Colourful cones: how did flower colour first evolve?

DcWRKY15 positively regulates anthocyanin biosynthesis during petal coloration in Dianthus caryophyllus

Petal pigmentation in carnations is closely associated with the biosynthesis of anthocyanins. This biosynthetic process is tightly regulated by transcription factors, which activate or repress key genes involved in anthocyanin production. Here, we aim to explore the mechanisms involved in the transcriptional regulation of anthocyanin biosynthesis in carnation petals. We identified DcWRKY15 as a critical regulator influencing anthocyanin production in these petals. DcWRKY15 expression showed a strong correlation with the expression levels of genes associated with anthocyanin biosynthesis, peaking during early petal development stages. The findings from the dual-LUC, VIGS, Y1H and EMSA assays demonstrated that DcWRKY15 played a positive regulatory role in anthocyanin biosynthesis. DcWRKY15 achieved this by binding directly to the promoters of DcCHS and DcF3H, thereby enhancing their expression. Additionally, DcWRKY15 interacts with the repressor DcMYB2, which reduces its capacity to enhance anthocyanin biosynthesis, particularly during the later stages of petal development. These findings offer new insights into the molecular mechanisms responsible for petal coloration in carnations, highlighting the complex interplay between activator and repressor transcription factors.

How life became colourful: colour vision, aposematism, sexual selection, flowers, and fruits

Plants and animals are often adorned with potentially conspicuous colours (e.g. red, yellow, orange, blue, purple). These include the dazzling colours of fruits and flowers, the brilliant warning colours of frogs, snakes, and invertebrates, and the spectacular sexually selected colours of insects, fish, birds, and lizards. Such signals are often thought to utilize pre-existing sensitivities in the receiver's visual systems. This raises the question: what was the initial function of conspicuous colouration and colour vision? Here, we review the origins of colour vision, fruit, flowers, and aposematic and sexually selected colouration. We find that aposematic colouration is widely distributed across animals but relatively young, evolving only in the last ~150 million years (Myr). Sexually selected colouration in animals appears confined to arthropods and chordates, and is also relatively young (generally <100 Myr). Colourful flowers likely evolved ~200 million years ago (Mya), whereas colourful fruits/seeds likely evolved ~300 Mya. Colour vision (sensu lato) appears to be substantially older, and likely originated ~400-500 Mya in both arthropods and chordates. Thus, colour vision may have evolved long before extant lineages with fruit, flowers, aposematism, and sexual colour signals. We also find that there appears to have been an explosion of colour within the last ~100 Myr, including >200 origins of aposematic colouration across nine animal phyla and >100 origins of sexually selected colouration among arthropods and chordates.

Flavonoids and anthocyanins in seagrasses: implications for climate change adaptation and resilience

Seagrasses are a paraphyletic group of marine angiosperms and retain certain adaptations from the ancestors of all embryophytes in the transition to terrestrial environments. Among these adaptations is the production of flavonoids, versatile phenylpropanoid secondary metabolites that participate in a variety of stress responses. Certain features, such as catalytic promiscuity and metabolon interactions, allow flavonoid metabolism to expand to produce novel compounds and respond to a variety of stimuli. As marine environments expose seagrasses to a unique set of stresses, these plants display interesting flavonoid profiles, the functions of which are often not completely clear. Flavonoids will likely prove to be effective and versatile agents in combating the new host of stress conditions introduced to marine environments by anthropogenic climate change, which affects marine environments differently from terrestrial ones. These new stresses include increased sulfate levels, changes in salt concentration, changes in herbivore distributions, and ocean acidification, which all involve flavonoids as stress response mechanisms, though the role of flavonoids in combatting these climate change stresses is seldom discussed directly in the literature. Flavonoids can also be used to assess the health of seagrass meadows through an interplay between flavonoid and simple phenolic levels, which may prove to be useful in monitoring the response of seagrasses to climate change. Studies focusing on the genetics of flavonoid metabolism are limited for this group, but the large chalcone synthase gene families in some species may provide an interesting topic of research. Anthocyanins are typically studied separately from other flavonoids. The phenomenon of reddening in certain seagrass species typically focuses on the importance of anthocyanins as a UV-screening mechanism, while the role of anthocyanins in cold stress is discussed less often. Both of these stress response functions would be useful for adaptation to climate change-induced deviations in tidal patterns and emersion. However, ocean warming will likely lead to a decrease in anthocyanin content, which may impact the performance of intertidal seagrasses. This review highlights the importance of flavonoids in angiosperm stress response and adaptation, examines research on flavonoids in seagrasses, and hypothesizes on the importance of flavonoids in these organisms under climate change.

Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies

Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.

Transcriptome and WGCNA Analyses Reveal Key Genes Regulating Anthocyanin Biosynthesis in Purple Sprout of Pak Choi (Brassica rapa L. ssp. chinensis)

Chinese cabbage is rich in vitamins, fibre, and nutrients and is one of the primary vegetables consumed in autumn and winter in South Asia. 'Purple pak choi' sprouts are particularly rich in anthocyanins and are favoured by consumers. However, reports on the regulation of anthocyanin synthesis in purple pak choi sprouts do not exist. In this study, we examined the phenotypic development of purple pak choi sprouts after germination. The total anthocyanin content increased from 0.02 to 0.52 mg/g FW from days 0 to 6. RNA-seq data analysis revealed an increase in differentially expressed genes corresponding to the development of purple pak choi sprouts. Expression pattern analysis of genes associated with the anthocyanin biosynthesis pathway revealed a significant upregulation of structural genes during the purple phase, suggesting that the transcription factors PAP2 and MYBL2 may play crucial regulatory roles. BraPAP2.A03, BraTT8.A09, and BraMYBL2.A07 exhibited strong interactions with key genes in the anthocyanin biosynthesis pathway, specifically BraDFR.A09. Furthermore, the expression of BraPAP2.A03 aligned with the expression patterns of most anthocyanin biosynthesis-related genes, whereas those of BraTT8.A09 and BraMYBL2.A07 corresponded with the expression pattern of BraDFR.A09. These results provide valuable insights into regulatory mechanisms underlying anthocyanin synthesis in purple pak choi sprouts.

Transcriptome Analysis Revealed the Anabolic Regulation of Chlorophyll and Carotenoids in Curcuma alismatifolia Bracts

Curcuma alismatifolia is an attractive ornamental plant in the ginger family. Its bracts come in a variety of colors and are commonly used as cut flowers, potted plants, and landscaping. To investigate the regulation of bract pigmentation in C. alismatifolia, we examined the pigment levels of chlorophyll and carotenoids in the pure color part (PC) and variegated part (VA) of three C. alismatifolia varieties, i.e., "Siam TM Sitrone," "Chiang Mai Pink," and "Snow White." To mine the color mechanisms of the pure color and variegated parts of the bract, we conducted RNA-seq analysis on C. alismatifolia. We identified a total of 89,975 unigenes, and there were 3584 differentially expressed genes identified post-screening. Furthermore, 1858 DEGs were annotated in the GO database and 681 in the KEGG database. We pinpointed key genes responsible for the diverse bract colors in C. alismatifolia, including ZEP for carotenoid synthesis and GAGA2 in the chlorophyll synthesis pathway. This study provides valuable insights into understanding the pigmentation mechanism of bracts in C. alismatifolia and the breeding process.

The impact of thermogenesis on the origin of insect pollination

Thermogenesis in plants is the ability to raise their temperature above that of the surrounding air through metabolic processes, and is especially detected in reproductive organs. Warming benefits plants by facilitating the transmission of odours and compounds that attract insects. As a result, these plants increase their odds of being pollinated by the attracted insect. Modern thermogenesis has been reported in extant cycads and a small number of angiosperm lineages. Although thermogenesis is not directly preserved in the fossil record, it can be inferred by examining extant thermogenic plant lineages and comparing their features with those of the fossil record. We suggest that thermogenesis has probably occurred in seed plants for at least the past 200 million years, long before the origin of angiosperms. Thermogenesis in plants is an important factor that facilitated entomophilous pollination by enhancing the attraction of insects, complementary to other factors, thereby participating in the success of the two groups of organisms and providing many facets of past and recent reproductive biology for future exploration.

Comparative analysis of sipeimine content, metabolome and chloroplast genome in cultivated and wild varieties of Fritillaria taipaiensis

BACKGROUND

The wild variety Fritillaria taipaiensis E.B (EB) is known for its superior therapeutic effects, but its limited production cannot meet demand. As a result, the cultivated variety F. taipaiensis P. Y. Li (PY) has been widely grown. In this study, we conducted a comprehensive analysis comparing EB and PY in terms of external features, sipeimine content, metabolome and chloroplast genome to differentiate these two varieties.

RESULTS

Our research revealed that the petals and pods of EB are green, while those of PY have purple markings. The bulbs of EB contain significantly higher levels of sipeimine compared to those of PY. Metabolomic analysis identified 56 differentially expressed metabolites (DMs), with 23 upregulated and 33 downregulated in EB bulbs. Particularly, 3-hydroxycinnamic acid and secoxyloganin may serve as distinctive DMs. These DMs were associated with 17 KEGG pathways, including pyrimidine metabolism, alanine, aspartate and glutamate metabolism, and galactose metabolism. Differences in the length of the chloroplast genome were primarily observed in the large single-copy (LSC) region, with the largest variation in the trnH-GUC-psbA region. The placement of the trnH gene and the rps gene in proximity to the LSC/IRb boundary differs between EB and PY.

CONCLUSION

The results of this study provide valuable insights for the introduction and comprehensive development of wild F. taipaiensis from a scientific perspective. © 2024 Society of Chemical Industry.

Application of artificial neural networks to classify Avena fatua and Avena sterilis based on seed traits: insights from European Avena populations primarily from the Balkan Region

BACKGROUND

Avena fatua and A. sterilis are challenging to distinguish due to their strong similarities. However, Artificial Neural Networks (ANN) can effectively extract patterns and identify these species. We measured seed traits of Avena species from 122 locations across the Balkans and from some populations from southern, western, and central Europe (total over 22 000 seeds). The inputs for the ANN model included seed mass, size, color, hairiness, and placement of the awn attachment on the lemma.

RESULTS

The ANN model achieved high classification accuracy for A. fatua and A. sterilis (R2 > 0.99, RASE < 0.0003) with no misclassification. Incorporating geographic coordinates as inputs also resulted in successful classification (R2 > 0.99, RASE < 0.000001) with no misclassification. This highlights the significant influence of geographic coordinates on the occurrence of Avena species. The models revealed hidden relationships between morphological traits that are not easily detectable through traditional statistical methods. For example, seed color can be partially predicted by other seed traits combined with geographic coordinates. When comparing the two species, A. fatua predominantly had the lemma attachment point in the upper half, while A. sterilis had it in the lower half. A. sterilis exhibited slightly longer seeds and hairs than A. fatua, while seed hairiness and mass were similar in both species. A. fatua populations primarily had brown, light brown, and black colors, while A. sterilis populations had black, brown, and yellow colors.

CONCLUSIONS

Distinguishing A. fatua from A. sterilis based solely on individual characteristics is challenging due to their shared traits and considerable variability of traits within each species. However, it is possible to classify these species by combining multiple seed traits. This approach also has significant potential for exploring relationships among different traits that are typically difficult to assess using conventional methods.

Selection and Validation of qRT-PCR Internal Reference Genes to Study Flower Color Formation in Camellia impressinervis

Real-time quantitative PCR (qRT-PCR) is a pivotal technique for gene expression analysis. To ensure reliable and accurate results, the internal reference genes must exhibit stable expression across varied experimental conditions. Currently, no internal reference genes for Camellia impressinervis have been established. This study aimed to identify stable internal reference genes from eight candidates derived from different developmental stages of C. impressinervis flowers. We employed geNorm, NormFinder, and BestKeeper to evaluate the expression stability of these candidates, which was followed by a comprehensive stability analysis. The results indicated that CiTUB, a tubulin gene, exhibited the most stable expression among the eight reference gene candidates in the petals. Subsequently, CiTUB was utilized as an internal reference for the qRT-PCR analysis of six genes implicated in the petal pigment synthesis pathway of C. impressinervis. The qRT-PCR results were corroborated by transcriptome sequencing data, affirming the stability and suitability of CiTUB as a reference gene. This study marks the first identification of stable internal reference genes within the entire genome of C. impressinervis, establishing a foundation for future gene expression and functional studies. Identifying such stable reference genes is crucial for advancing molecular research on C. impressinervis.

Integrated transcriptome and metabolome analysis revealed that HaMYB1 modulates anthocyanin accumulation to deepen sunflower flower color

KEY MESSAGE

HanMYB1 was found to play positive roles in the modulation of anthocyanins metabolism based on the integrative analysis of different color cultivars and the related molecular genetic analyses. As a high value ornamental and edible crop with various colors, sunflowers (Helianthus annuus L.) provide an ideal system to understand the formation of flower color. Anthocyanins are major pigments in higher plants, which is associated with development of flower colors and ability of oxidation resistance. Here, we performed an integrative analysis of the transcriptome and flavonoid metabolome in five sunflower cultivars with different flower colors. According to differentially expressed genes and differentially accumulated flavonoids, these cultivars could be grouped into yellow and red. The results showed that more anthocyanins were accumulated in the red group flowers, especially the chrysanthemin. Some anthocyanins biosynthesis-related genes like UFGT (UDP-glycose flavonoid glycosyltransferase) also expressed more in the red group flowers. A MYB transcriptional factor, HanMYB1, was found to play vital positive roles in the modulation of anthocyanins metabolism by the integrative analysis. Overexpressed HanMYB1 in tobacco could deepen the flower color, increase the accumulation of anthocyanins and directly active the express of UFGT genes. Our findings indicated that the MYB transcriptional factors provide new insight into the dynamic regulation of the anthocyanin biosynthesis in facilitating sunflower color formation and anthocyanin accumulation.

Pollination syndromes and the origins of floral traits

BACKGROUND

A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes.

SCOPE

The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century.

CONCLUSIONS

The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.

Detailed Seed Cone Morpho-Anatomy Provides New Insights into Seed Cone Origin and Evolution of Podocarpaceae; Podocarpoid and Dacrydioid Clades

The study of reproductive morphology and trait evolution provides a vital insight to understand the evolutionary history of plants. The conifer family Podocarpaceae has a remarkable diversity of seed cones, with distinct morphology among the genera and with conifers in general. However, we lack a good understanding of the seed cone morpho-anatomy and trait evolution of Podocarpaceae. We investigated detailed seed cone morpho-anatomy using staining and sectioning techniques to clarify the anatomical, morphological diversity and evolution of functional traits. The presence of a fleshy receptaculum is a characteristic feature of both clades. However, species of Retrophyllum, Afrocarpus and some species of Nageia and Podocarpus form a fleshy sarcotesta-like seed coat, lacking a fleshy receptaculum. The ancestral state reconstructions show a shift between and sometimes within the genus. Although both clades demonstrate fleshiness as an ancestral trait, the shift in fleshy structures provides evidence for complex multiple evolutions of fleshy morphologies. These seed cone traits (e.g., fleshiness and size), along with the broad, flattened and well-adapted (leaf dimorphism) foliage in both clades, are largely congruent with efficient light harvesting and bird dispersal. These traits make these two clades well adapted to their environment, when growing in communities including tall and broad-leaved angiosperms (closed-canopy angiosperm forests), compared to other podocarps, making them more successful in achieving a wider distribution and species richness.

Analyzing Morphology, Metabolomics, and Transcriptomics Offers Invaluable Insights into the Mechanisms of Pigment Accumulation in the Diverse-Colored Labellum Tissues of Alpinia

Alpinia plants are widely cherished for their vibrant and captivating flowers. The unique feature of this genus lies in their labellum, a specialized floral structure resulting from the fusion of two non-fertile staminodes. However, the intricate process of pigment formation, leading to distinct color patterns in the various labellum segments of Alpinia, remains a subject of limited understanding. In this study, labellum tissues of two Alpinia species, A. zerumbet (yellow-orange flowers) and A. oxyphylla (white-purple flowers), were sampled and analyzed through morphological structure observation, metabolite analysis, and transcriptome analyses. We found that hemispherical/spherical epidermal cells and undulate cell population morphology usually display darker flower colors, while flat epidermal cells and cell populations usually exhibit lighter flower colors. Metabolomic analysis identified a high concentration of anthocyanins, particularly peonidin derivatives, in segments with orange and purple pigments. Additionally, segments with yellow pigments showed significant accumulations of flavones, flavanols, flavanones, and xanthophylls. Furthermore, our investigation into gene expression levels through qRT-PCR revealed notable differences in several genes that participated in anthocyanin and carotenoid biosynthesis among the four pigmented segments. Collectively, these findings offer a comprehensive understanding of pigmentation in Alpinia flowers and serve as a valuable resource for guiding future breeding efforts aimed at developing Alpinia varieties with novel flower colors.

Phenylpropanoid Derivatives and Their Role in Plants' Health and as antimicrobials

Phenylpropanoids belong to a wide group of compounds commonly secreted by plants and involved in different roles related with plant growth and development and the defense against plant pathogens. Some key intermediates from shikimate pathway are used to synthesize these compounds. In this way, by the phenylpropanoid pathway several building blocks are achieved to obtain flavonoids, isoflavonoids, coumarins, monolignols, phenylpropenes, phenolic acids, stilbenes and stilbenoids, and lignin, suberin and sporopollenin for plant-microbe interactions, structural support and mechanical strength, organ pigmentation, UV protection and acting against pathogens. Some reviews have revised phenylpropanoid biosynthesis and regulation of the biosynthetic pathways. In this review, the most important chemical structures about phenylpropanoid derivatives are summarized grouping them in different sections according to their structure. We have put special attention on their different roles in plants especially in plant health, growth and development and plant-environment interactions. Their interaction with microorganisms is discussed including their role as antimicrobials. We summarize all new findings about new developed structures and their involvement in plants health.

Research progress and applications of colorful Brassica crops

MAIN CONCLUSION

We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.

The evolution of flower colour

Flowers are the most commonly seen colourful elements of the natural world, and in this primer we explain the evolution of their spectacular range of colours. To understand flower colour, we first explain what colour is and how a flower can have different colours in the eyes of different observers. We briefly introduce the molecular and biochemical basis of flower colour, which is primarily based on well-characterised pigment synthesis pathways. We then consider the evolution of flower colour over four timescales - its origin and deep evolution, its macroevolution, its microevolution and finally, the recent effects of human behaviour on flower colour and its evolution. Because flower colour is so evolutionarily labile, and at the same time so striking to the human eye, it is an exciting subject for current and future research efforts.

Advances in extraction and purification of citrus flavonoids

Flavonoids are the representative active substances of citrus with various biological activities and high nutritional value. In order to evaluate and utilize citrus flavonoids, isolation and purification are necessary steps. This manuscript reviewed the research advances in the extraction and purification of citrus flavonoids. The structure classification, the plant and nutritional functions, and the biosynthesis of citrus flavonoids were summarized. The characteristics of citrus flavonoids and the selection of separation strategies were explained. The technical system of extraction and purification of citrus flavonoids was systematically described. Finally, outlook and research directions were proposed.

The MYB transcription factor RcMYB1 plays a central role in rose anthocyanin biosynthesis

Rose (Rosa hybrida) is one of most famous ornamental plants in the world, and its commodity value largely depends on its flower color. However, the regulatory mechanism underlying rose flower color is still unclear. In this study, we found that a key R2R3-MYB transcription factor, RcMYB1, plays a central role in rose anthocyanin biosynthesis. Overexpression of RcMYB1 significantly promoted anthocyanin accumulation in both white rose petals and tobacco leaves. In 35S:RcMYB1 transgenic lines, a significant accumulation of anthocyanins occurred in leaves and petioles. We further identified two MBW complexes (RcMYB1-RcBHLH42-RcTTG1; RcMYB1-RcEGL1-RcTTG1) associated with anthocyanin accumulation. Yeast one-hybrid and luciferase assays showed that RcMYB1 could active its own gene promoter and those of other EBGs (early anthocyanin biosynthesis genes) and LBGs (late anthocyanin biosynthesis genes). In addition, both of the MBW complexes enhanced the transcriptional activity of RcMYB1 and LBGs. Interestingly, our results also indicate that RcMYB1 is involved in the metabolic regulation of carotenoids and volatile aroma. In summary, we found that RcMYB1 widely participates in the transcriptional regulation of ABGs (anthocyanin biosynthesis genes), indicative of its central role in the regulation of anthocyanin accumulation in rose. Our results provide a theoretical basis for the further improvement of the flower color trait in rose by breeding or genetic modification.

Chromosomal-level genome and multi-omics dataset provides new insights into leaf pigmentation in Acer palmatum

Acer palmatum (A. palmatum), a deciduous shrub or small arbour which belongs to Acer of Aceraceae, is an excellent greening species as well as a beautiful ornamental plant. In this study, a high-quality chromosome-level reference genome for A. palmatum was constructed using Oxford Nanopore sequencing and Hi-C technology. The assembly genome was ∼745.78 Mb long with a contig N50 length of 3.20 Mb, and 95.30 % (710.71 Mb) of the assembly was anchored into 13 pseudochromosomes. A total of 28,559 protein-coding genes were obtained, ∼90.02 % (25,710) of which could be functionally annotated. The genomic evolutionary analysis revealed that A. palmatum is most closely related to A. yangbiense and A. truncatum, and underwent only an ancient gamma whole-genome duplication event. Despite lacking a recent independent WGD, 25,795 (90.32 %) genes of A. palmatum were duplicated, and the unique/expanded gene families were linked with genes involved in plant-pathogen interaction and several metabolic pathways, which might underpin adaptability. A combined genomic, transcriptomic, and metabolomic analysis related to the biosynthesis of anthocyanin in leaves during the different season were characterized. The results indicate that the dark-purple colouration of the leaves in spring was caused by a high amount of anthocyanins, especially delphinidin and its derivatives; and the red colouration of the leaves in autumn by a high amount of cyanidin 3-O-glucoside. In conclusion, these valuable multi-omic resources offer important foundations to explore the molecular regulation mechanism in leaf colouration and also provide a platform for the scientific and efficient utilization of A. palmatum.

Evolution and function of red pigmentation in land plants

BACKGROUND

Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments.

SCOPE

In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues; theories on the functions of stress-induced pigmentation; the evolution of the biosynthetic pathways; and structure-function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants.

CONCLUSIONS

The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.

Evaluation of thermoregulation of different pine organs in early spring and estimation of heat reward for the western conifer seed bug (Leptoglossus occidentalis) on male cones

The western conifer seed bug (WCSB, Leptoglossus occidentalis) is a pest of many pine species and is invasive worldwide. WCSB directly and indirectly deteriorates pine nut production by sucking seeds from cones. Currently, researchers think that WCSBs search for food by a combination of cues from visible light, infrared radiation, and chemicals such as monoterpenes. Some research revealed that WCSBs prefer larger cones, and it was thought that WCSBs suck seeds from and obtain more heat on larger cones. However, in early spring, we observed that most WCSBs gathered on male cones rather than on female cones and young cones. We hypothesized that male pine cones were warmer than female cones and needles, and WCSBs sucking male cones may receive more heat. To test these hypotheses, we measured spectral reflectance with a hyperspectral sensor and temperature of pine organs with tiny thermocouples, and the data were analyzed by a heat budget model. Our results revealed that male cones were significantly warmer and more reflective than female cones and needles, which may attract WCSBs. These results supported our hypothesis that WCSBs on male cones were warmer than those on other organs. This study will help further understanding of WCSBs and the adaptive value of pine cone colors.

Heterochrony and repurposing in the evolution of gymnosperm seed dispersal units

Background

Plant dispersal units, or diaspores, allow the colonization of new environments expanding geographic range and promoting gene flow. Two broad categories of diaspores found in seed plants are dry and fleshy, associated with abiotic and biotic dispersal agents, respectively. Anatomy and developmental genetics of fleshy angiosperm fruits is advanced in contrast to the knowledge gap for analogous fleshy structures in gymnosperm diaspores. Improved understanding of the structural basis of modified accessory organs that aid in seed dispersal will enable future work on the underlying genetics, contributing to hypotheses on the origin of angiosperm fruits. To generate a structural framework for the development and evolution of gymnosperm fleshy diaspores, we studied the anatomy and histochemistry of Ephedra (Gnetales) seed cone bracts, the modified leaves surrounding the reproductive organs. We took an ontogenetic approach, comparing and contrasting the anatomy and histology of fleshy and papery-winged seed cone bracts, and their respective pollen cone bracts and leaves in four species from the South American clade.

Results

Seed bract fleshiness in Ephedra derives from mucilage accumulated in chlorenchyma cells, also found in the reduced young leaves before they reach their mature, dry stage. Cellulosic fibers, an infrequent cell type in gymnosperms, were found in Ephedra, where they presumably function as a source of supplementary apoplastic water in fleshy seed cone bracts. Papery-winged bract development more closely resembles that of leaves, with chlorenchyma mucilage cells turning into tanniniferous cells early on, and hyaline margins further extending into “wings”.

Conclusions

We propose an evolutionary developmental model whereby fleshy and papery-winged bracts develop from an early-stage anatomy shared with leaves that differs at the pollination stage. The ancestral fleshy bract state may represent a novel differentiation program built upon young leaf anatomy, while the derived dry, papery-winged state is likely built upon an existing differentiation pattern found in mature vegetative leaves. This model for the evolution of cone bract morphology in South American Ephedra hence involves a novel differentiation program repurposed from leaves combined with changes in the timing of leaf differentiation, or heterochrony, that can further be tested in other gymnosperms with fleshy diaspores.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13227-022-00191-8.

The Effects of Ozone on Visual Attraction Traits of Erodium paularense (Geraniaceae) Flowers: Modelled Perception by Insect Pollinators

Ozone (O₃) effects on the visual attraction traits (color, perception and area) of petals are described for Erodium paularense, an endangered plant species. Plants were exposed to three O₃ treatments: charcoal-filtered air (CFA), ambient (NFA) and ambient + 40 nL L^-1 O₃ (FU+) in open-top chambers. Changes in color were measured by spectral reflectance, from which the anthocyanin reflectance index (ARI) was calculated. Petal spectral reflectance was mapped onto color spaces of bees, flies and butterflies for studying color changes as perceived by different pollinator guilds. Ozone-induced increases in petal reflectance and a rise in ARI under NFA were observed. Ambient O₃ levels also induced a partial change in the color perception of flies, with the number of petals seen as blue increasing to 53% compared to only 24% in CFA. Butterflies also showed the ability to partially perceive petal color changes, differentiating some CFA petals from NFA and FU+ petals through changes in the excitation of the UV photoreceptor. Importantly, O₃ reduced petal area by 19.8 and 25% in NFA and FU+ relative to CFA, respectively. In sensitive species O₃ may affect visual attraction traits important for pollination, and spectral reflectance is proposed as a novel method for studying O₃ effects on flower color.

Photoprotection of Arabidopsis leaves under short-term high light treatment: The antioxidant capacity is more important than the anthocyanin shielding effect

Photoprotection strategies that have evolved in plants to cope with high light (HL) stress provide plants with the ability to resist HL. However, it has not been clearly confirmed which photoprotection strategy is the major HL resistance mechanism. To reveal the major photoprotection mechanism against short-term high light (STHL), the physiological and biochemical responses of three Arabidopsis mutants (Col, chi and ans) under STHL were analyzed in this study. After STHL treatment, the most serious photosynthetic pigment damage was observed in chi plants. At the same time, the degrees of membrane and Rubisco damage in chi was the highest, followed by Col, and ans was the smallest. The results showed that ans with high antioxidant capacity showed higher resistance to STHL treatment than Col containing anthocyanins, while chi with no anthocyanin accumulation and small antioxidant capacity had the lowest resistance. In addition, the gene expression results showed that plants tend to synthesize anthocyanin precursor flavonoids with antioxidant capacity under STHL stress. To further determine the major mechanism of photoprotection under STHL, we also analyzed Arabidopsis lines (Col, CHS1, CHS2 and tt4) that had the same anthocyanin content but different antioxidant capacities. It was found that CHS2 with high antioxidant capacity had higher cell viability, smaller maximal quantum yield of PSII photochemistry (F_v/F_m) reduction and less reactive oxygen species (ROS) accumulation under HL treatment of their mesophyll protoplasts. Therefore, the antioxidant capacity provided by antioxidant substances was the major mechanism of plant photoprotection under STHL treatment.

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

BACKGROUND

Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations.

RESULTS

We generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees.

CONCLUSIONS

Despite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.

CmNAC73 Mediates the Formation of Green Color in Chrysanthemum Flowers by Directly Activating the Expression of Chlorophyll Biosynthesis Genes HEMA1 and CRD1

Chrysanthemum is one of the most beautiful and popular flowers in the world, and the flower color is an important ornamental trait of chrysanthemum. Compared with other flower colors, green flowers are relatively rare. The formation of green flower color is attributed to the accumulation of chlorophyll; however, the regulatory mechanism of chlorophyll metabolism in chrysanthemum with green flowers remains largely unknown. In this study, we performed Illumina RNA sequencing on three chrysanthemum materials, Chrysanthemum vestitum and Chrysanthemum morifolium cultivars ‘Chunxiao’ and ‘Green anna’, which produce white, light green and dark green flowers, respectively. Based on the results of comparative transcriptome analysis, a gene encoding a novel NAC family transcription factor, CmNAC73, was found to be highly correlated to chlorophyll accumulation in the outer whorl of ray florets in chrysanthemum. The results of transient overexpression in chrysanthemum leaves showed that CmNAC73 acts as a positive regulator of chlorophyll biosynthesis. Furthermore, transactivation and yeast one-hybrid assays indicated that CmNAC73 directly binds to the promoters of chlorophyll synthesis-related genes HEMA1 and CRD1. Thus, this study uncovers the transcriptional regulation of chlorophyll synthesis-related genes HEMA1 and CRD1 by CmNAC73 and provides new insights into the development of green flower color in chrysanthemum and chlorophyll metabolism in plants.

Ephedra as a gymnosperm evo-devo model lineage

Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

Regulation of MYB Transcription Factors of Anthocyanin Synthesis in Lily Flowers

Flower color is the decisive factor that affects the commercial value of ornamental flowers. Therefore, it is important to study the regulation of flower color formation in lily to discover the positive and negative factors that regulate this important trait. In this study, MYB transcription factors (TFs) were characterized to understand the regulatory mechanism of anthocyanin biosynthesis in lily. Two R2R3-MYB TFs, LvMYB5, and LvMYB1, were found to regulate anthocyanin biosynthesis in lily flowers. LvMYB5, which has an activation motif, belongs to the SG6 MYB protein subgroup of Arabidopsis thaliana. Transient expression of LvMYB5 indicated that LvMYB5 can promote coloration in Nicotiana benthamiana leaves, and that expression of LvMYB5 increases the expression levels of NbCHS, NbDFR, and NbANS. VIGS experiments in lily petals showed that the accumulation of anthocyanins was reduced when LvMYB5 was silenced. Luciferase assays showed that LvMYB5 can promote anthocyanin synthesis by activating the ANS gene promoter. Therefore, LvMYB5 plays an important role in flower coloration in lily. In addition, the transient expression experiment provided preliminary evidence that LvMYB1 (an R2R3-MYB TF) inhibits anthocyanin synthesis in lily flowers. The discovery of activating and inhibitory factors related to anthocyanin biosynthesis in lily provides a theoretical basis for improving flower color through genetic engineering. The results of our study provide a new direction for the further study of the mechanisms of flower color formation in lilies.

Integrated metabolic profiling and transcriptome analysis of pigment accumulation in diverse petal tissues in the lily cultivar 'Vivian'

BACKGROUND

Petals are the colorful region of many ornamental plants. Quality traits of petal color directly affect the value of ornamental plants. Although the regulatory mechanism of flower color has been widely studied in many plants, that of lily flower color is still worth further exploration.

RESULTS

In this study, the pigmentation regulatory network in different regions of the petal of lily cultivar 'Vivian' was analyzed through tissue structure, metabolites biosynthesis, and gene expression. We found that cell morphology of the petal in un-pigmented region differed from that in pigmented region. The cell morphology tends to flatten in un-pigmented region where the color is lighter. Moreover, high level anthocyanin was found in the pigmented regions by metabonomic analysis, especially cyanidin derivatives. However, flavanones were accumulated, contrast with anthocyanin in the un-pigmented regions of lily petal. To understand the relationship of these different metabolites and lily flower color, RNA-Seq was used to analyze the differentially expressed genes-related metabolite biosynthesis. Among these genes, the expression levels of several genes-related cyanidin derivatives biosynthesis were significantly different between the pigmented and un-pigmented regions, such as LvMYB5, LvMYB7, LvF3'H, LvDFR, LvANS and Lv3GT.

CONCLUSIONS

This data will help us to further understand the regulation network of lily petal pigmentation and create different unique color species.