The Roles of the Sole Activator-Type Auxin Response Factor in Pattern Formation of Marchantia polymorpha

MpANT regulates meristem development in Marchantia polymorpha

Meristems are crucial for organ formation, but our knowledge of their molecular evolution is limited. Here, we show that AINTEGUMENTA (MpANT) in the euANT branch of the APETALA2-like transcription factor family is essential for meristem development in the nonvascular plant Marchantia polymorpha. MpANT is expressed in the thallus meristem. Mpant mutants show defects to maintain meristem identity and undergo meristem duplication, while MpANT overexpressers show ectopic thallus growth. MpANT directly upregulates MpGRAS9 in the SHORT-ROOT (SHR) branch of the GRAS family. In the vascular plant Arabidopsis thaliana, the euANT-branch genes PLETHORAs (AtPLTs) and AtANT are involved in the formation and maintenance of root/shoot apical meristems and lateral organ primordia, and AtPLTs directly target SHR-branch genes. In addition, euANTs bind through a similar DNA-binding motif to many conserved homologous genes in M. polymorpha and A. thaliana. Overall, the euANT pathway has an evolutionarily conserved role in meristem development.

Comparative transcriptome and functional analyses provide insights into the key factors regulating shoot regeneration in highbush blueberry

Establishing an efficient plant regeneration system is a crucial prerequisite for genetic engineering technology in plants. However, the regeneration rate exhibits considerable variability among genotypes, and the key factors underlying shoot regeneration capacity remain largely elusive. Blueberry leaf explants cultured on a medium rich in cytokinins exhibit direct shoot organogenesis without prominent callus formation, which holds promise for expediting genetic transformation while minimizing somatic mutations during culture. The objective of this study is to unravel the molecular and genetic determinants that govern cultivar-specific shoot regeneration potential in highbush blueberry (Vaccinium corymbosum L.). We conducted comparative transcriptome analysis using two highbush blueberry genotypes: 'Blue Muffin' ('BM') displaying a high regeneration rate (>80%) and 'O'Neal' ('ON') exhibiting a low regeneration rate (<10%). The findings revealed differential expression of numerous auxin-related genes; notably, 'BM' exhibited higher expression of auxin signaling genes compared to 'ON'. Among blueberry orthologs of transcription factors involved in meristem formation in Arabidopsis, expression of VcENHANCER OF SHOOT REGENERATION (VcESR), VcWUSCHEL (VcWUS), and VcCUP-SHAPED COTYLEDON 2.1 were significantly higher in 'BM' relative to 'ON'. Exogenous application of auxin promoted regeneration, as well as VcESR and VcWUS expression, whereas inhibition of auxin biosynthesis yielded the opposite effects. Overexpression of VcESR in 'BM' promoted shoot regeneration under phytohormone-free conditions by activating the expression of cytokinin- and auxin-related genes. These findings provide new insights into the molecular mechanisms underlying blueberry regeneration and have practical implications for enhancing plant regeneration and transformation techniques.

MdARF3 switches the lateral root elongation to regulate dwarfing in apple plants

Apple rootstock dwarfing and dense planting are common practices in apple farming. However, the dwarfing mechanisms are not understood. In our study, the expression of MdARF3 in the root system of dwarfing rootstock 'M9' was lower than in the vigorous rootstock from Malus micromalus due to the deletion of the WUSATAg element in the promoter of the 'M9' genotype. Notably, this deletion variation was significantly associated with dwarfing rootstocks. Subsequently, transgenic tobacco (Nicotiana tabacum) cv. Xanthi was generated with the ARF3 promoter from 'M9' and M. micromalus genotypes. The transgenic apple with 35S::MdARF3 was also obtained. The transgenic tobacco and apple with the highly expressed ARF3 had a longer root system and a higher plant height phenotype. Furthermore, the yeast one-hybrid, luciferase, electrophoretic mobility shift assays, and Chip-qPCR identified MdWOX4-1 in apples that interacted with the pMm-ARF3 promoter but not the pM9-ARF3 promoter. Notably, MdWOX4-1 significantly increased the transcriptional activity of MdARF3 and MdLBD16-2. However, MdARF3 significantly decreased the transcriptional activity of MdLBD16-2. Further analysis revealed that MdARF3 and MdLBD16-2 were temporally expressed during different stages of lateral root development. pMdLBD16-2 was mainly expressed during the early stage of lateral root development, which promoted lateral root production. On the contrary, pMmARF3 was expressed during the late stage of lateral root development to promote elongation. The findings in our study will shed light on the genetic causes of apple plant dwarfism and provide strategies for molecular breeding of dwarfing apple rootstocks.

Genomic survey and expression analysis of LcARFs reveal multiple functions to somatic embryogenesis in Liriodendron

BACKGROUND

Auxin response factors (ARFs) are critical transcription factors that mediate the auxin signaling pathway and are essential for regulating plant growth. However, there is a lack of understanding regarding the ARF gene family in Liriodendron chinense, a vital species in landscaping and economics. Thus, further research is needed to explore the roles of ARFs in L. chinense and their potential applications in plant development.

RESULT

In this study, we have identified 20 LcARF genes that belong to three subfamilies in the genome of L. chinense. The analysis of their conserved domains, gene structure, and phylogeny suggests that LcARFs may be evolutionarily conserved and functionally similar to other plant ARFs. The expression of LcARFs varies in different tissues. Additionally, they are also involved in different developmental stages of somatic embryogenesis. Overexpression of LcARF1, LcARF2a, and LcARF5 led to increased activity within callus. Additionally, our promoter-GFP fusion study indicated that LcARF1 may play a role in embryogenesis. Overall, this study provides insights into the functions of LcARFs in plant development and embryogenesis, which could facilitate the improvement of somatic embryogenesis in L. chinense.

CONCLUSION

The research findings presented in this study shed light on the regulatory roles of LcARFs in somatic embryogenesis in L. chinense and may aid in accelerating the breeding process of this tree species. By identifying the specific LcARFs involved in different stages of somatic embryogenesis, this study provides a basis for developing targeted breeding strategies aimed at optimizing somatic embryogenesis in L. chinense, which holds great potential for improving the growth and productivity of this economically important species.

Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution

The phytohormone auxin, and its directional transport through tissues, plays a fundamental role in the development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using a radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In the Arabidopsis root epidermis, bryophytic PINs have no defined polarity. Pharmacological interference revealed a strong cytoskeletal dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal the divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and the co-evolution of PIN sequence-based and cell-based polarity mechanisms.

Game of thrones among AUXIN RESPONSE FACTORs-over 30 years of MONOPTEROS research

For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.

To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes

Most plant growth and development processes are regulated in one way or another by auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through the nuclear auxin pathway (NAP). In this pathway, Auxin Response Factors (ARFs) are the transcription factors that ultimately determine which genes become auxin regulated by binding to specific DNA sequences. ARFs have primarily been studied in Arabidopsis thaliana, but recent studies in other species have revealed family-wide DNA binding specificities for different ARFs and the minimal functional system of the NAP system, consisting of a duo of competing ARFs of the A and B classes. In this review, we provide an overview of key aspects of ARF DNA binding such as auxin response elements (TGTCNN) and tandem repeat motifs, and consider how structural biology and in vitro studies help us understand ARF DNA preferences. We also highlight some recent aspects related to the regulation of ARF levels inside a cell, which may alter the DNA binding profile of ARFs in different tissues. We finally emphasize the need to study minimal NAP systems to understand fundamental aspects of ARF function, the need to characterize algal ARFs to understand how ARFs evolved, how cutting-edge techniques can increase our understanding of ARFs, and which remaining questions can only be answered by structural biology.

An enhancer trap system to track developmental dynamics in Marchantia polymorpha

A combination of streamlined genetics, experimental tractability and relative morphological simplicity compared to vascular plants makes the liverwort Marchantia polymorpha an ideal model system for studying many aspects of plant biology. Here we describe a transformation vector combining a constitutive fluorescent membrane marker with a nuclear marker that is regulated by nearby enhancer elements and use this to produce a library of enhancer trap lines for Marchantia. Screening gemmae from these lines allowed the identification and characterization of novel marker lines, including markers for rhizoids and oil cells. The library allowed the identification of a margin tissue running around the thallus edge, highlighted during thallus development. The expression of this marker is correlated with auxin levels. We generated multiple markers for the meristematic apical notch region, which have different spatial expression patterns, reappear at different times during meristem regeneration following apical notch excision and have varying responses to auxin supplementation or inhibition. This reveals that there are proximodistal substructures within the apical notch that could not be observed otherwise. We employed our markers to study Marchantia sporeling development, observing meristem emergence as defining the protonema-to-prothallus stage transition, and subsequent production of margin tissue during the prothallus stage. Exogenous auxin treatment stalls meristem emergence at the protonema stage but does not inhibit cell division, resulting in callus-like sporelings with many rhizoids, whereas pharmacologically inhibiting auxin synthesis and transport does not prevent meristem emergence. This enhancer trap system presents a useful resource for the community and will contribute to future Marchantia research.

Modulating auxin response stabilizes tomato fruit set

Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here, we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.

Insights into cryptochrome modulation of ABA signaling to mediate dormancy regulation in Marchantia polymorpha

The acquisition of dormancy capabilities has enabled plants to survive in adverse terrestrial environmental conditions. Dormancy accumulation and release is coupled with light signaling, which is well studied in Arabidopsis, but it is unclear in the distant nonvascular relative. We study the characteristics and function on dormancy regulation of a blue light receptor cryptochrome in Marchantia polymorpha (MpCRY). Here, we identified MpCRY via bioinformatics and mutant complement analysis. The biochemical characteristics were assessed by multiple protein-binding assays. The function of MpCRY in gemma dormancy was clarified by overexpression and mutation of MpCRY, and its mechanism was analyzed via RNA sequencing and quantitative PCR analyses associated with hormone treatment. We found that the unique MpCRY protein in M. polymorpha undergoes both blue light-promoted interaction with itself (self-interaction) and blue light-dependent phosphorylation. MpCRY has the specific characteristics of blue light-induced nuclear localization and degradation. We further demonstrated that MpCRY transcriptionally represses abscisic acid (ABA) signaling-related gene expression to suppress gemma dormancy, which is dependent on blue light signaling. Our findings indicate that MpCRY possesses specific biochemical and molecular characteristics, and modulates ABA signaling under blue light conditions to regulate gemma dormancy in M. polymorpha.

Auxin signaling is essential for organogenesis but not for cell survival in the liverwort Marchantia polymorpha

Auxin plays pleiotropic roles in plant development via gene regulation upon its perception by the receptors TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFBs). This auxin-regulated transcriptional control mechanism originated in the common ancestor of land plants. Although the complete loss of TIR1/AFBs causes embryonic lethality in Arabidopsis thaliana, it is unclear whether the requirement for TIR1-mediated auxin perception in cell viability can be generalized. The model liverwort Marchantia polymorpha has a minimal auxin signaling system with only a single TIR1/AFB, MpTIR1. Here we show by genetic, biochemical, and transcriptomic analyses that MpTIR1 functions as an evolutionarily conserved auxin receptor. Null mutants and conditionally knocked-out mutants of MpTIR1 were viable but incapable of forming any organs and grew as cell masses. Principal component analysis performed using transcriptomes at various developmental stages indicated that MpTIR1 is involved in the developmental transition from spores to organized thalli, during which apical notches containing stem cells are established. In Mptir1 cells, stem cell- and differentiation-related genes were up- and downregulated, respectively. Our findings suggest that, in M. polymorpha, auxin signaling is dispensable for cell division but is essential for three-dimensional patterning of the plant body by establishing pluripotent stem cells for organogenesis, a derived trait of land plants.

Evolution of wound-activated regeneration pathways in the plant kingdom

Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.

Comprehensive analysis of peptide-coding genes and initial characterization of an LRR-only microprotein in Marchantia polymorpha

In the past two decades, many plant peptides have been found to play crucial roles in various biological events by mediating cell-to-cell communications. However, a large number of small open reading frames (sORFs) or short genes capable of encoding peptides remain uncharacterized. In this study, we examined several candidate genes for peptides conserved between two model plants: Arabidopsis thaliana and Marchantia polymorpha. We examined their expression pattern in M. polymorpha and subcellular localization using a transient assay with Nicotiana benthamiana. We found that one candidate, MpSGF10B, was expressed in meristems, gemma cups, and male reproductive organs called antheridiophores. MpSGF10B has an N-terminal signal peptide followed by two leucine-rich repeat (LRR) domains and was secreted to the extracellular region in N. benthamiana and M. polymorpha. Compared with the wild type, two independent Mpsgf10b mutants had a slightly increased number of antheridiophores. It was revealed in gene ontology enrichment analysis that MpSGF10B was significantly co-expressed with genes related to cell cycle and development. These results suggest that MpSGF10B may be involved in the reproductive development of M. polymorpha. Our research should shed light on the unknown role of LRR-only proteins in land plants.

The origin of a land flora

The origin of a land flora fundamentally shifted the course of evolution of life on earth, facilitating terrestrialization of other eukaryotic lineages and altering the planet's geology, from changing atmospheric and hydrological cycles to transforming continental erosion processes. Despite algal lineages inhabiting the terrestrial environment for a considerable preceding period, they failed to evolve complex multicellularity necessary to conquer the land. About 470 million years ago, one lineage of charophycean alga evolved complex multicellularity via developmental innovations in both haploid and diploid generations and became land plants (embryophytes), which rapidly diversified to dominate most terrestrial habitats. Genome sequences have provided unprecedented insights into the genetic and genomic bases for embryophyte origins, with some embryophyte-specific genes being associated with the evolution of key developmental or physiological attributes, such as meristems, rhizoids and the ability to form mycorrhizal associations. However, based on the fossil record, the evolution of the defining feature of embryophytes, the embryo, and consequently the sporangium that provided a reproductive advantage, may have been most critical in their rise to dominance. The long timeframe and singularity of a land flora were perhaps due to the stepwise assembly of a large constellation of genetic innovations required to conquer the terrestrial environment.

The renaissance and enlightenment of Marchantia as a model system

The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.

Protein Kinase MpYAK1 Is Involved in Meristematic Cell Proliferation, Reproductive Phase Change and Nutrient Signaling in the Liverwort Marchantia polymorpha

Plant growth and development are regulated by environmental factors, including nutrient availability and light conditions, via endogenous genetic signaling pathways. Phosphorylation-dependent protein modification plays a major role in the regulation of cell proliferation in stress conditions, and several protein kinases have been shown to function in response to nutritional status, including dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). Although DYRKs are widely conserved in eukaryotes, the physiological functions of DYRKs in land plants are still to be elucidated. In the liverwort Marchantia polymorpha, a model bryophyte, four putative genes encoding DYRK homologous proteins, each of which belongs to the subfamily yet another kinase 1 (Yak1), plant-specific DYRK, DYRK2, or pre-mRNA processing protein 4 kinase, were identified. MpYAK1-defective male and female mutant lines generated by the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system showed smaller sizes of thalli than did the wild-type plants and repressed cell divisions in the apical notch regions. The Mpyak1 mutants developed rhizoids from gemmae in the gemma cup before release. The Mpyak1 lines developed sexual organs even in non-inductive short-day photoperiod conditions supplemented with far-red light. In nitrogen (N)-deficient conditions, rhizoid elongation was inhibited in the Mpyak1 mutants. In conditions of aeration with 0.08% CO2 (v/v) and N depletion, Mpyak1 mutants accumulated higher levels of sucrose and lower levels of starch compared to the wild type. Transcriptomic analyses revealed that the expression of peroxidase genes was differentially affected by MpYAK1. These results suggest that MpYAK1 is involved in the maintenance of plant growth and developmental responses to light conditions and nutrient signaling.

The wound-activated ERF15 transcription factor drives Marchantia polymorpha regeneration by activating an oxylipin biosynthesis feedback loop

The regenerative potential in response to wounding varies widely among species. Within the plant lineage, the liverwort Marchantia polymorpha displays an extraordinary regeneration capacity. However, its molecular pathways controlling the initial regeneration response are unknown. Here, we demonstrate that the MpERF15 transcription factor gene is instantly activated after wounding and is essential for gemmaling regeneration following tissue incision. MpERF15 operates both upstream and downstream of the MpCOI1 oxylipin receptor by controlling the expression of oxylipin biosynthesis genes. The resulting rise in the oxylipin dinor-12-oxo-phytodienoic acid (dn-OPDA) levels results in an increase in gemma cell number and apical notch organogenesis, generating highly disorganized and compact thalli. Our data pinpoint MpERF15 as a key factor activating an oxylipin biosynthesis amplification loop after wounding, which eventually results in reactivation of cell division and regeneration. We suggest that the genetic networks controlling oxylipin biosynthesis in response to wounding might have been reshuffled over evolution.

The liverwort Marchantia polymorpha, a model for all ages

The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.

Diminished Auxin Signaling Triggers Cellular Reprogramming by Inducing a Regeneration Factor in the Liverwort Marchantia polymorpha

Regeneration in land plants is accompanied by the establishment of new stem cells, which often involves reactivation of the cell division potential in differentiated cells. The phytohormone auxin plays pivotal roles in this process. In bryophytes, regeneration is enhanced by the removal of the apex and repressed by exogenously applied auxin, which has long been proposed as a form of apical dominance. However, the molecular basis behind these observations remains unexplored. Here, we demonstrate that in the liverwort Marchantia polymorpha, the level of endogenous auxin is transiently decreased in the cut surface of decapitated explants, and identify by transcriptome analysis a key transcription factor gene, LOW-AUXIN RESPONSIVE (MpLAXR), which is induced upon auxin reduction. Loss of MpLAXR function resulted in delayed cell cycle reactivation, and transient expression of MpLAXR was sufficient to overcome the inhibition of regeneration by exogenously applied auxin. Furthermore, ectopic expression of MpLAXR caused cell proliferation in normally quiescent tissues. Together, these data indicate that decapitation causes a reduction of auxin level at the cut surface, where, in response, MpLAXR is up-regulated to trigger cellular reprogramming. MpLAXR is an ortholog of Arabidopsis ENHANCER OF SHOOT REGENERATION 1/DORNRÖSCHEN, which has dual functions as a shoot regeneration factor and a regulator of axillary meristem initiation, the latter of which requires a low auxin level. Thus, our findings provide insights into stem cell regulation as well as apical dominance establishment in land plants.

The bryophytes Physcomitrium patens and Marchantia polymorpha as model systems for studying evolutionary cell and developmental biology in plants

Bryophytes are nonvascular spore-forming plants. Unlike in flowering plants, the gametophyte (haploid) generation of bryophytes dominates the sporophyte (diploid) generation. A comparison of bryophytes with flowering plants allows us to answer some fundamental questions raised in evolutionary cell and developmental biology. The moss Physcomitrium patens was the first bryophyte with a sequenced genome. Many cell and developmental studies have been conducted in this species using gene targeting by homologous recombination. The liverwort Marchantia polymorpha has recently emerged as an excellent model system with low genomic redundancy in most of its regulatory pathways. With the development of molecular genetic tools such as efficient genome editing, both P. patens and M. polymorpha have provided many valuable insights. Here, we review these advances with a special focus on polarity formation at the cell and tissue levels. We examine current knowledge regarding the cellular mechanisms of polarized cell elongation and cell division, including symmetric and asymmetric cell division. We also examine the role of polar auxin transport in mosses and liverworts. Finally, we discuss the future of evolutionary cell and developmental biological studies in plants.

The Systems and Synthetic Biology of Auxin

Auxin biology as a field has been at the forefront of advances in delineating the structures, dynamics, and control of plant growth networks. Advances have been enabled by combining the complementary fields of top-down, holistic systems biology and bottom-up, build-to-understand synthetic biology. Continued collaboration between these approaches will facilitate our understanding of and ability to engineer auxin's control of plant growth, development, and physiology. There is a need for the application of similar complementary approaches to improving equity and justice through analysis and redesign of the human systems in which this research is undertaken.

Development and Molecular Genetics of Marchantia polymorpha

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.

On the Evolutionary Origins of Land Plant Auxin Biology

Indole-3-acetic acid, that is, auxin, is a molecule found in a broad phylogenetic distribution of organisms, from bacteria to eukaryotes. In the ancestral land plant auxin was co-opted to be the paramount phytohormone mediating tropic responses and acting as a facilitator of developmental decisions throughout the life cycle. The evolutionary origins of land plant auxin biology genes can now be traced with reasonable clarity. Genes encoding the two enzymes of the land plant auxin biosynthetic pathway arose in the ancestral land plant by a combination of horizontal gene transfer from bacteria and possible neofunctionalization following gene duplication. Components of the auxin transcriptional signaling network have their origins in ancestral alga genes, with gene duplication and neofunctionalization of key domains allowing integration of a portion of the preexisting transcriptional network with auxin. Knowledge of the roles of orthologous genes in extant charophycean algae is lacking, but could illuminate the ancestral functions of both auxin and the co-opted transcriptional network.

Expansion and innovation in auxin signaling: where do we grow from here?

The phytohormone auxin plays a role in almost all growth and developmental responses. The primary mechanism of auxin action involves the regulation of transcription via a core signaling pathway comprising proteins belonging to three classes: receptors, co-receptor/co-repressors and transcription factors. Recent studies have revealed that auxin signaling can be traced back at least as far as the transition to land. Moreover, studies in flowering plants have highlighted how expansion of the gene families encoding auxin components is tied to functional diversification. As we review here, these studies paint a picture of auxin signaling evolution as a driver of innovation.

Physcomitrium patens: A Single Model to Study Oriented Cell Divisions in 1D to 3D Patterning

Development in multicellular organisms relies on cell proliferation and specialization. In plants, both these processes critically depend on the spatial organization of cells within a tissue. Owing to an absence of significant cellular migration, the relative position of plant cells is virtually made permanent at the moment of division. Therefore, in numerous plant developmental contexts, the (divergent) developmental trajectories of daughter cells are dependent on division plane positioning in the parental cell. Prior to and throughout division, specific cellular processes inform, establish and execute division plane control. For studying these facets of division plane control, the moss Physcomitrium (Physcomitrella) patens has emerged as a suitable model system. Developmental progression in this organism starts out simple and transitions towards a body plan with a three-dimensional structure. The transition is accompanied by a series of divisions where cell fate transitions and division plane positioning go hand in hand. These divisions are experimentally highly tractable and accessible. In this review, we will highlight recently uncovered mechanisms, including polarity protein complexes and cytoskeletal structures, and transcriptional regulators, that are required for 1D to 3D body plan formation.

Auxin Biology in Bryophyta: A Simple Platform with Versatile Functions

Bryophytes, including liverworts, mosses, and hornworts, are gametophyte-dominant land plants that are derived from a common ancestor and underwent independent evolution from the sporophyte-dominant vascular plants since their divergence. The plant hormone auxin has been shown to play pleiotropic roles in the haploid bodies of bryophytes. Pharmacological and chemical studies identified conserved auxin molecules, their inactivated forms, and auxin transport in bryophyte tissues. Recent genomic and molecular biological studies show deep conservation of components and their functions in auxin biosynthesis, inactivation, transport, and signaling in land plants. Low genetic redundancy in model bryophytes enable unique assays, which are elucidating the design principles of the auxin signaling pathway. In this article, the physiological roles of auxin and regulatory mechanisms of gene expression and development by auxin in Bryophyta are reviewed.

Studies of moss reproductive development indicate that auxin biosynthesis in apical stem cells may constitute an ancestral function for focal growth control

The plant hormone auxin is a key factor for regulation of plant development, and this function was probably reinforced during the evolution of early land plants. We have extended the available toolbox to allow detailed studies of how auxin biosynthesis and responses are regulated in moss reproductive organs, their stem cells and gametes to better elucidate the function of auxin in the morphogenesis of early land plants. We measured auxin metabolites and identified IPyA (indole-3-pyruvic acid) as the main biosynthesis pathway in Physcomitrium (Physcomitrella) patens and established knock-out, overexpressor and reporter lines for biosynthesis genes which were analyzed alongside previously reported auxin-sensing and transport reporters. Vegetative and reproductive apical stem cells synthesize auxin. Sustained stem cell activity depends on an inability to sense the auxin produced while progeny of the stem cells respond to the auxin, aiding in the control of cell division, expansion and differentiation. Gamete precursors are dependent on a certain degree of auxin sensing, while the final differentiation is a low auxin-sensing process. Tha data presented indicate that low auxin activity may represent a conserved hallmark of land plant gametes, and that local auxin biosynthesis in apical stem cells may be part of an ancestral mechanism to control focal growth.

Ethylene-independent functions of the ethylene precursor ACC in Marchantia polymorpha

The plant hormone ethylene has many roles in growth and development¹. In seed plants, the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is converted into ethylene by ACC oxidase (ACO), and treatment with ACC induces ethylene responses². However, non-seed plants lack ACO homologues^3-8, which led us to examine the relationship between ACC and ethylene in the liverwort Marchantia polymorpha. Here, we demonstrate that ACC and ethylene can induce divergent growth responses in Marchantia. Ethylene increases plant and gemma size, induces more gemma cups and promotes gemmae dormancy. As predicted, Mpctr1-knockout mutants display constitutive ethylene responses, whereas Mpein3-knockout mutants exhibit ethylene insensitivity. Compared with the wild type, Mpctr1 gemmae have more and larger epidermal cells, whereas Mpein3 gemmae have fewer and smaller epidermal cells, suggesting that ethylene promotes cell division and growth in developing gemmae. By contrast, ACC treatment inhibits gemma growth and development by suppressing cell division, even in the Mpein3-knockout alleles. Knockout mutants of one or both ACC SYNTHASE (ACS) gene homologues produce negligible levels of ACC, have more and larger gemma cups, and have more-expanded thallus branches. Mpacs2 and Mpacs1 Mpacs2 gemmae also display a high frequency of abnormal apical notches (meristems) that are not observed in ethylene mutants. These findings reveal that ethylene and ACC have distinct functions, and suggest that ACC is a signalling molecule in Marchantia. ACC may be an evolutionarily conserved signal that predates its efficient conversion to ethylene in higher plants.

A Comprehensive Toolkit for Quick and Easy Visualization of Marker Proteins, Protein-Protein Interactions and Cell Morphology in Marchantia polymorpha

Even though stable genomic transformation of sporelings and thalli of Marchantia polymorpha is straightforward and efficient, numerous problems can arise during critical phases of the process such as efficient spore production, poor selection capacity of antibiotics or low transformation efficiency. It is therefore also desirable to establish quick methods not relying on stable transgenics to analyze the localization, interactions and functions of proteins of interest. The introduction of foreign DNA into living cells via biolistic mechanisms has been first reported roughly 30 years ago and has been commonly exploited in established plant model species such as Arabidopsis thaliana or Nicotiana benthamiana. Here, we report the fast and reliable transient biolistic transformation of Marchantia thallus epidermal cells using fluorescent protein fusions. We present a catalog of fluorescent markers which can be readily used for tagging of a variety of subcellular compartments. Moreover, we report the functionality of the bimolecular fluorescence complementation (BiFC) in M. polymorpha with the example of the p-body markers MpDCP1/2. Finally, we provide standard staining procedures for live cell imaging in M. polymorpha, applicable to visualize cell boundaries or cellular structures, to complement or support protein localizations and to understand how results gained by transient transformations can be embedded in cell architecture and dynamics. Taken together, we offer a set of easy and quick tools for experiments that aim at understanding subcellular localization, protein-protein interactions and thus functions of proteins of interest in the emerging early diverging land plant model M. polymorpha.

Gemma cup and gemma development in Marchantia polymorpha

The basal land plant Marchantia polymorpha efficiently propagates in favourable environments through clonal progeny called gemmae. Gemmae develop in cup-shaped receptacles known as gemma cups, which are formed on the gametophyte body. Anatomical studies have described the developmental processes involved over a century ago; however, little is known about the underlying molecular mechanisms. Recent studies have started to unravel the mechanism underlying genetic and hormonal regulation of gemma cup and gemma development, showing that it shares some regulatory mechanisms with several sporophytic organs in angiosperms. Further study of these specialized organs will contribute to our understanding of the core regulatory modules underlying organ development in land plants and how these became so diversified morphologically over the course of evolution.

Genetic dissection of the auxin response network

The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.

Positional cues regulate dorsal organ formation in the liverwort Marchantia polymorpha

Bryophytes and vascular plants represent the broadest evolutionary divergence in the land plant lineage, and comparative analyses of development spanning this divergence therefore offer opportunities to identify truisms of plant development in general. In vascular plants, organs are formed repetitively around meristems at the growing tips in response to positional cues. In contrast, leaf formation in mosses and leafy liverworts occurs from clonal groups of cells derived from a daughter cell of the apical stem cell known as merophytes, and cell lineage is a crucial factor in repetitive organ formation. However, it remains unclear whether merophyte lineages are a general feature of repetitive organ formation in bryophytes as patterns of organogenesis in thalloid liverworts are unclear. To address this question, we developed a clonal analysis method for use in the thalloid liverwort Marchantia polymorpha, involving random low-frequency induction of a constitutively expressed nuclear-targeted fluorescent protein by dual heat-shock and dexamethasone treatment. M. polymorpha thalli ultimately derive from stem cells in the apical notch, and the lobes predominantly develop from merophytes cleft to the left and right of the apical cell(s). Sector induction in gemmae and subsequent culture occasionally generated fluorescent sectors that bisected thalli along the midrib and were maintained through several bifurcation events, likely reflecting the border between lateral merophytes. Such thallus-bisecting sectors traversed dorsal air chambers and gemma cups, suggesting that these organs arise independently of merophyte cell lineages in response to local positional cues.

Design principles of a minimal auxin response system

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity^1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development^1,3,4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. The expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned or prevented. This fundamental design probably represents the ancestral system and formed the basis for inflated, complex systems.

Morphological and stage-specific transcriptome analyses reveal distinct regulatory programs underlying yam (Dioscorea alata L.) bulbil growth

In yam (Dioscorea spp) species, bulbils at leaf axils are the most striking species-specific axillary structure and exhibit important ecological niches. Genetic regulation underlying bulbil growth remains largely unclear so far. Here, we characterize yam (Dioscorea alata L.) bulbil development using histological analysis, and perform full transcriptional profiling on key developmental stages together with phytohormone analyses. Using the stage-specific scoring algorithm, we have identified 3451 stage-specifically expressed genes that exhibit a tight link between major transcriptional changes and stages. Co-expressed gene clusters revealed an obvious over-representation of genes associated with cell division and expansion at the initiation stage of bulbils (T1). Transcriptional changes of hormone-related genes highly coincided with hormone levels, indicating that bulbil initiation and growth are coordinately controlled by multiple phytohormones. In particular, localized auxin is transiently required to trigger bulbil initiation, and be further depleted or exported from bulbils to promote growth by up-regulation of genes involved in auxinconjugation and efflux. The sharp increase in supply of sucrose and an enhanced trehalose-6-phophate pathway at T1 were observed, suggesting that sucrose probably functions as a key signal and promotes bulbil initiation. Analysis of the expression of transcription factors (TFs) predicated 149 TFs as stage-specifically expressed; several T1-specific TFs (from Aux/IAA, E2F, MYB, and bHLH families) have been shown to play key roles in triggering bulbil formation. Together, our work provides a crucial angle for in-depth understanding of the molecular programs underlying yam's unique bulbil development processes. Stage-specific gene sets can be queried to obtain key candidates regulating bulbil growth, serving as valuable resources for further functional research.

Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing

Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.

Minimal auxin sensing levels in vegetative moss stem cells revealed by a ratiometric reporter

Efforts to reveal ancestral functions of auxin, a key regulator of plant growth and development, and its importance for evolution have been hampered by a fragmented picture of auxin response domains in early-diverging land plants. We report the mapping of auxin sensing and responses during vegetative moss development using novel reporters. We established a moss-specific ratiometric reporter (PpR2D2) for Auxin Response Element- and AUXIN RESPONSE FACTOR-independent auxin sensing in Physcomitrella patens, and its readout during vegetative development was compared with new promoter-based GmGH3::GFPGUS and DR5revV2::GFPGUS auxin response reporters. The ratiometric reporter responds rapidly to auxin in a time-, dose- and TRANSPORT INHIBITOR RESISTANT1/AUXIN F-BOX-dependent manner and marks known, anticipated and novel auxin sensing domains. It reveals proximal auxin sensing maxima in filamentous tissues and sensing minima in all five vegetative gametophytic stem cell types as well as dividing cells. PpR2D2 readout is compliant with an ancestral function of auxin as a positive regulator of differentiation vs proliferation in stem cell regions. The PpR2D2 reporter is a sensitive tool for high-resolution mapping of auxin sensing, which can increase our knowledge of auxin function in early-diverging land plants substantially, thereby advancing our understanding of its importance for plant evolution.

Something ancient and something neofunctionalized-evolution of land plant hormone signaling pathways

The evolution of land plants from a charophycean algal ancestor was accompanied by an increased diversity of regulatory networks, including signaling pathways mediating cellular communication within plants and between plants and the environment. Canonical land plant hormone signaling pathways were originally identified in angiosperms, and comparative studies in basal taxa show that they have been assembled from both ancient and newly evolved components, both before and during land plant evolution. In this review we present our current understanding, and highlight several uncertainties, of the evolution of hormone signaling pathways, focusing on the biosynthetic pathways generating putative ligands and the downstream perception and signaling pathways often leading to transcriptional responses.

Highly efficient G-AgarTrap-mediated transformation of the Marchantia polymorpha model strains Tak-1 and Tak-2

The liverwort Marchantia polymorpha L. is an important model species for investigating land plant evolution. Effective genetic transformation techniques are crucial for plant molecular biology and simplified or improved techniques for specific cultivars or strains can accelerate research. Over the past several years, we developed a simple Agrobacterium-mediated transformation technique for M. polymorpha named AgarTrap (Agar-utilized transformation with pouring solutions). AgarTrap is an easy technique that involves pouring the appropriate solutions onto plant materials on a single solid plate of medium. We recently improved AgarTrap using gemmalings (G-AgarTrap) of the M. polymorpha female model strain BC3-38 and achieved a transformation efficiency of nearly 100%. Based on this improved technique, in the current study, we adopted two factors (sealing the Petri dish with Parafilm and dark treatment during co-cultivation) and optimized two factors (Agrobacterium strain and pre-culture period) of the improved G-AgarTrap for other model strains of M. polymorpha, the male strain Takaragaike-1 (Tak-1) and the female strain Takaragaike-2 (Tak-2). After optimization, the transformation efficiency of Tak-1 using G-AgarTrap was as high as 55% compared to approximately 30% using the previous protocol. Furthermore, using Tak-2, we achieved a transformation efficiency of nearly 100%. Our improved G-AgarTrap technique for Tak-1 and Tak-2 represents a promising tool for promoting the study of Marchantia.

An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha

Dormancy is a key process allowing land plants to adapt to changing conditions in the terrestrial habitat, allowing the cessation of growth in response to environmental or physiological cues, entrance into a temporary quiescent state, and subsequent reactivation of growth in more favorable environmental conditions [1-3]. Dormancy may be induced seasonally, sporadically (e.g., in response to drought), or developmentally (e.g., seeds and apical dominance). Asexual propagules, known as gemmae, derived via clonal reproduction in bryophytes, are often dormant until displaced from the parent plant. In the liverwort Marchantia polymorpha, gemmae are produced within specialized receptacles, gemma cups, located on the dorsal side of the vegetative thallus [4]. Mature gemmae are detached from the parent plant but may remain in the cup, with gemma growth suppressed as long as the gemmae remain in the gemma cup and the parental plant is alive [5]. Following dispersal of gemmae from gemma cups by rain, the gemmae germinate in the presence of light and moisture, producing clonal offspring [6]. In land plants, the plant hormone abscisic acid (ABA) regulates many aspects of dormancy and water balance [7]. Here, we demonstrate that ABA plays a central role in the control of gemma dormancy as transgenic M. polymorpha gemmae with reduced sensitivity to ABA fail to establish and/or maintain dormancy. Thus, the common ancestor of land plants used the ABA signaling module to regulate germination of progeny in response to environmental cues, with both gemmae and seeds being derived structures co-opting an ancestral response system.

Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha

Marchantia polymorpha is one of the model species of basal land plants. Although CRISPR/Cas9-based genome editing has already been demonstrated for this plant, the efficiency was too low to apply to functional analysis. In this study, we show the establishment of CRISPR/Cas9 genome editing vectors with high efficiency for both construction and genome editing. Codon optimization of Cas9 to Arabidopsis achieved over 70% genome editing efficiency at two loci tested. Systematic assessment revealed that guide sequences of 17 nt or shorter dramatically decreased this efficiency. We also demonstrated that a combinatorial use of this system and a floxed complementation construct enabled conditional analysis of a nearly essential gene. This study reports that simple, rapid, and efficient genome editing is feasible with the series of developed vectors.

Class C ARFs evolved before the origin of land plants and antagonize differentiation and developmental transitions in Marchantia polymorpha

A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss- and gain-of-function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss-of-function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR-resistant MpARF3 alleles are auxin-insensitive, suggesting that class C ARFs act in a context-dependent fashion. We conclude that two modules independently evolved to regulate a pre-existing ARF transcriptional network. Whereas the auxin-TIR1-AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.

Origin and evolution of the nuclear auxin response system

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

Across all kingdoms of life, signaling molecules like hormones, for example, control many aspects of the lives of organisms, including how they grow and develop. Cells have dedicated proteins that can recognize the signaling molecules, relay the information, and respond to the signal, for example by switching genes on or off. Such response systems usually consist of multiple components, and, throughout evolution, these response components have regularly been copied such that many species have multiple different versions of each one.

Auxin is a plant hormone that controls virtually all growth and developmental processes in plants, including many yield traits in crops. However, no one knows why it is involved in so many processes. This is partly because it is not clear how the response system for this central signaling molecule was first born, or how it has increased in its complexity.

To address this, Mutte, Kato et al. explored the genetic information of more than a thousand plant species, including algae, which span more than 700 million years of evolution. Their analysis showed that all auxin response components were assembled from pieces of much older genes, but that they first came together when plants conquered land. Indeed, the auxin response appears to have developed on top of a pre-existing genetic regulator that is still present in modern-day algae. Mutte, Kato et al. then used experiments to show how stepwise increases in the number and types of auxin response components have shaped sophisticated, complex responses in land plants, and to demonstrate how ancient components control auxin response.

Together these findings provide a framework for understanding the many functions of auxin in plants, and how this came to be. They also show how complexity can be accomplished in a signal response pathway, and how diversity evolves in gene families. Similar studies on other response systems in plants and beyond are likely to help reveal common principles of hormone response evolution and diversification of gene regulation systems.

Origin and evolution of the nuclear auxin response system

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module

We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.