Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land.

Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.

Green land: Multiple perspectives on green algal evolution and the earliest land plants.

Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.

Unexpected cryptic species among streptophyte algae most distant to land plants.

Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.

Draparnaldia: a chlorophyte model for comparative analyses of plant terrestrialization.

It is generally accepted that land plants evolved from streptophyte algae. However, there are also many chlorophytes (a sister group of streptophyte algae and land plants) that moved to terrestrial habitats and even resemble mosses. This raises the question of why no land plants evolved from chlorophytes. In order to better understand what enabled streptophyte algae to conquer the land, it is necessary to study the chlorophytes as well. This review will introduce the freshwater filamentous chlorophyte alga Draparnaldia sp. (Chaetophorales, Chlorophyceae) as a model for comparative analyses between these two lineages. It will also focus on current knowledge about the evolution of morphological complexity in chlorophytes versus streptophytes and their respective morphological/behavioural adaptations to semi-terrestrial habitats, and will show why Draparnaldia is needed as a new model system.

Immunofluorescence localization of the tubulin cytoskeleton during cell division and cell growth in members of the Coleochaetales (Streptophyta).

Study of charophycean green algae, including the Coleochaetales, may shed light on the evolutionary history of characters they share with their land plant relatives. We examined the tubulin cytoskeleton during mitosis, cytokinesis, and growth in members of the Coleochaetales with diverse morphologies to determine if phragmoplasts occurred throughout this order and to identify microtubular patterns associated with cell growth. Species representing three subgroups of Coleochaete and its sister genus Chaetosphaeridium were studied. Cytokinesis involving a phragmoplast was found in the four taxa examined. Differential interference contrast microscopy of living cells confirmed that polar cytokinesis like that described in the model flowering plant Arabidopsis occurred in all species when the forming cell plate traversed a vacuole. Calcofluor labeling of cell walls demonstrated directed growth from particular cell regions of all taxa. Electron microscopy confirmed directed growth in the unusual growth pattern of Chaetosphaeridium. All four species exhibited unordered microtubule patterns associated with diffuse growth in early cell expansion. In subsequent elongating cells, Coleochaete irregularis Pringsheim and Chaetosphaeridium globosum (Nordstedt) Klebahn exhibited tubulin cytoskeleton arrays corresponding to growth patterns associated with tip growth in plants, fungi, and other charophycean algae. Hoop-shaped microtubules frequently associated with diffuse growth of elongating cells in plants were not observed in any of these species. Presence of phragmoplasts in the diverse species studied supports the hypothesis that cytokinesis involving a phragmoplast originated in a common ancestor of the Coleochaetales, and possibly in a common ancestor of Charales, Coleochaetales, Zygnematales, and plants.

A DUF3494 ice-binding protein with a root cap domain in a streptophyte glacier ice alga.

Ice-binding proteins (IBPs) of the DUF3494 type have been found in many ice-associated unicellular photoautotrophs, including chlorophytes, haptophytes, diatoms and a cyanobacterium. Unrelated IBPs have been found in many land plants (streptophytes). Here we looked for IBPs in two streptophyte algae that grow only on glaciers, a group in which IBPs have not previously been examined. The two species, Ancylonema nordenskioeldii and Ancylonema. alaskanum, belong to the class Zygnematophyceae, whose members are the closest relatives to all land plants. We found that one of them, A. nordenskioeldii, expresses a DUF3494-type IBP that is similar to those of their chlorophyte ancestors and that has not previously been found in any streptophytes. The protein is unusual in having what appears to be a perfect array of TXT motifs that have been implicated in water or ice binding. The IBP strongly binds to ice and almost certainly has a role in mitigating the daily freeze-thaw cycles that the alga is exposed to during late summer. No IBP was found in the second species, A. alaskanum, which may rely more on glycerol production for its freeze-thaw tolerance. The IBP is also unusual in having a 280-residue domain with a ß sandwich structure (which we designate as the DPH domain) that is characteristic of root cap proteins of land plants, and that may have a role in forming IBP oligomers. We also examined existing transcriptome data obtained from land plants to better understand the tissue and temperature dependence of expression of this domain.

Major episodes of horizontal gene transfer drove the evolution of land plants.

How horizontal gene transfer (HGT) has contributed to the evolution of animals and plants remains a major puzzle. Despite recent progress, defining the overall scale and pattern of HGT events in land plants has been largely elusive. In this study, we performed systematic analyses for acquired genes in different plant groups and throughout land plant evolution. We found that relatively recent HGT events occurred in charophytes and all major land plant groups, but their frequency declined rapidly in seed plants. Two major episodes of HGT events occurred in land plant evolution, corresponding to the early evolution of streptophytes and the origin of land plants, respectively. Importantly, a vast majority of the genes acquired in the two episodes have been retained in descendant groups, affecting numerous activities and processes of land plants. We analyzed some of the acquired genes involved in stress responses, ion and metabolite transport, growth and development, and specialized metabolism, and further assessed the cumulative effects of HGT in land plants.

Horizontal gene transfer and the evolution of land plants.

Horizontal gene transfer (HGT) is the transfer of genetic material between organisms. It has been known for some time that HGT in eukaryotes is not a rare phenomenon. A recent study by Ma et al. has shown that HGT has played a crucial role in shaping the evolution of land plants.

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

Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.

Glacier Algae: A Dark Past and a Darker Future.

"Glacier algae" grow on melting glacier and ice sheet surfaces across the cryosphere, causing the ice to absorb more solar energy and consequently melt faster, while also turning over carbon and nutrients. This makes glacier algal assemblages, which are typically dominated by just three main species, a potentially important yet under-researched component of the global biosphere, carbon, and water cycles. This review synthesizes current knowledge on glacier algae phylogenetics, physiology, and ecology. We discuss their significance for the evolution of early land plants and highlight their impacts on the physical and chemical supraglacial environment including their role as drivers of positive feedbacks to climate warming, thereby demonstrating their influence on Earth's past and future. Four complementary research priorities are identified, which will facilitate broad advances in glacier algae research, including establishment of reliable culture collections, sequencing of glacier algae genomes, development of diagnostic biosignatures for remote sensing, and improved predictive modeling of glacier algae biological-albedo effects.

Regeneration and transient gene expression in protoplasts of Draparnaldia (chlorophytes), an emerging model for comparative analyses with basal streptophytes.

BACKGROUND: Green plants comprise two lineages: (1) the streptophytes that colonised land and (2) the chlorophytes that have adaptations to land but remained mostly aquatic. To better understand what made streptophytes so successful, we are currently establishing the chlorophyte alga Draparnaldia sp. (Chaetophorales, Chlorophyceae) as a model for comparative analyses between these two lineages. However, establishing Draparnaldia as a valuable model requires that it can be transformed. Thus, our goal is to develop a transformation protocol for this alga. RESULTS: We have established the first transformation protocol for Draparnaldia. This protocol is based on protoplast transformation by electroporation. It includes instructions on protoplast isolation, regeneration and transient transfection. It also provides a list of the effective selective agents for future Draparnaldia transformations. CONCLUSIONS: Our protocol opens a way for Draparnaldia functional genomics analyses. Moreover, it also provides an important base for establishment of stable transformation.

Streptophyte Terrestrialization in Light of Plastid Evolution.

Key steps in evolution are often singularities. The emergence of land plants is one such case and it is not immediately apparent why. A recent analysis found that the zygnematophycean algae represent the closest relative to embryophytes. Intriguingly, many exaptations thought essential to conquer land are common among various streptophytes, but zygnematophycean algae share with land plants the transfer of a few plastid genes to the nucleus. Considering the contribution of the chloroplast to terrestrialization highlights potentially novel exaptations that currently remain unexplored. We discuss how the streptophyte chloroplast evolved into what we refer to as the embryoplast, and argue this was as important for terrestrialization by freshwater algae as the host cell-associated exaptations that are usually focused upon.

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.

As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant-fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.