(Why) Does Evolution Favour Embryogenesis?

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.

The tri-flow adaptiveness of codes in major evolutionary transitions

Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.

A DELAY OF GERMINATION 1 (DOG1)-like protein regulates spore germination in the moss Physcomitrium patens

DELAY OF GERMINATION 1 is a key regulator of dormancy in flowering plants before seed germination. Bryophytes develop haploid spores with an analogous function to seeds. Here, we investigate whether DOG1 function during germination is conserved between bryophytes and flowering plants and analyse the underlying mechanism of DOG1 action in the moss Physcomitrium patens. Phylogenetic and in silico expression analyses were performed to identify and characterise DOG1 domain-containing genes in P. patens. Germination assays were performed to characterise a Ppdog1-like1 mutant, and replacement with AtDOG1 was carried out. Yeast two-hybrid assays were used to test the interaction of the PpDOG1-like protein with DELLA proteins from P. patens and A. thaliana. P. patens possesses nine DOG1 domain-containing genes. The DOG1-like protein PpDOG1-L1 (Pp3c3_9650) interacts with PpDELLAa and PpDELLAb and the A. thaliana DELLA protein AtRGA in yeast. Protein truncations revealed the DOG1 domain as necessary and sufficient for interaction with PpDELLA proteins. Spores of Ppdog1-l1 mutant germinate faster than wild type, but replacement with AtDOG1 reverses this effect. Our data demonstrate a role for the PpDOG1-LIKE1 protein in moss spore germination, possibly alongside PpDELLAs. This suggests a conserved DOG1 domain function in germination, albeit with differential adaptation of regulatory networks in seed and spore germination.

The greening ashore

More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.

Diverse and complex developmental mechanisms of early Ediacaran embryo-like fossils from the Weng'an Biota, southwest China

The origin and early evolution of animal development remain among the many deep, unresolved problems in evolutionary biology. As a compelling case for the existence of pre-Cambrian animals, the Ediacaran embryo-like fossils (EELFs) from the Weng'an Biota (approx. 609 Myr old, Doushantuo Formation, South China) have great potential to cast light on the origin and early evolution of animal development. However, their biological implications can be fully realized only when their phylogenetic positions are correctly established, and unfortunately, this is the key problem under debate. As a significant feature of developmental biology, the cell division pattern (CDP) characterized by the dynamic spatial arrangement of cells and associated developmental mechanisms is critical to reassess these hypotheses and evaluate the diversity of the EELFs; however, their phylogenetic implications have not been fully realized. Additionally, the scarcity of fossil specimens representing late developmental stages with cell differentiation accounts for much of this debate too. Here, we reconstructed a large number of EELFs using submicron resolution X-ray tomographic microscopy and focused on the CDPs and associated developmental mechanisms as well as features of cell differentiation. Four types of CDPs and specimens with cell differentiation were identified. Contrary to the prevailing view, our results together with recent studies suggest that the diversity and complexity of developmental mechanisms documented by the EELFs are much higher than is often claimed. The diverse CDPs and associated development features including palintomic cleavage, maternal nutrition, asymmetric cell divisions, symmetry breaking, establishment of polarity or axis, spatial cell migration and differentiation constrain some, if not all, EELFs as total-group metazoans.

This article is part of the theme issue ‘The impact of Chinese palaeontology on evolutionary research’.

Flowering plant embryos: How did we end up here?

The seeds of flowering plants are sexually produced propagules that ensure dispersal and resilience of the next generation. Seeds harbor embryos, three dimensional structures that are often miniatures of the adult plant in terms of general structure and primordial organs. In addition, embryos contain the meristems that give rise to post-embryonically generated structures. However common, flowering plant embryos are an evolutionary derived state. Flowering plants are part of a much larger group of embryo-bearing plants, aptly termed Embryophyta. A key question is what evolutionary trajectory led to the emergence of flowering plant embryos. In this opinion, we deconstruct the flowering plant embryo and describe the current state of knowledge of embryos in other plant lineages. While we are far yet from understanding the ancestral state of plant embryogenesis, we argue what current knowledge may suggest and how the knowledge gaps may be closed.

Genome sequencing of the multicellular alga Astrephomene provides insights into convergent evolution of germ-soma differentiation

Germ-soma differentiation evolved independently in many eukaryotic lineages and contributed to complex multicellular organizations. However, the molecular genetic bases of such convergent evolution remain unresolved. Two multicellular volvocine green algae, Volvox and Astrephomene, exhibit convergent evolution of germ-soma differentiation. The complete genome sequence is now available for Volvox, while genome information is scarce for Astrephomene. Here, we generated the de novo whole genome sequence of Astrephomene gubernaculifera and conducted RNA-seq analysis of isolated somatic and reproductive cells. In Volvox, tandem duplication and neofunctionalization of the ancestral transcription factor gene (RLS1/rlsD) might have led to the evolution of regA, the master regulator for Volvox germ-soma differentiation. However, our genome data demonstrated that Astrephomene has not undergone tandem duplication of the RLS1/rlsD homolog or acquisition of a regA-like gene. Our RNA-seq analysis revealed the downregulation of photosynthetic and anabolic gene expression in Astrephomene somatic cells, as in Volvox. Among genes with high expression in somatic cells of Astrephomene, we identified three genes encoding putative transcription factors, which may regulate somatic cell differentiation. Thus, the convergent evolution of germ-soma differentiation in the volvocine algae may have occurred by the acquisition of different regulatory circuits that generate a similar division of labor.

Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture

Functional and architectural diversification of transcription factor families has played a central role in the independent evolution of complex development in plants and animals. Here, we investigate the role of architectural constraints on evolution of B3 DNA binding domains that regulate plant embryogenesis. B3 domains of ABI3, FUS3, LEC2 and VAL1 proteins recognize the same cis-element. Complex architectures of ABI3 and VAL1 integrate cis-element recognition with other signals, whereas LEC2 and FUS3 have reduced architectures conducive to roles as pioneer activators. In yeast and plant in vivo assays, B3 domain functions correlate with architectural complexity of the parent transcription factor rather than phylogenetic relatedness. In a complex architecture, attenuated ABI3-B3 and VAL1-B3 activities enable integration of cis-element recognition with hormone signaling, whereas hyper-active LEC2-B3 and FUS3-B3 over-ride hormonal control. Three clade-specific amino acid substitutions (β4-triad) implicated in interactions with the DNA backbone account for divergence of LEC2-B3 and ABI3-B3. We find a striking correlation between differences in in vitro DNA binding affinity and in vivo activities of B3 domains in plants and yeast. Our results highlight the role of DNA backbone interactions that preserve DNA sequence specificity in adaptation of B3 domains to functional constraints associated with domain architecture.

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.

Embryo-Like Features in Developing Bacillus subtilis Biofilms

Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.

The Impacts of Symmetry in Architecture and Urbanism: Toward a New Research Agenda

Architecture has an ancient relationship to mathematics, and symmetry—in the broad sense of the term—is a core topic of both. Yet the contemporary application of theories of symmetry to architecture and built environments is a surprisingly immature area of research. At the same time, research is showing a divergence between the benefits of and preferences for natural environments on the one hand, and built environments on the other, demonstrating relatively deleterious effects of many contemporary built environments. Yet the research cannot yet pinpoint the actual geometric factors of architecture and urbanism that could produce such an important divergence. This paper explores this research gap, surveying the literature across a range of fields, and assessing current evidence for the impacts of symmetry in the built environment upon human perception and well-being. As an emerging case study, it considers the recent work by Christopher Alexander and Nikos Salingaros, two trained mathematicians who have made notable contributions to architecture and urbanism. The conclusion proposes a new research agenda toward further development of this immature subject area.

Molecular Mechanisms Involved in the Multicellular Growth of Ustilaginomycetes

Multicellularity is defined as the developmental process by which unicellular organisms became pluricellular during the evolution of complex organisms on Earth. This process requires the convergence of genetic, ecological, and environmental factors. In fungi, mycelial and pseudomycelium growth, snowflake phenotype (where daughter cells remain attached to their stem cells after mitosis), and fruiting bodies have been described as models of multicellular structures. Ustilaginomycetes are Basidiomycota fungi, many of which are pathogens of economically important plant species. These fungi usually grow unicellularly as yeasts (sporidia), but also as simple multicellular forms, such as pseudomycelium, multicellular clusters, or mycelium during plant infection and under different environmental conditions: Nitrogen starvation, nutrient starvation, acid culture media, or with fatty acids as a carbon source. Even under specific conditions, Ustilago maydis can form basidiocarps or fruiting bodies that are complex multicellular structures. These fungi conserve an important set of genes and molecular mechanisms involved in their multicellular growth. In this review, we will discuss in-depth the signaling pathways, epigenetic regulation, required polyamines, cell wall synthesis/degradation, polarized cell growth, and other cellular-genetic processes involved in the different types of Ustilaginomycetes multicellular growth. Finally, considering their short life cycle, easy handling in the laboratory and great morphological plasticity, Ustilaginomycetes can be considered as model organisms for studying fungal multicellularity.

Evo-physio: on stress responses and the earliest land plants

Embryophytes (land plants) can be found in almost any habitat on the Earth's surface. All of this ecologically diverse embryophytic flora arose from algae through a singular evolutionary event. Traits that were, by their nature, indispensable for the singular conquest of land by plants were those that are key for overcoming terrestrial stressors. Not surprisingly, the biology of land plant cells is shaped by a core signaling network that connects environmental cues, such as stressors, to the appropriate responses-which, thus, modulate growth and physiology. When did this network emerge? Was it already present when plant terrestrialization was in its infancy? A comparative approach between land plants and their algal relatives, the streptophyte algae, allows us to tackle such questions and resolve parts of the biology of the earliest land plants. Exploring the biology of the earliest land plants might shed light on exactly how they overcame the challenges of terrestrialization. Here, we outline the approaches and rationale underlying comparative analyses towards inferring the genetic toolkit for the stress response that aided the earliest land plants in their conquest of land.

TALE homeobox heterodimer GSM1/GSP1 is a molecular switch that prevents unwarranted genetic recombination in Chlamydomonas

Eukaryotic sexual life cycles alternate between haploid and diploid stages, the transitions between which are delineated by cell fusion and meiotic division. Transcription factors in the TALE-class homeobox family, GSM1 and GSP1, predominantly control gene expression for the haploid-to-diploid transition during sexual reproduction in the unicellular green alga, Chlamydomonas reinhardtii. To understand the roles that GSM1 and GSP1 play in zygote development, we used gsm1 and gsp1 mutants and examined fused gametes that normally undergo the multiple organellar fusions required for the genetic unity of the zygotes. In gsm1 and gsp1 zygotes, no fusion was observed for the nucleus and chloroplast. Surprisingly, mitochondria and endoplasmic reticulum, which undergo dynamic autologous fusion/fission, did not undergo heterologous fusions in gsm1 or gsp1 zygotes. Furthermore, the mutants failed to resorb their flagella, an event that normally renders the zygotes immotile. When gsm1 and gsp1 zygotes resumed the mitotic cycle, their two nuclei fused prior to mitosis, but neither chloroplastic nor mitochondrial fusion took place, suggesting that these fusions are specifically turned on by GSM1/GSP1. Taken together, this study shows that organellar restructuring during zygotic diploidization does not occur by default but is triggered by a combinatorial switch, the GSM1/GSP1 dyad. This switch may represent an ancient mechanism that evolved to restrict genetic recombination during sexual development.

Multicellular growth of the Basidiomycota phytopathogen fungus Sporisorium reilianum induced by acid conditions

Fungi are considered model organisms for the analysis of important phenomena of eukaryotes. For example, some of them have been described as models to understand the phenomenon of multicellularity acquisition by different unicellular organisms phylogenetically distant. Interestingly, in this work, we describe the multicellular development in the model fungus S. reilianum. We observed that Sporisorium reilianum, a Basidiomycota cereal pathogen that at neutral pH grows with a yeast-like morphology during its saprophytic haploid stage, when incubated at acid pH grew in the form of multicellular clusters. The multicellularity observed in S. reilianum was of clonal type, where buds of "stem" cells growing as yeasts remain joined by their cell wall septa, after cytokinesis. The elaboration and analysis of a regulatory network of S. reilianum showed that the putative zinc finger transcription factor CBQ73544.1 regulates a number of genes involved in cell cycle, cellular division, signal transduction pathways, and biogenesis of cell wall. Interestingly, homologous of these genes have been found to be regulated during Saccharomyces cerevisiae multicellular growth. In adddition, some of these genes were found to be negatively regulated during multicellularity of S. reilianum. With these data, we suggest that S. reilianum is an interesting model for the study of multicellular development.

Embryogenesis of flattened colonies implies the innovation required for the evolution of spheroidal colonies in volvocine green algae

Background

Volvocine algae provide a suitable model for investigation of the evolution of multicellular organisms. Within this group, evolution of the body plan from flattened to spheroidal colonies is thought to have occurred independently in two different lineages, Volvocaceae and Astrephomene. Volvocacean species undergo inversion to form a spheroidal cell layer following successive cell divisions during embryogenesis. During inversion, the daughter protoplasts change their shape and develop acute chloroplast ends (opposite to basal bodies). By contrast, Astrephomene does not undergo inversion; rather, its daughter protoplasts rotate during successive cell divisions to form a spheroidal colony. However, the evolutionary pathways of these cellular events involved in the two tactics for formation of spheroidal colony are unclear, since the embryogenesis of extant volvocine genera with ancestral flattened colonies, such as Gonium and Tetrabaena, has not previously been investigated in detail.

Results

We conducted time-lapse imaging by light microscopy and indirect immunofluorescence microscopy with staining of basal bodies, nuclei, and microtubules to observe embryogenesis in G. pectorale and T. socialis, which form 16-celled or 4-celled flattened colonies, respectively. In G. pectorale, a cup-shaped cell layer of the 16-celled embryo underwent gradual expansion after successive cell divisions, with the apical ends (position of basal bodies) of the square embryo’s peripheral protoplasts separated from each other. In T. socialis, on the other hand, there was no apparent expansion of the daughter protoplasts in 4-celled embryos after successive cell divisions, however the two pairs of diagonally opposed daughter protoplasts shifted slightly and flattened after hatching. Neither of these two species exhibited rotation of daughter protoplasts during successive cell divisions as in Astrephomene or the formation of acute chloroplast ends of daughter protoplasts as in volvocacean inversion.

Conclusions

The present results indicate that the ancestor of Astrephomene might have newly acquired the rotation of daughter protoplasts after it diverged from the ancestor of Gonium, while the ancestor of Volvocaceae might have newly acquired the formation of acute chloroplast ends to complete inversion after divergence from the ancestor of Goniaceae (Gonium and Astrephomene).

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1452-x) contains supplementary material, which is available to authorized users.

Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae

Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators. The genome-wide annotation of these protein families has been analyzed and made available via the novel TAPscan web interface. We find that many TAP families previously thought to be specific for land plants actually evolved in streptophyte (charophyte) algae; 26 out of 36 TAP family gains are inferred to have occurred in the common ancestor of the Streptophyta (uniting the land plants—Embryophyta—with their closest algal relatives). In contrast, expansions of TAP families were found to occur throughout streptophyte evolution. 17 out of 76 expansion events were found to be common to all land plants and thus probably evolved concomitant with the water-to-land-transition.

Great moments in evolution: the conquest of land by plants

500Ma ago the terrestrial habitat was a barren, unwelcoming place for species other than, for example, bacteria or fungi. Most probably, filamentous freshwater algae adapted to aerial conditions and eventually conquered land. Adaptation to a severely different habitat apparently included sturdy cell walls enabling an erect body plan as well as protection against abiotic stresses such as ultraviolet radiation, drought and varying temperature. To thrive on land, plants probably required more elaborate signaling pathways to react to diverse environmental conditions, and phytohormones to control developmental programs. Many such plant-typical features have been studied in flowering plants, but their evolutionary origins were long clouded. With the sequencing of a moss genome a decade ago, inference of ancestral land plant states using comparative genomics, phylogenomics and evolutionary developmental approaches began in earnest. In the past few years, the ever increasing availability of genomic and transcriptomic data of organisms representing the earliest common ancestors of the plant tree of life has much informed our understanding of the conquest of land by plants.

lncRNAs in Plant and Animal Sexual Reproduction

Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length with no discernible protein-coding potential. Multiple lines of evidence point to lncRNAs as master regulators, controlling the expression of protein-coding genes. Studies in plants and animals consistently show high expression of lncRNAs in reproductive organs in a cell- and tissue-specific manner. Sexual reproduction is a complex process that involves cell fate specification and specialized cell division requiring precise coordination of gene expression in response to intrinsic and extrinsic signals. The roles of lncRNAs as master regulators of gene expression and chromatin organization might make them particularly suited for coordination and control of molecular processes involved in sexual reproduction.

The cytoskeleton regulates symmetry transitions in moving amoeboid cells

Symmetry and symmetry breaking are essential in biology. Symmetry comes in different forms: rotational symmetry, mirror symmetry and alternating right/left symmetry. Especially the transitions between the different symmetry forms specify crucial points in cell biology, including gastrulation in development, formation of the cleavage furrow in cell division, or the front in cell polarity. However, the mechanisms of these symmetry transitions are not well understood. Here we have investigated the fundaments of symmetry and symmetry transitions of the cytoskeleton during cell movement. Our data show that the dynamic shape changes of amoeboid cells are far from random, but are the consequence of refined symmetries and symmetry changes that are orchestrated by small G-proteins and the cytoskeleton, with local stimulation by F-actin and Scar , and local inhibition by IQGAP2 and myosin.

Why we need more non-seed plant models

Contents 355 I. 355 II. 356 III. 356 IV. 357 V. 358 VI. 359 359 References 359 SUMMARY: Out of a hundred sequenced and published land plant genomes, four are not of flowering plants. This severely skewed taxonomic sampling hinders our comprehension of land plant evolution at large. Moreover, most genetically accessible model species are flowering plants as well. If we are to gain a deeper understanding of how plants evolved and still evolve, and which of their developmental patterns are ancestral or derived, we need to study a more diverse set of plants. Here, I thus argue that we need to sequence genomes of so far neglected lineages, and that we need to develop more non-seed plant model species.

The First Darwinian Phylogenetic Tree of Plants

In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first phylogenetic trees for the plant kingdom that Haeckel created as part of this two-volume work.

The evolution of the plant genome-to-morphology auxin circuit

In his Generelle Morphologie der Organismen (1866), 150 years ago, Ernst Haeckel (1834-1919) combined developmental patterns in animals with the concept of organismic evolution, and 50 years ago, a new era of plant research started when focus shifted from crop species (sunflower, maize etc.) to thale cress (Arabidopsis thaliana) as a model organism. In this contribution, we outline the general principles of developmental evolutionary biology sensu Haeckel and describe the evolutionary genome-to-morphology-plant hormone auxin (IAA, indole-3-acetic acid)-circuit with reference to other phytohormones and a focus on land plants (embryophytes) plus associated epiphytic microbes. Our primary conclusion is that a system-wide approach is required to truly understand the ontogeny of any organism, because development proceeds according to signal pathways that integrate and respond to external as well as internal stimuli. We also discuss IAA-regulated embryology in A. thaliana and epigenetic phenomena in the gametophyte development, and outline how these processes are connected to the seminal work of Ernst Haeckel.

A Comprehensive Phylogeny Reveals Functional Conservation of the UV-B Photoreceptor UVR8 from Green Algae to Higher Plants

Ultraviolet-B (UV-B) is present in sunlight (280-315 nm) and has diverse effects on living organisms. Low fluence rate of exposure induces a specific photomorphogenic response regulated by the UV-B response locus 8 (UVR8) receptor. UVR8 was first described in Arabidopsis thaliana. In the absence of stimuli it is located in the cytoplasm as a homodimer. However, upon UV-B irradiation, it switches to a monomer and interacts with the ubiquitin ligase E3 COP1 via the UVR8 β-propeller domain and the VP core. This induces the expression of the transcription factor HY5 leading to changes in the expression of genes associated with UV-B acclimation and stress tolerance. UVR8 senses UV-B through tryptophan residues being Trp233 and 285 the most important. Based on the comparison and analysis of UVR8 functionally important motifs, we report a comprehensive phylogeny of UVR8, trying to identify UVR8 homologs and the ancestral organism where this gene could be originated. Results obtained showed that Chlorophytes are the first organisms from the Viridiplantae group where UVR8 appears. UVR8 is present in green algae, bryophytes, lycophytes, and angiosperms. All the sequences identified contain tryptophans 233 and 285, arginines involved in homodimerization and the VP domain suggesting they are true UVR8 photoreceptors. We also determined that some species from bryophytes and angiosperms contain more than one UVR8 gene copy posing the question if UVR8 could constitute a gene family in these species. In conclusion, we described the functional conservation among UVR8 proteins from green algae to higher plants.