nubigena, although the time when gigantism evolved in this species cannot be precisely inferred. Our results support the previously hypothesized Asian origin of (1) the Hawaiian Lobelioideae, (2) Southeast Asian islands lobelias, and (3) the African Lobelia‐Rynchopetalum group, which also reached South America.