Periodic Reporting for period 4 - TerreStriAL (Terrestrialization: Stress Signalling Dynamics in the Algal Progenitors of Land Plants)
Reporting period: 2024-05-01 to 2025-04-30
Land plants are what constitutes our macroscopic flora—from bogs of mosses to fields of cereal crops to forests of towering trees. Plant terrestrialization marks the birth of land plants. It describes the evolutionary process in which streptophyte algae established a thriving population in the terrestrial habitat, thus creating the foundation for macroscopic life on land and forever changing the face of our planet. Our rationale is that a cornerstone in the success of plant terrestrialization was an adequate response to environmental challenges. Terrestrial stressors. In project TerresStriAL, we investigated genes and genomes to learn about shared molecular mechanisms of extant plants and algae related to responding environmental cues that are characteristic of the terrestrial environment. We used these data to infer what molecular toolkit was present in the last common ancestor of land plants and algae to successfully overcome terrestrial stressors. To trace their occurrences, we established functional genomic resources that we first used to build a robust phylogenomic backbone on which to map the distribution of traits and genes. Our co-expression analyses revealed that environmental inputs appear to converge at conserved hubs composed of transcriptional regulators and phosphorelay switches. We scrutinized several of these switches using molecular biological approaches, uncovering both divergent and conserved activities. Overall, we identified major homologous denominators in the stress-response networks shared by algae and land plants that diverged approximately 600 million years ago. These features were likely present in the earliest land plants and thus formed part of the terrestrialization toolkit.
Work on the project fell into three major categories that concertedly shed light on the evolution of plant stress physiology: (i) stress experiments on streptophyte algae—which include the closest algal relatives of land plants, (ii) scrutinization of key molecular switches, including specific compounds and proteins, and (iii) large-scale analyses of new and publicly available sequencing data to illuminate the evolution of stress response networks and pathways. We integrated all results in an evolutionary framework, mainly by means of computational biological tools and theoretical work. We have used a diverse set of innovative experimental work to elucidate how the closest algal relatives of land plants respond to environmental challenges. A major line of work was building on gradients–across different environmental conditions and time-course stress dynamics. Integrating stress physiological data on the algae with comparative computational approaches, we have pinpointed a range of denominators in molecular stress responses conserved across about 600 million years of evolution. This resulted in several publications (e.g. Dadras et al., 2023, Nature Plants; Feng et al., 2024, Nature Genetics; Rieseberg et al., 2025, Nature Communications; Zegers et al., in press at Nature Communications), interactive web tools for the community, and being featured in press. We have en route with this work—but also additionally—generated a series of new genomic data, filling important gaps in the streptophyte tree of life. We have learned about the deep evolutionary origins of a key phytohormone signaling cascade (the stress hormone abscisic acid); this cascade likely first emerged as a phytohormone-independent signaling cascade that was brought under hormonal control during plant terrestrialization. Further, we have explored this using proteomic work, pulling down key concertedly acting components in the algae that are homologous to the land plant chassis. Finally, we have conducted several phylogenomic studies to be able to aptly place our findings on a phylogenetic backbone. This established novel phylogenomic backbones for all major streptophyte algal classes (except Charophyceae) and, building on ancestral character state reconstruction, shed light on the origin as well as versatility in the evolutionary emergence of multicellularity.
Owing to seminal work that was carried out prior to project TerreStriAL by the international community of plant evolutionary biology, we have a good understanding of the relationships between land plants and algae. This knowledge allowed us to take a deep dive into the molecular physiology of the most informative species in order to understand the deep evolutionary roots of decisive features of plant molecular biology. Several steps have been taken towards understanding how plants acquired the cellular and physiological innovations required for life on land. We aimed to establish a phylogenetically informed evolutionary systems biology framework for investigating deep plant evolution, fundamentally advancing the field beyond these limitations. We demonstrated that core stress-response and signaling systems predate terrestrialization. By integrating fine-scale physiological measurements with transcriptomics, proteomics, and network analyses across environmental gradients, we showed that algal relatives of land plants already deploy stress-signaling hubs previously considered embryophyte-specific. We moved beyond static evolutionary comparisons by introducing time-resolved, cross-lineage systems analyses. By combining time-course RNA sequencing with machine learning and statistical modeling, we inferred gene regulatory networks shared across approximately 600 million years of streptophyte evolution. This revealed deep conservation of dynamic oxidative stress signaling logic across the algae–embryophyte divide, demonstrating that not only genes but regulatory behaviors are evolutionarily conserved. We delivered foundational genomic resources that did not previously exist, including the first chromosome-scale genomes of any streptophyte alga and the first genomes of filamentous algal sisters to land plants. These datasets, integrated with co-expression and comparative analyses, transformed streptophyte algae into tractable reference systems for functional and evolutionary biology and enabled community-wide hypothesis testing at the systems level. Simultaneously, we advanced the phylogenomic backbones for all major streptophyte algal lineages closest to land plants, including Zygnematophyceae, Klebsormidiophyceae, and Coleochaetophyceae. These frameworks enabled causal evolutionary inference, revealing that multicellularity arose multiple times independently and that iconic complex morphologies are often recent, derived traits. Molecular clock analyses further pushed the origin of multicellular streptophytes back to approximately one billion years, reshaping timelines of plant body plan evolution. Through several measures of theoretical work, we synthesized into a unifying conceptual framework. Collectively, this work shifts the field from a focus on isolated traits and genes to an understanding of how ancient, stress-responsive cellular systems were repurposed during the evolution of plants on land.