Algal origins of core land plant stress response subnetworks.

We computed co-expression networks from more than 2200 samples of nine species across 600 million years of divergent streptophyte evolution and infer that the streptophyte algal ancestors of land plants already had a remarkable fraction of the embryophytic stress response system. Despite its phytohormone-independent origin, homologs of all core components of the drought hormone abscisic acid (ABA) subnetwork are present, and we find that most are co-expressed in streptophyte algae and land plants; this subnetwork was thus co-opted in embryophytes by bringing it under the regime of ABA. The last common ancestor of embryophytes and Zygnematophyceae algae had ancient stress-responsive pathways, enabling it to face the stresses typical of the land environment - even before the origin of land plants - while evolution on land led to the adaptive refinement of these responses.

Protist genomics: key to understanding eukaryotic evolution.

All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution.

Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.

Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species.

Reply to Žárský and Eliáš.

The more we learn about the algal relatives of embryophytes (land plants), the more complex and fascinating the evolution of key streptophyte traits becomes. With the sequencing of the Klebsormidium nitens genome, a range of molecular traits shared with land plants were found - despite ca. 800 million years of divergence.

Accessible versatility underpins the deep evolution of plant specialized metabolism.

The evolution of several hallmark traits of land plants is underpinned by phytochemical innovations. The specialized metabolism of plants can appear like a teeming chaos that has yielded an ungraspable array of chemodiversity. Yet, this diversity is the result of evolutionary processes including neutral evolution, drift, and selection that have shaped the metabolomic networks.

Time-resolved oxidative signal convergence across the algae-embryophyte divide.

The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood.

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.

Evolving circuitries in plant signaling cascades.

Land plants are astounding processors of information; due to their sessile nature, they adjust the molecular programs that define their development and physiology in accordance with the environment in which they dwell. Transduction of the external input to the respective internal programs hinges to a large degree on molecular signaling cascades, many of which have deep evolutionary origins in the ancestors of land plants and its closest relatives, streptophyte algae. In this Review, we discuss the evolutionary history of the defining factors of streptophyte signaling cascades, circuitries that not only operate in extant land plants and streptophyte algae, but that also likely operated in their extinct algal ancestors hundreds of millions of years ago.

Evolutionary assembly of the plant terrestrialization toolkit from protein domains.

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty.

Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes.

Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure.

Species delimitation 4.0: integrative taxonomy meets artificial intelligence.

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.

Phylogeny and evolution of streptophyte algae.

The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants.

Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway.

Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo.

Sequence similarity networks bear out hierarchical relationships of green cytochrome P450.

Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes.

Phylogenomic insights into the first multicellular streptophyte.

Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants). Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out.

Divergent responses in desiccation experiments in two ecophysiologically different Zygnematophyceae.

Water scarcity can be considered a major stressor on land, with desiccation being its most extreme form. Land plants have found two different solutions to this challenge: avoidance and tolerance. The closest algal relatives to land plants, the Zygnematophyceae, use the latter, and how this is realized is of great interest for our understanding of the conquest of land.

Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia.

The phylum Rozellomycota has been proposed for a group of early-branching holomycotan lineages representing obligate parasites and hyperparasites of zoosporic fungi, oomycotes or phytoplankton. Given their predominantly intracellular lifestyle, rozellids are typically known from environmental ribosomal DNA data, except for the well-studied species. To date, the phylogenetic relationship between rozellids and microsporidians (Microsporidia) is not fully understood and most reliable hypotheses are based on phylogenomic analyses that incorporate the only publicly available rozellid genome of .

GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution.

IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria.

Environmental gradients reveal stress hubs pre-dating plant terrestrialization.

Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravelled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum.

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 .