The genome assembly of the duckweed fern, Azolla caroliniana.

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only 2 species are currently recognized but the actual diversity may include up to 6 species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly and annotation of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies.

Genome sequences of two cyanobacteria strains isolated from hornworts.

We report two complete genome assemblies of symbiotic cyanobacteria isolated from the hornwort species and . These new datasets will facilitate future comparative genomic studies across symbiotic cyanobacteria.

The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.

Premise: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

Methods: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.

Background And Aims: Resolving the phylogeny of hornworts is critical in understanding the evolution of key morphological characters that are unique to the group, including the pyrenoid. Extensive phylogenomic analyses have revealed unexpected complexities in the placement of Leiosporoceros, the previously identified sister taxon to other hornworts. We explore the role of incomplete lineage sorting (ILS) and ancient reticulation in resolving interrelationships and understanding the diversification and evolutionary processes within hornworts.

Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes.

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.

Hornworts reveal a spatial model for pyrenoid-based CO-concentrating mechanisms in land plants.

Pyrenoid-based CO-concentrating mechanisms (pCCMs) turbocharge photosynthesis by saturating CO around Rubisco. Hornworts are the only land plants with a pCCM. Owing to their closer relationship to crops, hornworts could offer greater translational potential than the green alga Chlamydomonas, the traditional model for studying pCCMs.

Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems.

Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco's CO fixation, yet hornwort Rubisco remains poorly characterized. Here we assembled the hornwort Anthoceros agrestis Rubisco (AaRubisco) using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates, prompting us to develop a new SynBio system with A. agrestis cognate chaperones.

 var. (Notothyladaceae, Anthocerotophyta), a new taxon from northern Thailand.

A new variety of hornwort from northern Thailand, Phaeocerosperpusillusvar.scabrellus is described based on morphological characters and molecular phylogenetic analyses. In this study, phylogenetic analyses supported that the new variety is closely related to P.

Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants.

Plant-herbivore interactions reciprocally influence species' evolutionary trajectories. These interactions have led to many physical and chemical defenses across the plant kingdom. Some plants have even evolved indirect defense strategies to outsource their protection to ant bodyguards by bribing them with a sugary reward (nectar).

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes.

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes ( and ) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid and the diploid .

Twelve new metagenome-assembled genomes from non-axenic culture of (Rhodophyta).

We report 12 metagenome-assembled genomes from a non-axenic culture of the red alga Harvey, some of which are distantly related to publicly available genomes.

Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.

Background And Aims: Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast majority may constitute evolutionary 'dead ends'. This has important implications for conservation efforts where polyploids and diploid progenitors often compete for wildlife management resources.

Genome sequence of a symbiotic cyanobacterium from the flowering plant .

Metagenomic analysis of the symbiotic cyanobacteria colonies within stems revealed a new strain of . Here, we report its genome sequence.

The ancestral chromatin landscape of land plants.

Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss Physcomitrium patens and the liverwort Marchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants.

An ancient route towards salicylic acid and its implications for the perpetual Trichormus-Azolla symbiosis.

Despite its small size, the water fern Azolla is a giant among plant symbioses. Within each of its leaflets, a specialized leaf cavity is home to a population of nitrogen-fixing cyanobacteria (cyanobionts). Although a number of plant-cyanobiont symbioses exist, Azolla is unique in that its symbiosis is perpetual: the cyanobionts are inherited during sexual and vegetative propagation.

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution.

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of and one strain of ) and generated chromosome-scale assemblies for all strains of the emerging model system .

PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem.

Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatics problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs).