Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae)

Analysis of Flavonoid Metabolism during the Process of Petal Discoloration in Three Malus Crabapple Cultivars

Malus crabapple has high ornamental and ecological value. Here, the flavonoids in the petals of three pink Malus crabapple cultivars, Malus 'Strawberry Parfait' (GD), M. 'Pink Spire' (FY), and M. 'Hongyi' (HY), at the bud stage (flower buds are swollen, and the pistils and stamens are about to appear; L), full bloom stage (the flowers are fully open, and the stigma and anthers have recently appeared; S), and end bloom stage (the stigma and anthers are dry; M) were identified, and their abundances were determined. First, Kodak Color Control Patches were used to describe the colors of petals, and a colorimeter was used to determine the phenotypic values of flower colors. Flavonoids were determined using ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). In all three crabapple cultivars, the red and yellow hues of the petals gradually disappeared, the color of the flowers changed from bright to dull, and the petals gradually faded. The extent of fading of the red hue of the petals was highest in GD, followed by FY and HY. A total of 302 metabolites were detected in the three cultivars. The content of total flavonoids in the three cultivars significantly differed, but there were no significant differences among species. The total flavonoid content of the three crabapple varieties was highest in HY, followed by FY and GD. The content of the anthocyanins delphinidin-3-O-sophoricoside-5-O-glucoside, pelargonidin-3-O-(6″-O-malonyl)glucoside, pelargonidin-3-O-glucoside, peonidin-3-O-glucoside, and cyanidin-3-O-arabinoside decreased significantly, which resulted in the discoloration of GD petals from L to M. The flavonoids and flavonols in FY might interact with anthocyanins in metabolic pathways. The content of these five anthocyanins decreased slowly, which resulted in the weaker discoloration of FY and HY compared with GD. The content of the five anthocyanins in HY did not decrease significantly, but the content of chalcone increased significantly, which might facilitate the production of anthocyanin auxiliary pigments and result in less pronounced fading of the petals. Cyanidin-3-O-arabinoside and pelargonidin-3-O-glucoside were the key flavonoids of the three crabapple cultivars. The total content and changes in anthocyanins were the key factors affecting petal color development and fading. Nonanthocyanin polyphenols, such as flavonoids, flavonols, and chalcone, are auxiliary pigments that affect petal fading. Overall, the results of this study provide new insights into the mechanism underlying the fading of the color of Malus crabapple flowers, and these new insights could aid the breeding of cultivars with different flower colors.

Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism

Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.

Transcriptomic and metabolomic analyses reveal the altitude adaptability and evolution of different-colored flowers in alpine Rhododendron species

Understanding the molecular mechanisms and evolutionary process of plant adaptation to the heterogeneous environment caused by altitude gradients in plateau mountain ecosystems can provide novel insight into species' responses to global changes. Flower color is the most conspicuous and highly diverse trait in nature. Herein, the gene expression patterns, evolutionary adaptation and metabolites changes of different-colored flowers of alpine Rhododendron L. species along altitude gradients were investigated based on a combined analysis of transcriptomics and metabolomics. Differentially expressed genes were found to be related to the biosynthesis of carbohydrates, fatty acids, amino acids and flavonoids, suggesting their important roles in the altitude adaptability of Rhododendron species. The evolution rate of high-altitude species was faster than that of low-altitude species. Genes related to DNA repair, mitogen-activated protein kinase and ABA signal transduction, and lipoic acid and propanoate metabolism were positively selected in the flowers of high-altitude Rhododendron species and those associated with carotenoid biosynthesis pathway, ABA signal transduction and ethylene signal transduction were positively selected in low-altitude species. These results indicated that the genes with differentiated expressions or functions exhibit varying evolution during the adaptive divergence of heterogeneous environment caused by altitude gradients. Flower-color variation might be attributed to the significant differences in gene expression or metabolites related to sucrose, flavonoids and carotenoids at the transcription or metabolism levels of Rhododendron species. This work suggests that Rhododendron species have multiple molecular mechanisms in their adaptation to changing environments caused by altitude gradients.

A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose (Hibiscus mutabilis)

Hibiscus mutabilis (cotton rose) is a deciduous shrub or small tree of the Malvaceae family. Here, we report a chromosome-scale assembly of the H. mutabilis genome based on a combination of single-molecule sequencing and Hi-C technology. We obtained an optimized assembly of 2.68 Gb with a scaffold N50 length of 54.7 Mb. An integrated strategy of homology-based, de novo, and transcriptome-based gene predictions identified 118,222 protein-coding genes. Repetitive DNA sequences made up 58.55% of the genome, and LTR retrotransposons were the most common repetitive sequence type, accounting for 53.15% of the genome. Through the use of Hi-C data, we constructed a chromosome-scale assembly in which Nanopore scaffolds were assembled into 46 pseudomolecule sequences. We identified important genes involved in anthocyanin biosynthesis and documented copy number variation in floral regulators. Phylogenetic analysis indicated that H. mutabilis was closely related to H. syriacus, from which it diverged approximately 15.3 million years ago. The availability of cotton rose genome data increases our understanding of the species' genetic evolution and will support further biological research and breeding in cotton rose, as well as other Malvaceae species.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.

The effects of pollination, herbivory and autonomous selfing on the maintenance of flower colour variation in Silenelittorea

Intraspecific flower colour variation has been generally proposed to evolve as a result of selection driven by biotic or abiotic agents. In a polymorphic population of Silene littorea with pink- and white-flowered plants, we studied pollinators, analysed flower colour perception and tested for differences in pollinator visitation. We also experimentally analysed pollinator limitation in fruit and seed set, and the degree of autonomous selfing. The incidence of florivory and leaf herbivory was compared over 3-4 years. Silene littorea is mainly pollinated by bees and butterflies. Pollinators preferred pink flowers, which did not show pollinator limitation. On the contrary, white flowers showed pollinator limitation in fruit set. White-flowered plants had less floral display and higher levels of florivory than pink plants. Flower colour morphs of S. littorea can reproduce in the absence of pollinators by autonomous selfing, setting 20% and 12% of fruit and seeds in the pink morph and 27% and 20% in the white morph, respectively. Fruit set of white flowers produced by autonomous selfing did not differ from open-pollinated flowers. In conclusion, S. littorea is pollinated by insects of different orders that more frequently visit pink flowers, which is reflected in pollinator limitation of fruit set in white flowers. Moreover, this species has a mixed mating system in which both colour morphs can reproduce in the absence of pollinators by autonomous selfing, although white flowers mainly produce fruits by autogamy. We suggest that reproductive assurance by autonomous selfing helps to maintain flower colour polymorphism in this population.

Changes at a Critical Branchpoint in the Anthocyanin Biosynthetic Pathway Underlie the Blue to Orange Flower Color Transition in Lysimachia arvensis

Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical analysis for blue and orange petals. Among a set of 140 structural and regulatory genes broadly representing the flavonoid biosynthetic pathway, we found 39 genes with significant differential expression including some that have previously been reported to be involved in similar flower color transitions. In particular, F3'5'H and DFR, two genes at a critical branchpoint in the ABP for determining flower color, showed differential expression. The expression results were complemented by careful examination of the SNPs that differentiate the two color types for these two critical genes. The decreased expression of F3'5'H in orange petals and differential expression of two distinct copies of DFR, which also exhibit amino acid changes in the color-determining substrate specificity region, strongly correlate with the blue to orange transition. Our biochemical analysis was consistent with the transcriptome data indicating that the shift from blue to orange petals is caused by a change from primarily malvidin to largely pelargonidin forms of anthocyanins. Overall, we have identified several flavonoid biosynthetic pathway loci likely involved in the shift in flower color in L. arvensis and even more loci that may represent the complex network of genetic and physiological consequences of this flower color polymorphism.

Integrated Metabolomics and Transcriptome Analysis of Flavonoid Biosynthesis in Safflower (Carthamus tinctorius L.) With Different Colors

Safflower is widely used in dying and in traditional medicine, and C-glucosylquinochalcones are the main metabolic species in the red color of safflower. Various safflower cultivars have flowers with different colors. However, the metabolic and transcriptional differences among safflower cultivars with different-colored flowers and the genes participating in C-glucosylquinochalcone biosynthesis are largely unknown. To provide insights on this issue, we performed integrated metabolomics and transcriptome analyses on the flavonoid biosynthesis of flowers of different colors in safflower (white-W, yellow-Y, light red-LR, and deep red-DR). The metabolic analysis showed that flavonoid metabolites showed great differences among the different colors of safflower. More flavonoid metabolic species were detected in Y and W, while C-glucosylquinochalcones were not detected in W. The content of C-glucosylquinochalcones increased with increasing color. Transcriptional analysis showed that most of the annotated flavonoid biosynthesis genes were significantly increased in W. The expression of genes related to flavonoid biosynthesis decreased with increasing color. We analyzed the candidate genes associated with C-glucosylquinochalcones, and an integration of the metabolic and transcriptional analyses indicated that the differential expression of the chalcone synthase (CHS) gene is one of the main reasons for the difference in flavonoid species and content among the different colors of safflower. Combined with the expression pattern analysis, these results indicated that HH_035319, HH_032689, and HH_018025 are likely involved in C-glucosylquinochalcones biosynthesis. In addition, we found that their expression showed greatly increased after the methyl jasmonate (MeJA) treatment. Therefore, HH_035319, HH_032689, and HH_018025 might participate in C-glucosylquinochalcone biosynthesis, which ultimately leads to the red color in safflower.

Indirect Selection on Flower Color in Silene littorea

Flower color, as other floral traits, may suffer conflicting selective pressures mediated by both mutualists and antagonists. The maintenance of intraspecific flower color variability has been usually explained as a result of direct selection by biotic agents. However, flower color might also be under indirect selection through correlated traits, since correlations among flower traits are frequent. In this study, we aimed to find out how flower color variability is maintained in two nearby populations of Silene littorea that consistently differ in the proportions of white-flowered plants. To do that, we assessed natural selection on floral color and correlated traits by means of phenotypic selection analysis and path analysis. Strong directional selection on floral display and flower production was found in both populations through either male or female fitness. Flower color had a negative indirect effect on the total male and female fitness in Melide population, as plants with lighter corollas produced more flowers. In contrast, in Barra population, plants with darker corollas produced more flowers and have darker calices, which in turn were selected. Our results suggest that the prevalence of white-flowered plants in Melide and pink-flowered plants in Barra is a result of indirect selection through correlated flower traits and not a result of direct selection of either pollinators or herbivores on color.

Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis

BACKGROUND

To understand the gene expression networks controlling flower color formation in alfalfa, flowers anthocyanins were identified using two materials with contrasting flower colors, namely Defu and Zhongtian No. 3, and transcriptome analyses of PacBio full-length sequencing combined with RNA sequencing were performed, across four flower developmental stages.

RESULTS

Malvidin and petunidin glycoside derivatives were the major anthocyanins in the flowers of Defu, which were lacking in the flowers of Zhongtian No. 3. The two transcriptomic datasets provided a comprehensive and systems-level view on the dynamic gene expression networks underpinning alfalfa flower color formation. By weighted gene coexpression network analyses, we identified candidate genes and hub genes from the modules closely related to floral developmental stages. PAL, 4CL, CHS, CHR, F3'H, DFR, and UFGT were enriched in the important modules. Additionally, PAL6, PAL9, 4CL18, CHS2, 4 and 8 were identified as hub genes. Thus, a hypothesis explaining the lack of purple color in the flower of Zhongtian No. 3 was proposed.

CONCLUSIONS

These analyses identified a large number of potential key regulators controlling flower color pigmentation, thereby providing new insights into the molecular networks underlying alfalfa flower development.

Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants.

Stability of petal color polymorphism: the significance of anthocyanin accumulation in photosynthetic tissues

BACKGROUND

Anthocyanins are the primary source of colour in flowers and also accumulate in vegetative tissues, where they have multiple protective roles traditionally attributed to early compounds of the metabolic pathway (flavonols, flavones, etc.). Petal-specific loss of anthocyanins in petals allows plants to escape from the negative pleiotropic effects of flavonoid and anthocyanins loss in vegetative organs, where they perform a plethora of essential functions. Herein, we investigate the degree of pleiotropy at the biochemical scale in a pink-white flower colour polymorphism in the shore campion, Silene littorea. We report the frequencies of pink and white individuals across 21 populations and underlying biochemical profiles of three flower colour variants: anthocyanins present in all tissues (pink petals), petal-specific loss of anthocyanins (white petals), and loss of anthocyanins in all tissues (white petals).

RESULTS

Individuals lacking anthocyanins only in petals represent a stable polymorphism in two populations at the northern edge of the species range (mean frequency 8-21%). Whereas, individuals lacking anthocyanins in the whole plant were found across the species range, yet always at very low frequencies (< 1%). Biochemically, the flavonoids detected were anthocyanins and flavones; in pigmented individuals, concentrations of flavones were 14-56× higher than anthocyanins across tissues with differences of > 100× detected in leaves. Loss of anthocyanin pigmentation, either in petals or in the whole plant, does not influence the ability of these phenotypes to synthesize flavones, and this pattern was congruent among all sampled populations.

CONCLUSIONS

We found that all colour variants showed similar flavone profiles, either in petals or in the whole plant, and only the flower colour variant with anthocyanins in photosynthetic tissues persists as a stable flower colour polymorphism. These findings suggest that anthocyanins in photosynthetic tissues, not flavonoid intermediates, are the targets of non-pollinator mediated selection.

Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

Comparative analysis of whole flower transcriptomes in the Zingiberales

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.

Global gene expression and pigment analysis of two contrasting flower color cultivars of Canna

Development of flower color in plants is a complex process. Among others, it is an important trait for ornamental flowering plants. Canna is a flowering ornamental plant of family Cannaceae. To understand the molecular mechanism of flower color development in Canna, RNA sequencing from flower tissues of two contrasting flower color cultivars, Red President (RP) and Tropical Sunrise (TS) was performed. More than 27.0 million and 19.0 million clean reads were obtained from RP and TS, respectively. The combined clean reads were assembled into 147,295 unigenes. The Canna unigenes showed maximum homology with Populus trichocarpa (26.79%). A total of 2702 unigenes expressed differentially between the two cultivars of which 1972 were up-regulated and 730 were down-regulated in RP. Phenylpropanoid and flavonoid biosynthetic processes were the significant processes in RP. Expression of a vast number of transcription factors including MYB, bHLH, ARF, and WRKY were higher in RP than TS. The expression analysis of RNA sequencing data was validated by qRT-PCR analysis. Further, concentration of measured anthocyanidins and flavonols were very low or absent in TS, corroborating largely with our transcriptome data. These findings may help in understanding flower color development in Canna and in future crop breeding program.

Digital photography provides a fast, reliable, and noninvasive method to estimate anthocyanin pigment concentration in reproductive and vegetative plant tissues

Anthocyanin pigments have become a model trait for evolutionary ecology as they often provide adaptive benefits for plants. Anthocyanins have been traditionally quantified biochemically or more recently using spectral reflectance. However, both methods require destructive sampling and can be labor intensive and challenging with small samples. Recent advances in digital photography and image processing make it the method of choice for measuring color in the wild. Here, we use digital images as a quick, noninvasive method to estimate relative anthocyanin concentrations in species exhibiting color variation. Using a consumer‐level digital camera and a free image processing toolbox, we extracted RGB values from digital images to generate color indices. We tested petals, stems, pedicels, and calyces of six species, which contain different types of anthocyanin pigments and exhibit different pigmentation patterns. Color indices were assessed by their correlation to biochemically determined anthocyanin concentrations. For comparison, we also calculated color indices from spectral reflectance and tested the correlation with anthocyanin concentration. Indices perform differently depending on the nature of the color variation. For both digital images and spectral reflectance, the most accurate estimates of anthocyanin concentration emerge from anthocyanin content‐chroma ratio, anthocyanin content‐chroma basic, and strength of green indices. Color indices derived from both digital images and spectral reflectance strongly correlate with biochemically determined anthocyanin concentration; however, the estimates from digital images performed better than spectral reflectance in terms of r² and normalized root‐mean‐square error. This was particularly noticeable in a species with striped petals, but in the case of striped calyces, both methods showed a comparable relationship with anthocyanin concentration. Using digital images brings new opportunities to accurately quantify the anthocyanin concentrations in both floral and vegetative tissues. This method is efficient, completely noninvasive, applicable to both uniform and patterned color, and works with samples of any size.

Transcriptome sequencing of Paeonia suffruticosa 'Shima Nishiki' to identify differentially expressed genes mediating double-color formation

Paeonia suffruticosa 'Shima Nishiki' is one of extremely rare double-color cultivars in the world. It usually shows the two beautiful colors of red and white in the same flower, and this trait undoubtedly makes the flowers more charming for the ornamental market. However, few studies have been done to unravel the molecular mechanisms of double-color formation in P. suffruticosa 'Shima Nishiki'. In this study, we measured the anthocyanin composition and concentration, and sequenced the transcriptomes of the red and white petals. We found that the total content of Pg-based glycosides was at a significantly higher level in the red petals. Furthermore, we assembled and annotated 92,671 unigenes. Comparative analyses of the two transcriptomes showed 227 differentially expressed genes (DEGs), among which 57 were up-regulated, and 170 were down-regulated in the red petals. Subsequently, we identified 3 DEGs and the other 6 structural genes in the anthocyanin biosynthetic pathway including PsCHS, PsCHI, PsF3H, PsF3'H, PsDFR, PsANS, PsAOMT, PsMYB, and PsWD40. Among them, PsDFR and PsMYB expressed at a significantly higher level and showed positive correlations between their expression and anthocyanin concentration in the red petals. However, PsWD40 expressed at a significantly lower level and exhibited an inverse relationship in the red petals. Furthermore, we further confirmed the relative expression of the 9 candidate genes using quantitative real-time PCR. Based on the above results, we concluded that the significant differential expression of PsDFR, PsMYB and PsWD40 may play a key role in anthocyanin concentration in the red and white petals, thereby mediating double-color formation. These data will provide a valuable resource to better understand the molecular mechanisms of double-color formation of P. suffruticosa 'Shima Nishiki'.

Flower colour polymorphism in the Mediterranean Basin: occurrence, maintenance and implications for speciation

Flower colour polymorphism (FCP) is the occurrence of at least two discrete flower colour variants in the same population. Despite a vast body of research concerning the maintenance and evolutionary consequences of FCP, only recently has the spatial variation in morph frequencies among populations been explored. Here we summarise the biochemical and genetic basis of FCP, the factors that have been proposed to explain their maintenance, and the importance of FCP and its geographic variation in the speciation process. We also review the incidence of FCP in the environmentally heterogeneous Mediterranean Basin. Nearly 88% of Mediterranean FCP species showed anthocyanin-based polymorphisms. Concerning the evolutionary mechanisms that contribute to maintain FCP, selection by pollinators is suggested in some species, but in others, selection by non-pollinator agents, genetic drift or gene flow are also found; in some cases different processes interact in the maintenance of FCP. We emphasise the role of both autonomous selfing and clonal reproduction in FCP maintenance. Mediterranean polymorphic species show mainly monomorphic populations with only a few polymorphic ones, which generate clinal or mosaic patterns of variation in FCP. No cases of species with only polymorphic populations were found. We posit that different evolutionary processes maintaining polymorphism the Mediterranean Basin will result in a continuum of geographic patterns in morph compositions and relative frequencies of FCP species.