The evolution of plant regulatory networks: what Arabidopsis cannot say for itself

How to utilize comparative transcriptomics to dissect morphological diversity in plants

Comparative transcriptomics has emerged as a powerful approach that allows us to unravel the genetic basis of organ morphogenesis and its diversification processes during evolution. However, the application of comparative transcriptomics in studying plant morphological diversity addresses challenges such as identifying homologous gene pairs, selecting appropriate developmental stages for comparison, and extracting biologically meaningful networks. Methods such as phylostratigraphy, clustering, and gene co-expression networks are explored to identify functionally equivalent genes, align developmental stages, and uncover gene regulatory relationships. In the current review, we highlight the importance of these approaches in overcoming the complexity of plant genomes, the impact of heterochrony on stage alignment, and the integration of gene networks with additional data for a comprehensive understanding of morphological evolution.

Measurements of the number of specified and unspecified cells in the shoot apical meristem during a plastochron in rice (Oryza sativa) reveal the robustness of cellular specification process in plant development

The shoot apical meristem (SAM) is composed of a population of stem cells giving rise to the aboveground parts of plants. It maintains itself by controlling the balance of cell proliferation and specification. Although knowledge of the mechanisms maintaining the SAM has been accumulating, the processes of cellular specification to form leaves and replenishment of unspecified cells in the SAM during a plastochron (the time interval between which two successive leaf primordia are formed) is still obscure. In this study, we developed a method to quantify the number of specified and unspecified cells in the SAM and used it to elucidate the dynamics of cellular specification in the SAM during a plastochron in rice. OSH1 is a KNOX (KNOTTED1-like homeobox) gene in rice that is expressed in the unspecified cells in the SAM, but not in specified cells. Thus, we could visualize and count the nuclei of unspecified cells by fluorescent immunohistochemical staining with an anti-OSH1 antibody followed by fluorescein isothiocyanate detection. By double-staining with propidium iodide (which stains all nuclei) and then overlaying the images, we could also detect and count the specified cells. By using these measurements in combination with morphological observation, we defined four developmental stages of SAM that portray cellular specification and replenishment of unspecified cells in the SAM during a plastochron. In addition, through the analysis of mutant lines with altered size and shape of the SAM, we found that the number of specified cells destined to form a leaf primordium is not affected by mild perturbations of meristem size and shape. Our study highlights the dynamism and flexibility in stem cell maintenance in the SAM during a plastochron and the robustness of plant development.

Auxin Does the SAMba: Auxin Signaling in the Shoot Apical Meristem

Plants, in contrast to animals, are unique in their capacity to postembryonically develop new organs due to the activity of stem cell populations, located in specialized tissues called meristems. Above ground, the shoot apical meristem generates aerial organs and tissues throughout plant life. It is well established that auxin plays a central role in the functioning of the shoot apical meristem. Auxin distribution in the meristem is not uniform and depends on the interplay between biosynthesis, transport, and degradation. Auxin maxima and minima are created, and result in transcriptional outputs that drive the development of new organs and contribute to meristem maintenance. To uncover and understand complex signaling networks such as the one regulating auxin responses in the shoot apical meristem remains a challenge. Here, we will discuss our current understanding and point to important research directions for the future.

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits

The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.

Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Identification of putative homologs of Larix decidua to BABYBOOM (BBM), LEAFY COTYLEDON1 (LEC1), WUSCHEL-related HOMEOBOX2 (WOX2) and SOMATIC EMBRYOGENESIS RECEPTOR-like KINASE (SERK) during somatic embryogenesis

Embryogenesis-related genes ( LdBBM, LdLEC1, LdWOX2 and LdSERK ) were confirmed in sequence and expression abundance for Larix decidua —these findings are valid for somatic as well as for zygotic embryo development.S omatic embryogenesis is a reliable source of high-quality genotypes as it presents an advantageous alternative for conifers in forestry, independent from seed production. Although this propagation method is already being applied, molecular factors initiating and controlling the process remain to be understood. The embryogenesis-associated genes BABYBOOM (BBM), LEAFY COTYLEDON1 (LEC1), WUSCHEL-related HOMEOBOX2 (WOX2) and SOMATIC EMBRYOGENESIS RECEPTOR-like KINASE (SERK) were identified and analyzed in somatic embryos of the European larch, L. decidua Mill. Subsequent comparisons with annotated sequences displayed similarities with angiosperm homologs. Transcript accumulation of the identified genes during embryogenesis has been analyzed. LdLEC1 and LdWOX2 are mainly expressed during early embryogenesis, whereas LdBBM and LdSERK reveal increased expression during later development. Temporal and spatial expression studies revealed a specific LdLEC1 signal in the outer cell layer of young embryo heads, whereas mature embryos showed a homogeneous expression. The overexpression of LdLEC1 in Arabidopsis influences germination and cotyledon formation, thus indicating the interspecific importance of LEC1 for proper embryo and specifically cotyledon development. Our data support a conserved role of principal regulators during plant embryogenesis that may be used as molecular markers for embryogenicity and to further determine initiating processes of somatic embryogenesis.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Plant development regulation: Overview and perspectives

Plant development, as occur in other eukaryotes, is conducted through a complex network of hormones, transcription factors, enzymes and micro RNAs, among other cellular components. They control developmental processes such as embryo, apical root and shoot meristem, leaf, flower, or seed formation, among others. The research in these topics has been very active in last decades. Recently, an explosion of new data concerning regulation mechanisms as well as the response of these processes to environmental changes has emerged. Initially, most of investigations were carried out in the model eudicot Arabidopsis but currently data from other plant species are available in the literature, although they are still limited. The aim of this review is focused on summarize the main molecular actors involved in plant development regulation in diverse plant species. A special attention will be given to the major families of genes and proteins participating in these regulatory mechanisms. The information on the regulatory pathways where they participate will be briefly cited. Additionally, the importance of certain structural features of such proteins that confer ductility and flexibility to these mechanisms will also be reported and discussed.

Genome-wide evolutionary characterization and analysis of bZIP transcription factors and their expression profiles in response to multiple abiotic stresses in Brachypodium distachyon

BACKGROUND

Plant basic leucine zipper (bZIP) transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes. Brachypodium distachyon is emerging as a widely recognized model plant for the temperate grass family and the herbaceous energy crops, however there is no comprehensive analysis of bZIPs in B. distachyon, especially those involved in stress tolerances.

RESULTS

In this study, 96 bZIP genes (BdbZIPs) were identified distributing unevenly on each chromosome of B. distachyon, and most of them were scattered in the low CpG content regions. Gene duplications were widespread throughout B. distachyon genome. Evolutionary comparisons suggested B. distachyon and rice's bZIPs had the similar evolutionary patterns. The exon splicing in BdbZIP motifs were more complex and diverse than those in other plant species. We further revealed the potential close relationships between BdbZIP gene expressions and items including gene structure, exon splicing pattern and dimerization features. In addition, multiple stresses expression profile demonstrated that BdbZIPs exhibited significant expression patterns responding to 14 stresses, and those responding to heavy metal treatments showed opposite expression pattern comparing to the treatments of environmental factors and phytohormones. We also screened certain up- and down-regulated BdbZIP genes with fold changes ≥2, which were more sensitive to abiotic stress conditions.

CONCLUSIONS

BdbZIP genes behaved diverse functional characters and showed discrepant and some regular expression patterns in response to abiotic stresses. Comprehensive analysis indicated these BdbZIPs' expressions were associated not only with gene structure, exon splicing pattern and dimerization feature, but also with abiotic stress treatments. It is possible that our findings are crucial for revealing the potentialities of utilizing these candidate BdbZIPs to improve productivity of grass plants and cereal crops.

Genome-wide evolutionary characterization and analysis of bZIP transcription factors and their expression profiles in response to multiple abiotic stresses in Brachypodium distachyon

BACKGROUND

Plant basic leucine zipper (bZIP) transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes. Brachypodium distachyon is emerging as a widely recognized model plant for the temperate grass family and the herbaceous energy crops, however there is no comprehensive analysis of bZIPs in B. distachyon, especially those involved in stress tolerances.

RESULTS

In this study, 96 bZIP genes (BdbZIPs) were identified distributing unevenly on each chromosome of B. distachyon, and most of them were scattered in the low CpG content regions. Gene duplications were widespread throughout B. distachyon genome. Evolutionary comparisons suggested B. distachyon and rice's bZIPs had the similar evolutionary patterns. The exon splicing in BdbZIP motifs were more complex and diverse than those in other plant species. We further revealed the potential close relationships between BdbZIP gene expressions and items including gene structure, exon splicing pattern and dimerization features. In addition, multiple stresses expression profile demonstrated that BdbZIPs exhibited significant expression patterns responding to 14 stresses, and those responding to heavy metal treatments showed opposite expression pattern comparing to the treatments of environmental factors and phytohormones. We also screened certain up- and down-regulated BdbZIP genes with fold changes ≥2, which were more sensitive to abiotic stress conditions.

CONCLUSIONS

BdbZIP genes behaved diverse functional characters and showed discrepant and some regular expression patterns in response to abiotic stresses. Comprehensive analysis indicated these BdbZIPs' expressions were associated not only with gene structure, exon splicing pattern and dimerization feature, but also with abiotic stress treatments. It is possible that our findings are crucial for revealing the potentialities of utilizing these candidate BdbZIPs to improve productivity of grass plants and cereal crops.

WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens

Many differentiated plant cells can dedifferentiate into stem cells, reflecting the remarkable developmental plasticity of plants. In the moss Physcomitrella patens, cells at the wound margin of detached leaves become reprogrammed into stem cells. Here, we report that two paralogous P. patens WUSCHEL-related homeobox 13-like (PpWOX13L) genes, homologs of stem cell regulators in flowering plants, are transiently upregulated and required for the initiation of cell growth during stem cell formation. Concordantly, Δppwox13l deletion mutants fail to upregulate genes encoding homologs of cell wall loosening factors during this process. During the moss life cycle, most of the Δppwox13l mutant zygotes fail to expand and initiate an apical stem cell to form the embryo. Our data show that PpWOX13L genes are required for the initiation of cell growth specifically during stem cell formation, in analogy to WOX stem cell functions in seed plants, but using a different cellular mechanism.

Shoot meristems of deciduous woody perennials: self-organization and morphogenetic transitions

Shoot apical meristems of deciduous woody perennials share gross structural features with other angiosperms, but are unique in the seasonal regulation of vegetative and floral meristems. Supporting longevity, flowering is postponed to the adult phase, and restricted to some axillary meristems. In cold climates, photoperiodic timing mechanisms and chilling are recruited to schedule end-of-season growth arrest, dormancy cycling and flowering. We review recently uncovered generic meristem properties, perennial meristem fate, and the role of CENL1, FT1 and FT2 in bud formation and flowering. We also highlight novel findings, suggesting that dormancy release is mediated by mobile lipid bodies that deliver enzymes to plasmodesmata to recover symplasmic communication and meristem function.

Plant science and agricultural productivity: why are we hitting the yield ceiling?

Trends in conventional plant breeding and in biotechnology research are analyzed with a focus on production and productivity of individual organisms. Our growing understanding of the productive/adaptive potential of (crop) plants is a prerequisite to increasing this potential and also its expression under environmental constraints. This review concentrates on growth rate, ribosome activity, and photosynthetic rate to link these key cellular processes to plant productivity. Examples of how they may be integrated in heterosis, organ growth control, and responses to abiotic stresses are presented. The yield components in rice are presented as a model. The ultimate goal of research programs, that concentrate on yield and productivity and integrating the panoply of systems biology tools, is to achieve "low input, high output" agriculture, i.e. shifting from a conventional "productivist" agriculture to an efficient sustainable agriculture. This is of critical, strategic importance, because the extent to which we, both locally and globally, secure and manage the long-term productive potential of plant resources will determine the future of humanity.

Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints

Background

The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa) formed ten clusters of orthologous groups (COG) with genes from the monocot sorghum (Sorghum bicolor) and dicot Arabidopsis (Arabidopsis thaliana). The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns.

Results

The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS) classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic) or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis.

Conclusions

Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in conjunction with lineage-specific or species-specific regulatory fine-tuners. This synergy may be critical for finer-scale spatio-temporal regulation, hence unique expression profiles of homologous transcription factors from different species with distinct zones of ecological adaptation such as rice, sorghum and Arabidopsis. The patterns revealed from these comparisons set the stage for further empirical validation by functional genomics.

Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage

MicroRNAs (miRNAs) are small 21-nucleotide RNAs that post-transcriptionally regulate gene expression. MiR396 controls leaf development by targeting GRF and bHLH transcription factors in Arabidopsis. WRKY transcription factors, unique to plants, have been identified as mediating varied stress responses. The sunflower (Helianthus annuus) HaWRKY6 is a particularly divergent WRKY gene exhibiting a putative target site for the miR396. A possible post-transcriptional regulation of HaWRKY6 by miR396 was investigated. Here, we used expression analyses, performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and northern blots together with computational approaches to establish the regulatory interaction between HaWRKY6 and the identified sunflower miR396. Arabidopsis plants expressing a mi396-resistant version of HaWRKY6 confirmed the miRNA-dependency of the HaWRKY6 silencing. Sunflower plants exposed to high temperatures or salicylic acid presented opposite expression of HaWRKY6 and miR396. Experiments using the wildtype and miRNA-resistant versions of HaWRKY6 showed altered stress responses. Our results showed a role of the recently evolved miR396 regulation of HaWRKY6 during early responses to high temperature. Our study reveals how a miRNA that normally regulates development has been recruited for high-temperature protection in sunflower, a plant particularly well adapted to this type of stress.

Stem cells: a view from the roots

In both plants and animals, regeneration requires the activation of stem cells. This is possibly related to the origin and requirements of multicellularity. Although long diverged from a common ancestry, plant and animal models such as Arabidopsis, Drosophila and mouse share considerable similarities in stem cell regulation. This includes stem cell niche organisation, epigenetic modification of DNA and histones, and the role of small RNA machinery in differentiation and pluripotency states. Dysregulation of any of these can lead to premature ageing, patterning and specification defects, as well as cancers. Moreover, emerging basal animal and plant systems are beginning to provide important clues concerning the diversity and evolutionary history of stem cell regulatory mechanisms in eukaryotes. This review provides a comparative framework, highlighting both the commonalities and differences among groups, which should promote the intelligent design of artificial stem cell systems, and thereby fuel the field of biomaterials science.

Lobe-generating centres in the simple leaves of Myriophyllum aquaticum: evidence for KN1-like activity

BACKGROUND AND AIMS

The mature morphology of most plants can usually be said to consist of three mutually exclusive organs: leaves, stems, and roots. The vast majority of mature morphologies may be easily grouped into one of these mutually exclusive categories. However, during very early stages of development and in many instances from inception, the division between organ categories becomes fuzzy due to the overlap in developmental processes that are shared between the aforementioned mutually exclusive categories. One such overlap has been described at the gene level where KNOXI homologues, transcription factors responsible for maintaining indeterminate cell fate, are expressed in the shoot apical meristem and during early stages of compound leaf development. This study characterizes the occurrence and spatial localization of mRNA of a KNOXI homologue, MaKN1, during the early stages of development in the simple leaves of Myriophyllum aquaticum, an aquatic angiosperm from the family Haloragaceae exhibiting pentamerous whorls of finely lobed leaves.

METHODS

A 300-bp KNOXI fragment was sequenced from M. aquaticum and used in an RNA localization study to determine the temporal and spatial expression of KNOXI during the early stages of leaf lobe development in M. aquaticum. The developmental sequence of leaves of M. aquaticum was also described using scanning electron microscopy.

KEY RESULTS

Lobe development of M. aquaticum occurs in two very distinct regions at the leaf base in an alternating fashion reminiscent of a distichous shoot system. It was discovered that MaKN1 expression is localized to both the shoot apical meristem and early stages of leaf primordia development (P1-P7). Initially, MaKN1 is expressed ubiquitously throughout primordia (P1-P3); however, as lobes develop, MaKN1 becomes localized to recently emerged lobe primordia, and disappears as lobes develop basipetally.

CONCLUSIONS

The pattern of gene expression is indicative of shared developmental processes during early development between shoots, compound leaves, highly lobed simple leaves and unifoliate simple leaves which lack KNOXI expression. These findings are supportive of Arber's less rigid 'partial shoot' theory, which conceptualizes compound leaves as having shoot-like elements.

Genetic control of leaf-blade morphogenesis by the INSECATUS gene in Pisum sativum

To understand the role of INSECATUS (INS) gene in pea, the leaf blades of wild-type, ins mutant and seven other genotypes, constructed by recombining ins with uni-tac, af, tl and mfp gene mutations, were quantitatively compared. The ins was inherited as a recessive mutant allele and expressed its phenotype in proximal leaflets of full size leaf blades. In ins leaflets, the midvein development was arrested in distal domain and a cleft was formed in lamina above this point. There was change in the identity of ins leaflets such that the intercalary interrupted midvein bore a leaf blade. Such adventitious blades in ins, ins tl and ins tl mfp were like the distal segment of respective main leaf blade. The ins phenotype was not seen in ins af and ins af uni-tac genotypes. There was epistasis of uni-tac over ins. The ins, tl and mfp mutations interacted synergistically to produce highly pronounced ins phenotype in the ins tl mfp triple mutant. The role(s) of INS in leaf-blade organogenesis are: positive regulation of vascular patterning in leaflets, repression of UNI activity in leaflet primordia for ectopic growth and in leaf-blade primordium for indeterminate growth of rachis, delimitation of proximal leaflet domain and together with TL and MFP homeostasis for meristematic activity in leaflet primordia. The variant apically bifid shape of the affected ins leaflets demonstrated that the leaflet shape is dependent on the venation pattern.

Genome-wide analysis of gene expression in soybean shoot apical meristem

The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs. The nature of genetic programs and the regulatory networks underlying SAM function in a major legume crop, soybean was investigated here. We used soybean GeneChip (containing 37,744 probe sets) to examine the transcript profiles associated with micro-dissected, actively growing SAMs or growth arrested axillary meristems (AMs) experiencing apical dominance, in comparison to that of non-meristem (NM) tissue. A total of 1,090 and 1,523 transcripts were identified to be significantly up- or down-regulated in the SAM in comparison to the NM. RT-PCR and in situ hybridization analysis were also carried out to verify the experimental approach. The resulting gene expression profiles point to the combinatorial role of diverse regulatory pathways including those associated with cell division and proliferation, epigenetic regulation, auxin-mediated responses and microRNA regulation in meristem function. In situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene, ANGUSITFOLIA3 that could potentially serve as a novel marker for differentiating cells in the meristem. Computational analysis on the promoter regions of Arabidopsis thaliana orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our data show that plant meristems possess a unique transcriptional profile, with shared "molecular signatures" in apical and axillary meristems providing a rich source of novel target genes for further studies into a fundamental process that impacts plant growth and crop productivity.

Megaphylls, microphylls and the evolution of leaf development

Originally coined to emphasize morphological differences, 'microphyll' and 'megaphyll' became synonymous with the idea that vascular plant leaves are not homologous. Although it is now accepted that leaves evolved independently in several euphyllophyte lineages, 'megaphyll' has grown to reflect another type of homology, that of euphyllophyte leaf precursor structures. However, evidence from the fossil record and developmental pathways fails to indicate homology and suggests homoplasy of precursor structures. Thus, as I discuss here, 'megaphyll' should be abandoned because it perpetuates an unsupported idea of homology, leading to misconceptions that pervade plant biology thinking and can bias hypothesis and inference in developmental and phylogenetic studies. Alternative definitions are needed that are based on development and phylogeny for different independently evolved leaf types.

Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

BACKGROUND

The Wuschel related homeobox (WOX) family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG) using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken.

RESULTS

The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation.

CONCLUSION

Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most likely by preventing premature differentiation. The future use of Ostreococcus tauri and Physcomitrella patens as biological models should allow us to obtain a better insight into the functional importance of WOX13 OG genes.

Plant development revolves around axes

Arabidopsis thaliana has become a paradigm for dicot embryo development, despite its embryology being non-representative of dicots in general. The recent cloning of heterologous genes involved in embryonic development from maize and construction of robust phylogenies has shed light on the conservation of transcription factor function and now facilitates a comparison of maize and Arabidopsis embryogenesis orthology. In this review, we focus on a comparison of expression domains of WUSCHEL HOMEOBOX LIKE (WOX), SHOOTMERISTEMLESS (STM), DORNROESCHEN (DRN) and CUP-SHAPED COTYLEDON (CUC) genes and their role in axialization in both species, showing that despite significantly divergent modes of embryogenesis, most notably in terms of axes and planes of symmetry, there is considerable conservation of function as well as notable differences between maize and Arabidopsis.