An Evolutionarily Conserved Plant RKD Factor Controls Germ Cell Differentiation

The BNB-GLID module regulates germline fate determination in Marchantia polymorpha

Germline fate determination is a critical event in sexual reproduction. Unlike animals, plants specify the germline by reprogramming somatic cells at the late stages of their development. However, the genetic basis of germline fate determination and how it evolved during the land plant evolution are still poorly understood. Here, we report that the plant homeodomain finger protein GERMLINE IDENTITY DETERMINANT (GLID) is a key regulator of the germline specification in liverwort, Marchantia polymorpha. Loss of the MpGLID function causes failure of germline initiation, leading to the absence of sperm and egg cells. Remarkably, the overexpression of MpGLID in M. polymorpha induces the ectopic formation of cells with male germline cell features exclusively in male thalli. We further show that MpBONOBO (BNB), with an evolutionarily conserved function, can induce the formation of male germ cell-like cells through the activation of MpGLID by directly binding to its promoter. The Arabidopsis (Arabidopsis thaliana) MpGLID ortholog, MALE STERILITY1 (AtMS1), fails to replace the germline specification function of MpGLID in M. polymorpha, demonstrating that a derived function of MpGLID orthologs has been restricted to tapetum development in flowering plants. Collectively, our findings suggest the presence of the BNB-GLID module in complex ancestral land plants that has been retained in bryophytes, but rewired in flowering plants for male germline fate determination.

NIN-like proteins (NLPs) as crucial nitrate sensors: an overview of their roles in nitrogen signaling, symbiosis, abiotic stress, and beyond

Nitrogen is an essential macronutrient critical for plant growth and productivity. Plants have the capacity to uptake inorganic nitrate and ammonium, with nitrate playing a crucial role as a signaling molecule in various cellular processes. The availability of nitrate and the signaling pathways involved finely tune the processes of nitrate uptake and assimilation. NIN-like proteins (NLPs), a group of transcription factors belonging to the RWP-RK gene family, act as major nitrate sensors and are implicated in the primary nitrate response (PNR) within the nucleus of both non-leguminous and leguminous plants through their RWP-RK domains. In leguminous plants, NLPs are indispensable for the initiation and development of nitrogen-fixing nodules in symbiosis with rhizobia. Moreover, NLPs play pivotal roles in plant responses to abiotic stresses, including drought and cold. Recent studies have identified NLP homologs in oomycete pathogens, suggesting their potential involvement in pathogenesis and virulence. This review article delves into the conservation of RWP-RK genes, examining their significance and implications across different plant species. The focus lies on the role of NLPs as nitrate sensors, investigating their involvement in various processes, including rhizobial symbiosis in both leguminous and non-leguminous plants. Additionally, the multifaceted functions of NLPs in abiotic stress responses, developmental processes, and interactions with plant pathogens are explored. By comprehensively analyzing the role of NLPs in nitrate signaling and their broader implications for plant growth and development, this review sheds light on the intricate mechanisms underlying nitrogen sensing and signaling in various plant lineages.

MpMLO1 controls sperm discharge in liverwort

In bryophytes, sexual reproduction necessitates the release of motile sperm cells from a gametophyte into the environment. Since 1856, this process, particularly in liverworts, has been known to depend on water. However, the molecular mechanism underlying this phenomenon has remained elusive. Here we identify the plasma membrane protein MpMLO1 in Marchantia polymorpha, a model liverwort, as critical for sperm discharge from antheridia. The MpMLO1-expressing tip cells among the sperm-wrapping jacket cells undergo programmed cell death upon antheridium maturation to facilitate sperm discharge after the application of water and even hypertonic solutions. The absence of MpMLO1 leads to reduced cytoplasmic Ca2+ levels in tip cells, preventing cell death and consequently sperm discharge. Our findings reveal that MpMLO1-mediated programmed cell death in antheridial tip cells, regulated by cytosolic Ca2+ dynamics, is essential for sperm release, elucidating a key mechanism in bryophyte sexual reproduction and providing insights into terrestrial plant evolution.

A non-canonical BZR/BES transcription factor regulates the development of haploid reproductive organs in Marchantia polymorpha

Gametogenesis, which is essential to the sexual reproductive system, has drastically changed during plant evolution. Bryophytes, lycophytes and ferns develop reproductive organs called gametangia-antheridia and archegonia for sperm and egg production, respectively. However, the molecular mechanism of early gametangium development remains unclear. Here we identified a 'non-canonical' type of BZR/BES transcription factor, MpBZR3, as a regulator of gametangium development in a model bryophyte, Marchantia polymorpha. Interestingly, overexpression of MpBZR3 induced ectopic gametangia. Genetic analysis revealed that MpBZR3 promotes the early phase of antheridium development in male plants. By contrast, MpBZR3 is required for the late phase of archegonium development in female plants. We demonstrate that MpBZR3 is necessary for the successful development of both antheridia and archegonia but functions in a different manner between the two sexes. Together, the functional specialization of this 'non-canonical' type of BZR/BES member may have contributed to the evolution of reproductive systems.

Divergent outcomes of genetic conflict on the UV sex chromosomes of Marchantia polymorpha and Ceratodon purpureus

In species with separate sexes, the genome must produce two distinct developmental programs. Sexually dimorphic development may be controlled by either sex-limited loci or biased expression of loci transmitted through both sexes. Variation in the gene content of sex-limited chromosomes demonstrates that eukaryotic species differ markedly in the roles of these two mechanisms in governing sexual dimorphism. The bryophyte model systems Marchantia polymorpha and Ceratodon purpureus provide a particularly striking contrast. Although both species possess a haploid UV sex chromosome system, in which females carry a U chromosome and males carry a V, M. polymorpha relies on biased autosomal expression, while in C. purpureus, sex-linked genes drive dimorphism. Framing these genetic architectures as divergent outcomes of genetic conflict highlights comparative genomic analyses to better understand the evolution of sexual dimorphism.

Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.

Control of cellularization, nuclear localization, and antipodal cell cluster development in maize embryo sacs

The maize female gametophyte contains four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In maize, these cells are produced after three rounds of free-nuclear divisions followed by cellularization, differentiation, and proliferation of the antipodal cells. Cellularization of the eight-nucleate syncytium produces seven cells with two polar nuclei in the central cell. Nuclear localization is tightly controlled in the embryo sac. This leads to precise allocation of the nuclei into the cells upon cellularization. Nuclear positioning within the syncytium is highly correlated with their identity after cellularization. Two mutants are described with extra polar nuclei, abnormal antipodal cell morphology, and reduced antipodal cell number, as well as frequent loss of antipodal cell marker expression. Mutations in one of these genes, indeterminate gametophyte2 encoding a MICROTUBULE ASSOCIATED PROTEIN65-3 homolog, shows a requirement for MAP65-3 in cellularization of the syncytial embryo sac as well as for normal seed development. The timing of the effects of ig2 suggests that the identity of the nuclei in the syncytial female gametophyte can be changed very late before cellularization.

The fate of sex chromosomes during the evolution of monoicy from dioicy in liverworts

Liverworts comprise one of six primary land plant lineages, with the predicted origin of extant liverwort diversity dating to the Silurian. The ancestral liverwort has been inferred to have been dioicous (unisexual) with chromosomal sex determination in which the U chromosome of females and the V chromosome of males were dimorphic with an extensive non-recombining region. In liverworts, sex is determined by a U chromosomal "feminizer" gene that promotes female development, and in its absence, male development ensues. Monoicy (bisexuality) has independently evolved multiple times within liverworts. Here, we explore the evolution of monoicy, focusing on the monoicous species Ricciocarpos natans, and propose that the evolution of monoicy in R. natans involved the appearance of an aneuploid spore that possessed both U and V chromosomes. Chromosomal rearrangements involving the U chromosome resulted in distribution of essential U chromosome genes, including the feminizer, to several autosomal locations. By contrast, we infer that the ancestral V chromosome was inherited largely intact, probably because it carries numerous dispersed "motility" genes distributed across the chromosome. The genetic networks for sex differentiation in R. natans appear largely unchanged except that the feminizer is developmentally regulated, allowing for temporally separated differentiation of female and male reproductive organs on a single plant. A survey of other monoicous liverworts suggests that similar genomic rearrangements may have occurred repeatedly in lineages transitioning to monoicy from dioicy. These data provide a foundation for understanding how genetic networks controlling sex determination can be subtly rewired to produce profound changes in sexual systems.

Genome-Wide Survey of the RWP-RK Gene Family in Cassava (Manihot esculenta Crantz) and Functional Analysis

The plant-specific RWP-RK transcription factor family plays a central role in the regulation of nitrogen response and gametophyte development. However, little information is available regarding the evolutionary relationships and characteristics of the RWP-RK family genes in cassava, an important tropical crop. Herein, 13 RWP-RK proteins identified in cassava were unevenly distributed across 9 of the 18 chromosomes (Chr), and these proteins were divided into two clusters based on their phylogenetic distance. The NLP subfamily contained seven cassava proteins including GAF, RWP-RK, and PB1 domains; the RKD subfamily contained six cassava proteins including the RWP-RK domain. Genes of the NLP subfamily had a longer sequence and more introns than the RKD subfamily. A large number of hormone- and stress-related cis-acting elements were found in the analysis of RWP-RK promoters. Real-time quantitative PCR revealed that all MeNLP1-7 and MeRKD1/3/5 genes responded to different abiotic stressors (water deficit, cold temperature, mannitol, polyethylene glycol, NaCl, and H2O2), hormonal treatments (abscisic acid and methyl jasmonate), and nitrogen starvation. MeNLP3/4/5/6/7 and MeRKD3/5, which can quickly and efficiently respond to different stresses, were found to be important candidate genes for further functional assays in cassava. The MeRKD5 and MeNLP6 proteins were localized to the cell nucleus in tobacco leaf. Five and one candidate proteins interacting with MeRKD5 and MeNLP6, respectively, were screened from the cassava nitrogen starvation library, including agamous-like mads-box protein AGL14, metallothionein 2, Zine finger FYVE domain containing protein, glyceraldehyde-3-phosphate dehydrogenase, E3 Ubiquitin-protein ligase HUWE1, and PPR repeat family protein. These results provided a solid basis to understand abiotic stress responses and signal transduction mediated by RWP-RK genes in cassava.

A conserved RWP-RK transcription factor VSR1 controls gametic differentiation in volvocine algae

Volvocine green algae are a model for understanding the evolution of mating types and sexes. They are facultatively sexual, with gametic differentiation occurring in response to nitrogen starvation (-N) in most genera and to sex inducer hormone in Volvox. The conserved RWP-RK family transcription factor (TF) MID is encoded by the minus mating-type locus or male sex-determining region of heterothallic volvocine species and dominantly determines minus or male gametic differentiation. However, the factor(s) responsible for establishing the default plus or female differentiation programs have remained elusive. We performed a phylo-transcriptomic screen for autosomal RWP-RK TFs induced during gametogenesis in unicellular isogamous Chlamydomonas reinhardtii (Chlamydomonas) and in multicellular oogamous Volvox carteri (Volvox) and identified a single conserved ortho-group we named Volvocine Sex Regulator 1 (VSR1). Chlamydomonas vsr1 mutants of either mating type failed to mate and could not induce expression of key mating-type-specific genes. Similarly, Volvox vsr1 mutants in either sex could initiate sexual embryogenesis, but the presumptive eggs or androgonidia (sperm packet precursors) were infertile and unable to express key sex-specific genes. Yeast two-hybrid assays identified a conserved domain in VSR1 capable of self-interaction or interaction with the conserved N terminal domain of MID. In vivo coimmunoprecipitation experiments demonstrated association of VSR1 and MID in both Chlamydomonas and Volvox. These data support a new model for volvocine sexual differentiation where VSR1 homodimers activate expression of plus/female gamete-specific-genes, but when MID is present, MID-VSR1 heterodimers are preferentially formed and activate minus/male gamete-specific-genes.

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress

BACKGROUND

NIN-like protein (NLP) transcription factors (TFs) compose a plant-specific gene family whose members play vital roles in plant physiological processes, especially in the regulation of plant growth and the response to nitrate-nitrogen. However, no systematic identification or analysis of the NLP gene family has been reported in alfalfa. The recently completed whole-genome sequence of alfalfa has allowed us to investigate genome-wide characteristics and expression profiles.

RESULTS

53 MsNLP genes were identified from alfalfa and renamed according to their respective chromosome distributions. Phylogenetic analysis demonstrated that these MsNLPs can be classified into three groups on the basis of their conserved domains. Gene structure and protein motif analyses showed that closely clustered MsNLP genes were relatively conserved within each subgroup. Synteny analysis revealed four fragment duplication events of MsNLPs in alfalfa. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of gene pairs indicated that the MsNLP genes underwent purifying selection during evolution. Examination of the expression patterns of different tissues revealed specific expression patterns of the MsNLP genes in the leaves, indicating that these genes are involved in plant functional development. Prediction of cis-acting regulatory elements and expression profiles further demonstrated that the MsNLP genes might play important roles in the response to abiotic stress and in phytohormone signal transduction processes.

CONCLUSION

This study represents the first genome-wide characterization of MsNLP in alfalfa. Most MsNLPs are expressed mainly in leaves and respond positively to abiotic stresses and hormonal treatments. These results provide a valuable resource for an improved understanding of the characteristics and biological roles of the MsNLP genes in alfalfa.

RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice

BACKGROUND

Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown.

RESULTS

In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50% were up-regulated while the other half were down-regulated. Notably, approximately 37.5% of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways.

CONCLUSIONS

Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice.

Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis

Symmetric tissue alignment is pivotal to the functions of plant vascular tissue, such as long-distance molecular transport and lateral organ formation. During the vascular development of the Arabidopsis roots, cytokinins initially determine cell-type boundaries among vascular stem cells and subsequently promote cell proliferation to establish vascular tissue symmetry. Although it is unknown whether and how the symmetry of initially defined boundaries is progressively refined under tissue growth in plants, such boundary shapes in animal tissues are regulated by cell fluidity, e.g., cell migration and intercalation, lacking in plant tissues. Here, we uncover that cell proliferation during vascular development produces anisotropic compressive stress, smoothing, and symmetrizing cell arrangement of the vascular-cell-type boundary. Mechanistically, the GATA transcription factor HANABA-TARANU cooperates with the type-B Arabidopsis response regulators to form an incoherent feedforward loop in cytokinin signaling. The incoherent feedforward loop fine-tunes the position and frequency of vascular cell proliferation, which in turn restricts the source of mechanical stress to the position distal and symmetric to the boundary. By combinatorial analyses of mechanical simulations and laser cell ablation, we show that the spatially constrained environment of vascular tissue efficiently entrains the stress orientation among the cells to produce a tissue-wide stress field. Together, our data indicate that the localized proliferation regulated by the cytokinin signaling circuit is decoded into a globally oriented mechanical stress to shape the vascular tissue symmetry, representing a reasonable mechanism controlling the boundary alignment and symmetry in tissue lacking cell fluidity.

A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium

The Closterium peracerosum-strigosum-littorale complex (Closterium, Zygnematophyceae) has an isogamous mating system. Members of the Zygnematophyceae are the closest relatives to extant land plants and are distantly related to chlorophytic models, for which a genetic basis of mating type (MT) determination has been reported. We thus investigated MT determination in Closterium. We sequenced genomes representing the two MTs, mt+ and mt-, in Closterium and identified CpMinus1, a gene linked to the mt- phenotype. We analyzed its function using reverse genetics methods. CpMinus1 encodes a divergent RWP-RK domain-containing-like transcription factor and is specifically expressed during gamete differentiation. Introduction of CpMinus1 into an mt+ strain was sufficient to convert it to a phenotypically mt- strain, while CpMinus1-knockout mt- strains were phenotypically mt+. We propose that CpMinus1 is the major MT determinant that acts by evoking the mt- phenotype and suppressing the mt+ phenotype in heterothallic Closterium. CpMinus1 likely evolved independently in the Zygnematophyceae lineage, which lost an egg-sperm anisogamous mating system. mt- specific regions possibly constitute an MT locus flanked by common sequences that undergo some recombination.

Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean.

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.

MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha is equipped with a wide range of molecular and genetic tools and resources that have led to its wide use to explore the evo-devo aspects of land plants. Although its diverse transcriptome data are rapidly accumulating, there is no extensive yet user-friendly tool to exploit such a compilation of data and to summarize results with the latest annotations. Here, we have developed a web-based suite of tools, MarpolBase Expression (MBEX, https://marchantia.info/mbex/), where users can visualize gene expression profiles, identify differentially expressed genes, perform co-expression and functional enrichment analyses and summarize their comprehensive output in various portable formats. Using oil body biogenesis as an example, we demonstrated that the results generated by MBEX were consistent with the published experimental evidence and also revealed a novel transcriptional network in this process. MBEX should facilitate the exploration and discovery of the genetic and functional networks behind various biological processes in M. polymorpha and promote our understanding of the evolution of land plants.

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.

Remodeling of organelles and microtubules during spermiogenesis in the liverwort Marchantia polymorpha

Gametogenesis is an essential event for sexual reproduction in various organisms. Bryophytes employ motile sperm (spermatozoids) as male gametes, which locomote to the egg cells to accomplish fertilization. The spermatozoids of bryophytes harbor distinctive morphological characteristics, including a cell body with a helical shape and two flagella. During spermiogenesis, the shape and cellular contents of the spermatids are dynamically reorganized. However, the reorganization patterns of each organelle remain obscure. In this study, we classified the developmental processes during spermiogenesis in the liverwort Marchantia polymorpha according to changes in cellular and nuclear shapes and flagellar development. We then examined the remodeling of microtubules and the reorganization of endomembrane organelles. The results indicated that the state of glutamylation of tubulin changes during formation of the flagella and spline. We also found that the plasma membrane and endomembrane organelles are drastically reorganized in a precisely regulated manner, which involves the functions of endosomal sorting complexes required for transport (ESCRT) machineries in endocytic and vacuolar transport. These findings are expected to provide useful indices to classify developmental and subcellular processes of spermiogenesis in bryophytes.

RWP-RK domain-containing transcription factors in the Viridiplantae: biology and phylogenetic relationships

The RWP-RK protein family is a group of transcription factors containing the RWP-RK DNA-binding domain. This domain is an ancient motif that emerged before the establishment of the Viridiplantae-the green plants, consisting of green algae and land plants. The domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which are seemingly unrelated phenomena but possibly interdependent in autotrophs. Consistent with related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Thus, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge of the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and procurement of sophisticated mechanisms for adaptation to the terrestrial environment.

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.

The Physcomitrium patens egg cell expresses several distinct epigenetic components and utilizes homologues of BONOBO genes for cell specification

Although land plant germ cells have received much attention, knowledge about their specification is still limited. We thus identified transcripts enriched in egg cells of the bryophyte model species Physcomitrium patens, compared the results with angiosperm egg cells, and selected important candidate genes for functional analysis. We used laser-assisted microdissection to perform a cell-type-specific transcriptome analysis on egg cells for comparison with available expression profiles of vegetative tissues and male reproductive organs. We made reporter lines and knockout mutants of the two BONOBO (PbBNB) genes and studied their role in reproduction. We observed an overlap in gene activity between bryophyte and angiosperm egg cells, but also clear differences. Strikingly, several processes that are male-germline specific in Arabidopsis are active in the P. patens egg cell. Among those were the moss PbBNB genes, which control proliferation and identity of both female and male germlines. Pathways shared between male and female germlines were most likely present in the common ancestors of land plants, besides sex-specifying factors. A set of genes may also be involved in the switches between the diploid and haploid moss generations. Nonangiosperm gene networks also contribute to the specification of the P. patens egg cell.

Transcriptional dynamics of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP-RK transcription factor linked to reproduction

BACKGROUND

The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications.

RESULTS

Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, was studied. We analyzed transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrated that 45% of the genes in the genome were differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionarily conserved transcription factor containing an RWP-RK domain suggested a key role during Ulva gametogenesis.

CONCLUSIONS

Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in the induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

Switching it up: algal insights into sexual transitions

While the process of meiosis is highly conserved across eukaryotes, the sexual systems that govern life cycle phase transitions are surprisingly labile. Switches between sexual systems have profound evolutionary and ecological consequences, in particular for plants, but our understanding of the fundamental mechanisms and ultimate causes underlying these transitions is still surprisingly incomplete. We explore here the idea that brown and green algae may be interesting comparative models that can increase our understanding of relevant processes in plant reproductive biology, from evolution of gamete dimorphism, gametogenesis, sex determination and transitions in sex-determining systems.

Regulation of gametangia and gametangiophore initiation in the liverwort Marchantia polymorpha

The liverwort Marchantia polymorpha regulates gametangia and gametangiophore development by using evolutionarily conserved regulatory modules that are shared with angiosperm mechanisms regulating flowering and germ cell differentiation. Bryophytes, the earliest diverged lineage of land plants comprised of liverworts, mosses, and hornworts, produce gametes in gametangia, reproductive organs evolutionarily conserved but lost in extant angiosperms. Initiation of gametangium development is dependent on environmental factors such as light, although the underlying mechanisms remain elusive. Recent studies showed that the liverwort Marchantia polymorpha regulates development of gametangia and stalked receptacles called gametangiophores by using conserved regulatory modules which, in angiosperms, are involved in light signaling, microRNA-mediated flowering regulation, and germ cell differentiation. These findings suggest that these modules were acquired by a common ancestor of land plants before divergence of bryophytes, and were later recruited to flowering mechanism in angiosperms.

From birth to function: Male gametophyte development in flowering plants

Male germline development in flowering plants involves two distinct and successive phases, microsporogenesis and microgametogenesis, which involve one meiosis followed by two rounds of mitosis. Many aspects of distinctions after mitosis between the vegetative cell and the male germ cells are seen, from morphology to structure, and the differential functions of the two cell types in the male gametophyte are differentially needed and required for double fertilization. The two sperm cells, carriers of the hereditary substances, depend on the vegetative cell/pollen tube to be delivered to the female gametophyte for double fertilization. Thus, the intercellular communication and coordinated activity within the male gametophyte probably represent the most subtle regulation in flowering plants to guarantee the success of reproduction. This review will focus on what we have known about the differentiation process and the functional diversification of the vegetative cell and the male germ cell, the most crucial cell types for plant fertility and crop production.

Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants

KNOX and BELL transcription factors regulate distinct steps of diploid development in plants. In the green alga Chlamydomonas reinhardtii, KNOX and BELL proteins are inherited by gametes of the opposite mating types and heterodimerize in zygotes to activate diploid development. By contrast, in land plants such as Physcomitrium patens and Arabidopsis thaliana, KNOX and BELL proteins function in sporophyte and spore formation, meristem maintenance and organogenesis during the later stages of diploid development. However, whether the contrasting functions of KNOX and BELL were acquired independently in algae and land plants is currently unknown. Here, we show that in the basal land plant species Marchantia polymorpha, gamete-expressed KNOX and BELL are required to initiate zygotic development by promoting nuclear fusion in a manner strikingly similar to that in C. reinhardtii. Our results indicate that zygote activation is the ancestral role of KNOX/BELL transcription factors, which shifted toward meristem maintenance as land plants evolved.

Gene expression variation in Arabidopsis embryos at single-nucleus resolution

Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.

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.

Reproduction Multitasking: The Male Gametophyte

The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.

Comparative Embryogenesis in Angiosperms: Activation and Patterning of Embryonic Cell Lineages

Following fertilization in flowering plants (angiosperms), egg and sperm cells unite to form the zygote, which generates an entire new organism through a process called embryogenesis. In this review, we provide a comparative perspective on early zygotic embryogenesis in flowering plants by using the Poaceae maize and rice as monocot grass and crop models as well as Arabidopsis as a eudicot model of the Brassicaceae family. Beginning with the activation of the egg cell, we summarize and discuss the process of maternal-to-zygotic transition in plants, also taking recent work on parthenogenesis and haploid induction into consideration. Aspects like imprinting, which is mainly associated with endosperm development and somatic embryogenesis, are not considered. Controversial findings about the timing of zygotic genome activation as well as maternal versus paternal contribution to zygote and early embryo development are highlighted. The establishment of zygotic polarity, asymmetric division, and apical and basal cell lineages represents another chapter in which we also examine and compare the role of major signaling pathways, cell fate genes, and hormones in early embryogenesis. Except for the model Arabidopsis, little is known about embryopatterning and the establishment of the basic body plan in angiosperms. Using available in situ hybridization, RNA-sequencing, and marker data, we try to compare how and when stem cell niches are established. Finally, evolutionary aspects of plant embryo development are discussed.

HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants

KEY MESSAGE

Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1, and analyzed loss-of-function mutants in the moss P. patens. In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pphag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mphag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.

The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes

Short secreted plant peptides act as key signaling molecules and control a plethora of developmental and physiological processes. The ROOT GROWTH FACTOR (RGF)/GOLVEN (GLV)/CLE-Like (CLEL) family of peptides was discovered to be involved in root development in Arabidopsis thaliana. In contrast to active research efforts, which have been revealing receptors and downstream signaling components, little attention has been paid to evolutionary processes that shaped the RGF signaling system as we know it in angiosperms today. As a first step toward understanding how RGF signaling emerged and evolved, this study aimed to elucidate the phylogenetic distribution and functional conservation of RGF-like sequences. Using publicly available, genome and transcriptome data, RGF-like sequences were searched in 27 liverworts, 22 mosses, 8 hornworts, 23 lycophytes, 23 ferns, 38 gymnosperms, and 8 angiosperms. This led to the identification of more than four hundreds of RGF-like sequences in all major extant land plant lineages except for hornworts. Sequence comparisons within and between taxonomic groups identified lineage-specific characters. Notably, one of the two major RGF subgroups, represented by A. thaliana RGF6/GLV1/CLEL6, was found only in vascular plants. This subgroup, therefore, likely emerged in a common ancestor of vascular plants after its divergence from bryophytes. In bryophytes, our results infer independent losses of RGF-like sequences in mosses and hornworts. On the other hand, a single, highly similar RGF-like sequence is conserved in liverworts, including Marchantia polymorpha, a genetically tractable model species. When constitutively expressed, the M. polymorpha RGF-like sequence (MpRGF) affected plant development and growth both in A. thaliana and M. polymorpha. This suggests that MpRGF can exert known RGF-like effects and that MpRGF is under transcriptional control so that its potent activities are precisely controlled. These data suggest that RGFs are conserved as signaling molecules in both vascular plants and bryophytes and that lineage-specific diversification has increased sequence variations of RGFs. All together, our findings form a basis for further studies into RGF peptides and their receptors, which will contribute to our understandings of how peptide signaling pathways evolve.

A study of male fertility control in Medicago truncatula uncovers an evolutionarily conserved recruitment of two tapetal bHLH subfamilies in plant sexual reproduction

Male sterility is an important tool for plant breeding and hybrid seed production. Male-sterile mutants are largely due to an abnormal development of either the sporophytic or gametophytic anther tissues. Tapetum, a key sporophytic tissue, provides nutrients for pollen development, and its delayed degeneration induces pollen abortion. Numerous bHLH proteins have been documented to participate in the degeneration of the tapetum in angiosperms, but relatively little attention has been given to the evolution of the involved developmental pathways across the phylogeny of land plants. A combination of cellular, molecular, biochemical and evolutionary analyses was used to investigate the male fertility control in Medicago truncatula. We characterized the male-sterile mutant empty anther1 (ean1) and identified EAN1 as a tapetum-specific bHLH transcription factor necessary for tapetum degeneration. Our study uncovered an evolutionarily conserved recruitment of bHLH subfamily II and III(a + c)1 in the regulation of tapetum degeneration. EAN1 belongs to the subfamily II and specifically forms heterodimers with the subfamily III(a + c)1 members, which suggests a heterodimerization mechanism conserved in angiosperms. Our work suggested that the pathway of two tapetal-bHLH subfamilies is conserved in all land plants, and likely was established before the divergence of the spore-producing land plants.

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.

Conserved Subgroups of the Plant-Specific RWP-RK Transcription Factor Family Are Present in Oomycete Pathogens

Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12-15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach

MAIN CONCLUSION

This study shows differences in gene expression between male and female gametophytes of the simple thalloid liverwort with a distinction between the vegetative and reproductive phases of growth. Pellia endiviifolia is a simple thalloid liverwort that, together with hornworts and mosses, represents the oldest living land plants. The limited taxon sampling for genomic and functional studies hampers our understanding of processes governing evolution of these plants. RNA sequencing represents an attractive way to elucidate the molecular mechanisms of non-model species development. In the present study, RNA-seq was used to profile the differences in gene expression between P. endiviifolia male and female gametophytes, with a distinction between the vegetative and reproductive phases of growth. By comparison of the gene expression profiles from individuals producing sex organs with the remaining thalli types, we have determined a set of genes whose expression might be important for the development of P. endiviifolia reproductive organs. The selected differentially expressed genes (DEGs) were categorized into five main pathways: metabolism, genetic information processing, environmental information processing, cellular processes, and organismal systems. A comparison of the obtained data with the Marchantia polymorpha transcriptome resulted in the identification of genes exhibiting a similar expression pattern during the reproductive phase of growth between members of the two distinct liverwort classes. The common expression profile of  87 selected genes suggests a common mechanism governing sex organ development in both liverwort species. The obtained RNA-seq results were confirmed by RT-qPCR for the DEGs with the highest differences in expression level. Five Pellia-female-specific and two Pellia-male-specific DEGs showed enriched expression in archegonia and antheridia, respectively. The identified genes are promising candidates for functional studies of their involvement in liverwort sexual reproduction.

Can We Use Gene-Editing to Induce Apomixis in Sexual Plants?

Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.

Plant science's next top models

BACKGROUND

Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models.

SCOPE

Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers.

CONCLUSIONS

Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

Reproductive Multitasking: The Female Gametophyte

Fertilization of flowering plants requires the organization of complex tasks, many of which become integrated by the female gametophyte (FG). The FG is a few-celled haploid structure that orchestrates division of labor to coordinate successful interaction with the sperm cells and their transport vehicle, the pollen tube. As reproductive outcome is directly coupled to evolutionary success, the underlying mechanisms are under robust molecular control, including integrity check and repair mechanisms. Here, we review progress on understanding the development and function of the FG, starting with the functional megaspore, which represents the haploid founder cell of the FG. We highlight recent achievements that have greatly advanced our understanding of pollen tube attraction strategies and the mechanisms that regulate plant hybridization and gamete fusion. In addition, we discuss novel insights into plant polyploidization strategies that expand current concepts on the evolution of flowering plants.

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.

Square one: zygote polarity and early embryogenesis in flowering plants

In the last two decades, work on auxin signaling has helped to understand many aspects of the fundamental process underlying the specification of tissue types in the plant embryo. However, the immediate steps after fertilization including the polarization of the zygote and the initial body axis formation remained poorly understood. Valuable insight into these enigmatic processes has been gained by studying fertilization in grasses. Recent technical advances in transcriptomics of developing embryos with high spatial and temporal resolution give an emerging picture of the rapid changes of the zygotic developmental program. Together with the use of live imaging of novel fluorescent marker lines, these data are now the basis of unraveling the very first steps of the embryonic patterning process.

Suspensor-derived somatic embryogenesis in Arabidopsis

In many flowering plants, asymmetric division of the zygote generates apical and basal cells with different fates. In Arabidopsis thaliana, the apical cell generates the embryo while the basal cell divides anticlinally, leading to a suspensor of 6-9 cells that remain extra-embryonic and eventually senesce. In some genetic backgrounds, or upon ablation of the embryo, suspensor cells can undergo periclinal cell divisions and eventually form a second, twin embryo. Likewise, embryogenesis can be induced from somatic cells by various genes, but the relation to suspensor-derived embryos is unclear. Here, we addressed the nature of the suspensor to embryo fate transformation, and its genetic triggers. We expressed most known embryogenesis-inducing genes specifically in suspensor cells. We next analyzed morphology and fate marker expression in embryos in which suspensor division were activated by different triggers to address the developmental paths towards reprogramming. Our results show that reprogramming of Arabidopsis suspensor cells towards embryonic identity is a specific cellular response that is triggered by defined regulators, follows a conserved developmental trajectory and shares similarity to the process of somatic embryogenesis from post-embryonic tissues.

Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling

Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.

Algal Sex Determination and the Evolution of Anisogamy

Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.

Building new insights in plant gametogenesis from an evolutionary perspective

Extant bryophytes are thought to preserve characteristics of ancestral land plants, with a life cycle dominated by the haploid gametophyte. The gametophyte produces gametes in specialized organs that differentiate after an extensive phase of vegetative development. During land plant evolution, these organs became extremely reduced. As a result, in flowers of angiosperms the haploid phase of the life cycle is reduced to few-celled gametophytes, namely the embryo sac (female) and pollen (male). Although many factors contributing to gametogenesis have been identified in flowering plants, the extreme reduction of the gametophytes has prevented a clear molecular dissection of key processes of gametogenesis. Recent studies in the model bryophyte Marchantia polymorpha have identified conserved transcription factors regulating the equivalent steps in the sexual reproduction of land plants. These include FEMALE GAMETOPHYTE MYB for female gametophyte development, BONOBO for gamete progenitor cell specification, DUO POLLEN1 for sperm differentiation and members of the RWP-RK domain family for female gamete formation. These studies demonstrate that M. polymorpha is a powerful model to untangle the core processes of gametogenesis in land plants. We anticipate that a deeper understanding of gametogenesis in bryophytes will circumscribe the origin of plant germ cells and define the differentiation programmes of sperm and eggs.

Reproductive Induction is a Far-Red High Irradiance Response that is Mediated by Phytochrome and PHYTOCHROME INTERACTING FACTOR in Marchantia polymorpha

Land plants have evolved a series of photoreceptors to precisely perceive environmental information. Among these, phytochromes are the sole photoreceptors for red light (R) and far-red light (FR), and play pivotal roles in modulating various developmental processes. Most extant land plants possess multiple phytochromes that probably evolved from a single phytochrome in the common ancestor of land plants. However, the ancestral phytochrome signaling mechanism remains unknown due to a paucity of knowledge regarding phytochrome functions in basal land plants. It has recently been reported that Mpphy, a single phytochrome in the liverwort Marchantia polymorpha, regulates typical photoreversible responses collectively classified as low fluence response (LFR). Here, we show that Mpphy also regulates the gametangiophore formation analogous to the mode of action of the far-red high irradiance response (FR-HIR) in angiosperms. Our phenotypic analyses using mutant plants obtained by CRISPR/Cas9-based genome editing revealed that MpFHY1, an ortholog of FAR-RED ELONGATED HYPOCOTYL1, as well as Mpphy is critical for the FR-HIR signaling in M. polymorpha. In addition, knockout of MpPIF, a single PHYTOCHROME INTERACTING FACTOR gene in M. polymorpha, completely abolished the FR-HIR-dependent gametangiophore formation, while overexpression of MpPIF accelerated the response. FR-HIR-dependent transcriptional regulation was also disrupted in the Mppif mutant. Our findings suggest that plants had already acquired the FR-HIR signaling mediated by phytochrome and PIF at a very early stage during the course of land plant evolution, and that a single phytochrome in the common ancestor of land plants could mediate both LFR and FR-HIR.

A cis-acting bidirectional transcription switch controls sexual dimorphism in the liverwort

Plant life cycles alternate between haploid gametophytes and diploid sporophytes. While regulatory factors determining male and female sexual morphologies have been identified for sporophytic reproductive organs, such as stamens and pistils of angiosperms, those regulating sex‐specific traits in the haploid gametophytes that produce male and female gametes and hence are central to plant sexual reproduction are poorly understood. Here, we identified a MYB‐type transcription factor, MpFGMYB, as a key regulator of female sexual differentiation in the haploid‐dominant dioicous liverwort, Marchantia polymorpha. MpFGMYB is specifically expressed in females and its loss resulted in female‐to‐male sex conversion. Strikingly, MpFGMYB expression is suppressed in males by a cis‐acting antisense gene SUF at the same locus, and loss‐of‐function suf mutations resulted in male‐to‐female sex conversion. Thus, the bidirectional transcription module at the MpFGMYB/SUF locus acts as a toggle between female and male sexual differentiation in M. polymorpha gametophytes. Arabidopsis thaliana MpFGMYB orthologs are known to be expressed in embryo sacs and promote their development. Thus, phylogenetically related MYB transcription factors regulate female gametophyte development across land plants.