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.
