Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures

Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), in Arabidopsis. FT is expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed with FT and whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, the FT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The master FT regulator, CONSTANS (CO), controls FLP1 expression, suggesting FLP1's involvement in the photoperiod pathway. FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA 3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions.

High promoter sequence variation in subgroup 6 members of R2R3-MYB genes is involved in different floral anthocyanin color patterns in Lilium spp

The spatially and temporally distinct expression of R2R3-MYB positive regulators is among the major mechanisms that create various anthocyanin color patterns in many flowers. However, we do not know how these positive regulators have gained different expression profiles. In the Asiatic hybrid lily 'Lollypop' (derived from the crosses of species belonging to Sinomartagon/Daurolirion section), MYB12 and MYB19S regulate the pigmentation at whole tepals and raised tepal spots, respectively. In the Oriental hybrid lily 'Sorbonne' (derived from the crosses of species belonging to the Archelirion section), MYB12 regulates both whole tepal and raised spot pigmentation. The genes have similar amino acid sequences with similar protein functions but exhibit different expression profiles in lily flowers. As promoters are among the most significant factors affecting gene expression profiles, their promoter sequences were determined in this study. The three genes had very different promoter sequences, and putative cis-regulatory elements were not conserved in numbers or order. To further confirm the promoter functions, tobacco plants were transformed with native promoter-driven MYB12 or MYB19S genes of 'Lollypop.' Expression levels of MYB12 were higher in corolla tubes than in lobes, while those of MYB19S were higher in corolla lobes than in tubes. Thus, the diverse promoter functions were likely to be the leading causes of their different expression profiles and generation of unique color patterns. Finally, the history of R2R3-MYB gene establishment during lily evolution was estimated using sequence data.

Homologs of LEAFY and UNUSUAL FLORAL ORGANS Promote the Transition From Inflorescence to Floral Meristem Identity in the Cymose Aquilegia coerulea

Homologs of the transcription factor LEAFY (LFY) and the F-box family member UNUSUAL FLORAL ORGANS (UFO) have been found to promote floral meristem identity across diverse dicot model systems. The lower eudicot model Aquilegia produces cymose inflorescences that are independently evolved from the well-studied cymose models Petunia and tomato. We have previously characterized the expression pattern of the Aquilegia homolog AqLFY but in the current study, we add expression data on the two UFO homologs, AqUFO1 and 2, and conduct virus-induced gene silencing of all the loci. Down-regulation of AqLFY or AqUFO1 and 2 does not eliminate floral meristem identity but, instead, causes the transition from inflorescence to floral identity to become gradual rather than discrete. Inflorescences in down-regulated plants generate several nodes of bract/sepal chimeras and, once floral development does commence, flowers initiate several whorls of sepals before finally producing the wildtype floral whorls. In addition, silencing of AqUFO1/2 appears to specifically impact petal identity and/or the initiation of petal and stamen whorls. In general, however, there is no evidence for an essential role of AqLFY or AqUFO1/2 in transcriptional activation of the B or C gene homologs. These findings highlight differences between deeply divergent dicot lineages in the functional conservation of the floral meristem identity program.

Interspersed 5'cis-regulatory elements ascertain the spatio-temporal transcription of cytoskeletal profilin gene family in Arabidopsis

Spatio-temporal expression patterns of cytoskeleton-associated profilin (PRF) family proteins in response to varied environmental stimuli are tightly regulated. Functional analyses of PRFs have revealed their crucial roles in varied developmental and stress related traits, but very little is implicit pertaining to cis-acting regulatory elements that regulate such intricate expression patterns. Here, we identified cis-elements with their varying distribution frequencies by scanning 1.5kbp upstream sequences of 5'regulatory regions of PRFs of dicot and monocot plant species. Predicted cis-elements in the regulatory sub-regions of Arabidopsis PRFs (AtPRFs) were predominantly associated with development-responsive motifs (DREs), light responsive elements (LREs), hormonal responsive elements (HREs), core motifs and stress-responsive elements (SREs). Interestingly, DREs, LREs and core promoter motifs, were extensively distributed up to the distal end of 5'regulatory regions on contrary to HREs present closer to the translational start site in Arabidopsis. The evolutionary footprints of predicted orthologous cis-elements were conserved, and preferably located in the proximal regions of 5'regulatory regions of evolutionarily diverged plant species. We also explored comprehensive tissue-specific global gene expression levels of PRFs under diverse hormonal and abiotic stress regimes. In response, the PRFs exhibited large transcriptional biases in a time- and organ-dependent manner. Further, the methodical elucidation of spatial expression analysis of predicted cis-elements binding transcription factors and relevant PRFs showed notable correlation. Results indicate that binding transcription factors' expression data is largely informative for envisaging their precise roles in the spatial regulation of target PRFs. These results highlight the importance of PRFs during plant development; and establish a relationship between their spatial expression patterns and presence of respective regulatory motifs in their promoter sequences. This information could be employed in future studies and field-utilization of cell wall structural genes.

Chromatin Evolution-Key Innovations Underpinning Morphological Complexity

The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.

Two genetic changes in cis-regulatory elements caused evolution of petal spot position in Clarkia

A major premise in evolutionary developmental biology is that regulatory changes, often involving cis-regulatory elements, are responsible for much morphological evolution. This premise is supported by recent investigations of animal development, but information is just beginning to accumulate regarding whether it also applies to the evolution of plant morphology^1-4. Here, we identify the genetic differences between species in the genus Clarkia that are responsible for evolutionary change in an ecologically important element of floral colour patterns: spot position. The evolutionary shift in spot position was due to two simple genetic changes that resulted in the appearance of a transcription factor binding site mutation in the R2R3 Myb gene that changes spot formation. These genetic changes caused R2R3 Myb to be activated by a different transcription factor that is expressed in a different position in the petal. These results suggest that the regulatory rewiring paradigm is as applicable to plants as it is to animals, and support the hypothesis that cis-regulatory changes may often play a role in plant morphological evolution.

Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta

A conserved genetic toolkit underlies the development of diverse floral forms among angiosperms. However, the degree of conservation vs divergence in the configuration of these gene regulatory networks is less clear. We addressed this question in a parallel genetic study between the closely related species Arabidopsis thaliana and Cardamine hirsuta. We identified leafy (lfy) and apetala1 (ap1) alleles in a mutant screen for floral regulators in C. hirsuta. C. hirsuta lfy mutants showed a complete homeotic conversion of flowers to leafy shoots, mimicking lfy ap1 double mutants in A. thaliana. Through genetic and molecular experiments, we showed that AP1 activation is fully dependent on LFY in C. hirsuta, by contrast to A. thaliana. Additionally, we found that LFY influences heteroblasty in C. hirsuta, such that loss or gain of LFY function affects its progression. Overexpression of UNUSUAL FLORAL ORGANS also alters C. hirsuta leaf shape in an LFY-dependent manner. We found that LFY and AP1 are conserved floral regulators that act nonredundantly in C. hirsuta, such that LFY has more obvious roles in floral and leaf development in C. hirsuta than in A. thaliana.

Key developmental transitions during flower morphogenesis and their regulation

The arrangement of flowers on flowering stems called inflorescences contributes to the beauty of the natural world and enhances seed yield, impacting species survival and human sustenance. During the reproductive phase, annual/monocarpic plants like Arabidopsis and most crops form two types of lateral structures: indeterminate lateral inflorescences and determinate flowers. Their stereotypical arrangement on the primary inflorescence stem determines the species-specific inflorescence architecture. This architecture can be modulated in response to environmental cues to enhance reproductive success. Early botanists already appreciated that flowers and lateral inflorescences are analogous structures that are interconvertible. Here I will discuss the molecular underpinnings of these observations and explore the regulatory logic of the developmental fate transitions that lead to the formation of a flower.

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation

One of the most remarkable manifestations of plant evolution is the diversity for floral branching systems. These “inflorescences” arise from stem cell populations in shoot meristems that mature gradually to reproductive states in response to environmental and endogenous signals. The morphology of the shoot meristem maturation process is conserved across distantly related plants, raising the question of how diverse inflorescence architectures arise from seemingly common maturation programs. In tomato and related nightshades (Solanaceae), inflorescences range from solitary flowers to highly branched structures bearing hundreds of flowers. Since reproductive barriers between even closely related Solanaceae have precluded a genetic dissection, we captured and compared meristem maturation transcriptomes from five domesticated and wild species reflecting the evolutionary continuum of inflorescence complexity. We find these divergent species share hundreds of dynamically expressed genes, enriched for transcription factors. Meristem stages are defined by distinct molecular states and point to modified maturation schedules underlying architectural variation. These modified schedules are marked by a peak of transcriptome expression divergence during the reproductive transition, driven by heterochronic shifts of dynamic genes, including transcriptional regulators with known roles in flowering. Thus, evolutionary diversity in Solanaceae inflorescence complexity is determined by subtle modifications of transcriptional programs during a critical transitional window of meristem maturation, which we propose underlies similar cases of plant architectural variation. More broadly, our findings parallel the recently described transcriptome “inverse hourglass” model for animal embryogenesis, suggesting both plant and animal morphological variation is guided by a mid-development period of transcriptome divergence.

Petunia, Your Next Supermodel?

Plant biology in general, and plant evo-devo in particular would strongly benefit from a broader range of available model systems. In recent years, technological advances have facilitated the analysis and comparison of individual gene functions in multiple species, representing now a fairly wide taxonomic range of the plant kingdom. Because genes are embedded in gene networks, studying evolution of gene function ultimately should be put in the context of studying the evolution of entire gene networks, since changes in the function of a single gene will normally go together with further changes in its network environment. For this reason, plant comparative biology/evo-devo will require the availability of a defined set of 'super' models occupying key taxonomic positions, in which performing gene functional analysis and testing genetic interactions ideally is as straightforward as, e.g., in Arabidopsis. Here we review why petunia has the potential to become one of these future supermodels, as a representative of the Asterid clade. We will first detail its intrinsic qualities as a model system. Next, we highlight how the revolution in sequencing technologies will now finally allows exploitation of the petunia system to its full potential, despite that petunia has already a long history as a model in plant molecular biology and genetics. We conclude with a series of arguments in favor of a more diversified multi-model approach in plant biology, and we point out where the petunia model system may further play a role, based on its biological features and molecular toolkit.