During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered - in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, likely signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.

Vascular plants provide most of the biomass, food, and feed on earth, yet the molecular innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is rate-limiting for vascular cell proliferation inArabidopsis thaliana. Both regulators have origins predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 evolved its modern function, including dimerization with LHW, at the origin of land plants. A second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate heterodimerization and generated the critical function in vascular development inArabidopsis. In summary, our results suggest that the division potential of vascular cells may have been an important factor contributing to the evolution of vascular plants.

Chapter 1 as the closest living relatives to Embryophytes (Figure 2A). Charophytic algae can be divided in six main lineages: Mesostigmatophyceae, Chlorokybophyceae, Klebsormidiophyceae, Charophyceae, Zygnematophyceae and Coleochaetophyceae (Figure 2A) (Mattox and Stewart, 1984; McCourt et al., 2004). Phylogenetic studies have indicated that Mesostigmatophyceae and Chlorokybophyceae are the earliest diverging lineages within the Charophytes (Figure 2A) (Bhattacharya and Medlin, 1998; Lemieux et al., 2007; Simon et al., 2006). Indeed, morphologically, these are the simplest two Streptophyte algae: Mesostigma (the only genus in the Mesostigmatophyceae) is unicellular containing two flagella and Chlorokybus (the only member of the Chlorokybophyceae) forms packets of a few cells. Filamentous algae are found in the Klebsormidiophyceae lineage (Figure 2C), which diverged after Mesostigmatophyceae and Chlorokybophyceae (Figure 2A). These filamentous algae generally do not contain specialized or differentiated cells and branching is very rare (Mikhailyuk et al., 2014). Instead, branching as well as increased morphological complexity in general, is mostly observed in the three later diverging Charophytes. Charales (the only order in the Charophyceae) for example, are large morphologically complex macroscopic algae with differentiated cells and an apical meristem (Figure 2D). They generally contain a central stalk with many branches (Figure 2D). Furthermore, other innovations are present in the later diverging Charophytes, contributing to complexity. For example, Charales and Coleochaetophyceae develop plasmodesmata, allowing cell-cell communication. While the three early diverging lineages use furrowing during the cytokinesis step of cell division, Zygnematophyceae, Charophyceae and Coleochaetophyceae, produce a phragmoplast, similar to Embryophytes. Zygnematophyceae and Coleochaete are thought to be the closest related to Embryophytes (Figure 2A). However, the Zygnematophyceae lineage appears to have lost many traits such as plasmodesmata, flagella and extensive branching. Lycophytes Pterophytes Pteridophytes (Seedless) Gymnosperms Angiosperms Charophytes Chlorophytes Streptophytes Viridiplantae (The green lineage) Embryophytes (Land plants) Tracheophytes (Vascular) Spermatophytes (Seeds) Bryophytes (Non-vascular) Eudicots Monocots Ferns Horstails Liverworts Hornworts Mosses Figure 1. Overview of the plant taxonomy within the plant kingdom. 12 Chapter 1 The colonization of land by an ancestor related to Charophyte algae, was followed by the emergence of the first land plants, approximately 460 million years ago (Lemieux et al., 2007; Lewis and McCourt, 2004; Wellman et al., 2003). The earliest diverging Embryophytes are mosses, liverworts and hornworts, collectively known as Bryophytes (Figure 1). This lineage holds a key position in evolution, as they diverged after the transition from water to land, but prior to the emergence of vascular tissues. Indeed, Bryophytes are plants without lignified vascular systems or true ...

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16Vascular plants provide most of the biomass, food and feed on earth; yet the molecular 17 innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the 18 evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is 19 rate-limiting for vascular cell proliferation in Arabidopsis thaliana. Both regulators have origins 20 predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 21 evolved its modern function, including dimerization with LHW, at the origin of land plants. A 22 second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate 23 heterodimerization and generated the critical function in vascular development. In summary, our 24 results suggest that division potential of vascular cells may have been a major driver in the 25 evolution of vascular plants. 26 27 28 485 486 Evolution of vascular plants through redeployment of ancient developmental 487 regulators 488