Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de

Summary Dispersal is a key step in land plant life cycles, usually via formation of spores or seeds. Regulation of spore‐ or seed‐germination allows control over the timing of transition from one generation to the next, enabling plant dispersal. A combination of environmental and genetic factors determines when seed germination occurs. Endogenous hormones mediate this decision in response to the environment. Less is known about how spore germination is controlled in earlier‐evolving nonseed plants.Here, we present an in‐depth analysis of the environmental and hormonal regulation of spore germination in the model bryophyte Physcomitrella patens (Aphanoregma patens).Our data suggest that the environmental signals regulating germination are conserved, but also that downstream hormone integration pathways mediating these responses in seeds were acquired after the evolution of the bryophyte lineage. Moreover, the role of abscisic acid and diterpenes (gibberellins) in germination assumed much greater importance as land plant evolution progressed.We conclude that the endogenous hormone signalling networks mediating germination in response to the environment may have evolved independently in spores and seeds. This paves the way for future research about how the mechanisms of plant dispersal on land evolved.

Green Ulvophyte macroalgae represent attractive model systems for understanding growth, development, and evolution. They are untapped resources for food, fuel, and high-value compounds, but can also form nuisance blooms. To fully analyze green seaweed morphogenesis, controlled laboratory-based culture of these organisms is required. To date, only a single Ulvophyte species, Ulva mutabilis Føyn, has been manipulated to complete its whole life cycle in laboratory culture and to grow continuously under axenic conditions. Such cultures are essential to address multiple key questions in Ulva development and in algal–bacterial interactions. Here we show that another Ulva species, U. linza, with a broad geographical distribution, has the potential to be grown in axenic culture similarly to U. mutabilis. U. linza can be reliably induced to sporulate (form gametes and zoospores) in the laboratory, by cutting the relevant thallus tissue into small pieces and removing extracellular inhibitors (sporulation and swarming inhibitors). The germ cells work as an ideal feed stock for standardized algae cultures. The requirement of U. linza for bacterial signals to induce its normal morphology (particularly of the rhizoids) appears to have a species-specific component. The axenic cultures of these two species pave the way for future comparative studies of algal–microbial interactions.

Summary Armadillo‐related proteins regulate development throughout eukaryotic kingdoms. In the flowering plant Arabidopsis thaliana, Armadillo‐related ARABIDILLO proteins promote multicellular root branching. ARABIDILLO homologues exist throughout land plants, including early‐diverging species lacking true roots, suggesting that early‐evolving ARABIDILLOs had additional biological roles.Here we investigated, using molecular genetics, the conservation and diversification of ARABIDILLO protein function in plants separated by c. 450 million years of evolution.We demonstrate that ARABIDILLO homologues in the moss Physcomitrella patens regulate a previously undiscovered inhibitory effect of abscisic acid (ABA) on spore germination. Furthermore, we show that A. thaliana ARABIDILLOs function similarly during seed germination. Early‐diverging ARABIDILLO homologues from both P. patens and the lycophyte Selaginella moellendorffii can substitute for ARABIDILLO function during A. thaliana root development and seed germination.We conclude that (1) ABA was co‐opted early in plant evolution to regulate functionally analogous processes in spore‐ and seed‐producing plants and (2) plant ARABIDILLO germination functions were co‐opted early into both gametophyte and sporophyte, with a specific rooting function evolving later in the land plant lineage.

Summary Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non‐degradable DELLA proteins underpinned the development of high‐yielding ‘Green Revolution’ dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss‐specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as ‘hubs’ for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.

Plants live in close association with microorganisms that can have beneficial or detrimental effects. The activity of bacteria in association with flowering plants has been extensively analysed. Bacteria use quorum-sensing as a way of monitoring their population density and interacting with their environment. A key group of quorum sensing molecules in Gram-negative bacteria are the Nacylhomoserine lactones (AHLs), which are known to affect the growth and development of both flowering plants, including crops, and marine algae. Thus, AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated bacterial-plant/algal interactions is unknown. In this paper, we show that AHLs can affect spore germination in a representative of the earliest plants on land, the Bryophyte moss Physcomitrella patens. Furthermore, we demonstrate that sporophytes of some wild isolates of Physcomitrella patens are associated with AHL-producing bacteria. Plants do not exist in isolation in the environment, but interact with a wide array of organisms from all kingdoms including bacteria, fungi, animals and other plants. These interactions can have profound effects on plant fitness, growth and development. In addition to pathogenicity or parasitism, interactions between plants and other organisms can be beneficial. Examples include interactions between fungi and plants in the form of mycorrhizae and interactions between plants and bacteria 1-3. Interactions between plants and microorganisms have become more elaborate during plant evolution. Mycorrhizal interactions are beneficial in liverworts, one of the earliest diverging groups of land plants, where the association between liverworts and fungi boosts plant photosynthesis, growth, fitness and nitrogen/phosphorus uptake 4,5. In later-diverging plants including flowering plants, interactions with microorganisms have increased in complexity. For example, in legumes (Fabaceae, including beans and pulses) plant root cells are surrounded by a group of proteobacteria (Rhizobia) and form a symbiotic root nodule 6 while actinobacteria from the Frankia genus can form nodules with a wide range of plant families 7,8. The bacteria gain carbon from the plant, while the plant gains nitrogen from the bacteria. Not all plant-bacterial interactions are so highly specialised: many bacteria in the rhizosphere contribute to plant productivity and gain from plants in return 9. It has become clear that flowering plants can respond to bacterial signalling molecules that alter plant growth and development, representing inter-kingdom interaction 10,11. The perception of bacteria by plants is of significant importance in terms of monitoring their surroundings and thus being able to respond accordingly to enhance their chances of survival 12. A key way in which bacteria communicate with one another is via diffusible quorum sensing (QS) molecules that are used to monitor and respond to population d...

23Plants live in close association with microorganisms that can have beneficial or detrimental 24 effects. The activity of bacteria in association with flowering plants has been extensively 25analysed. Bacteria use quorum-sensing as a way of monitoring their population density and 26interacting with their environment. A key group of quorum sensing molecules in Gram-27 negative bacteria are the N-acylhomoserine lactones (AHLs), which are known to affect the 28 growth and development of both flowering plants, including crops, and marine algae. Thus, 29AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about 30 the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated 31 bacterial-plant-and algal interactions is unknown. In this paper, we show that AHLs can affect 32 spore germination in a representative of the earliest plants on land, the Bryophyte moss 33Physcomitrella patens. Furthermore, we demonstrate that sporophytes of wild isolates of 34Physcomitrella patens are associated with AHL-producing bacteria. 35 36

Proteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding Green Revolution dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood. We have examined the function and interactions of DELLA proteins in the moss Physcomitrium (Physcomitrella) patens, in the sister group of vascular plants (Bryophytes). PpDELLAs do not undergo the same regulation as flowering plant DELLAs. PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress. PpDELLAs do share a function with vascular plant DELLAs during reproductive development. PpDELLAs also regulate spore germination. PpDELLAs interact with moss-specific photoreceptors although a function for PpDELLAs in light responses was not detected. PpDELLAs likely act as hubs for transcriptional regulation similarly to their homologues across the plant kingdom. Taken together, these data demonstrate that PpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.