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

De novo genome assembly and population genomics of a shrub tree Barthea barthei (Hance) krass provide insights into the adaptive color variations

Flower color is a classic example of an ecologically important trait under selection in plants. Understanding the genetic mechanisms underlying shifts in flower color can provide key insights into ecological speciation. In this study, we investigated the genetic basis of flower color divergence in Barthea barthei, a shrub tree species exhibiting natural variation in flower color. We assembled a high-quality genome assembly for B. barthei with a contig N50 of 2.39 Mb and a scaffold N50 of 16.21 Mb. The assembly was annotated with 46,430 protein-coding genes and 1,560 non-coding RNAs. Genome synteny analysis revealed two recent tetraploidization events in B. barthei, estimated to have occurred at approximately 17 and 63 million years ago. These tetraploidization events resulted in massive duplicated gene content, with over 70% of genes retained in collinear blocks. Gene family members of the core regulators of the MBW complex were significantly expanded in B. barthei compared to Arabidopsis, suggesting that these duplications may have provided raw genetic material for the evolution of novel regulatory interactions and the diversification of anthocyanin pigmentation. Transcriptome profiling of B. barthei flowers revealed differential expression of 9 transcription factors related to anthocyanin biosynthesis between the two ecotypes. Six of these differentially expressed transcription factors were identified as high-confidence candidates for adaptive evolution based on positive selection signals. This study provides insights into the genetic basis of flower color divergence and the evolutionary mechanisms underlying ecological adaptation in plants.

kakapo: easy extraction and annotation of genes from raw RNA-seq reads

kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank's single-gene databases and help assemble datasets for a variety of phylogenetic analyses.

Plant morpho evo-devo

Evo-devo is often thought of as being the study of which genes underlie which phenotypes. However, evo-devo is much more than this, especially in plant science. In leaf scars along stems, cell changes across wood growth rings, or flowers along inflorescences, plants trace a record of their own development. Plant morpho evo-devo provides data that genes could never furnish on themes such as heterochrony, the evolution of temporal phenotypes, modularity, and phenotype-first evolution. As plant science surges into increasingly -omic realms, it is essential to keep plant morpho evo-devo in full view as an honored member of the evo-devo canon, ensuring that plant scientists can, wherever they are, generate fundamental insights at the appropriate level of biological organization.

Transcriptome and metabolome analysis reveals the effect of flavonoids on flower color variation in Dendrobium nobile Lindl

Introduction

Dendrobium nobile L. is a rare orchid plant with high medicinal and ornamentalvalue, and extremely few genetic species resources are remaining in nature. In the normal purple flower population, a type of population material with a white flower variation phenotype has been discovered, and through pigment component determination, flavonoids were preliminarily found to be the main reason for the variation.

Methods

This study mainly explored the different genes and metabolites at different flowering stages and analysed the flower color variation mechanism through transcriptome- and flavonoid-targeted metabolomics. The experimental materials consisted of two different flower color phenotypes, purple flower (PF) and white flower (WF), observed during three different periods.

Results and discussion

The results identified 1382, 2421 and 989 differentially expressed genes (DEGs) in the white flower variety compared with the purple flower variety at S1 (bud stage), S2 (chromogenic stage) and S3 (flowering stage), respectively. Among these, 27 genes enriched in the ko00941, ko00942, ko00943 and ko00944 pathways were screened as potential functional genes affecting flavonoid synthesis and flower color. Further analysis revealed that 15 genes are potential functional genes that lead to flavonoid changes and flower color variations. The metabolomics results at S3 found 129 differentially accumulated metabolites (DAMs), which included 8 anthocyanin metabolites, all of which (with the exception of delphinidin-3-o-(2'''-o-malonyl) sophoroside-5-o-glucoside) were found at lower amounts in the WF variety compared with the PF variety, indicating that a decrease in the anthocyanin content was the main reason for the inability to form purple flowers. Therefore, the changes in 19 flavone and 62 flavonol metabolites were considered the main reasons for the formation of white flowers. In this study, valuable materials responsible for flower color variation in D. nobile were identified and further analyzed the main pathways and potential genes affecting changes in flavonoids and the flower color. This study provides a material basis and theoretical support for the hybridization and molecular-assisted breeding of D. nobile.

Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant-pollinator interactions

Flowering plants have evolved extraordinarily diverse metabolites that underpin the floral visual and olfactory signals enabling plant-pollinator interactions. In some cases, these metabolites also provide unusual rewards that specific pollinators depend on. While some metabolites are shared by most flowering plants, many have evolved in restricted lineages in response to the specific selection pressures encountered within different niches. The latter are designated as specialized metabolites. Recent investigations continue to uncover a growing repertoire of unusual specialized metabolites. Increased accessibility to cutting-edge multi-omics technologies (e.g. genome, transcriptome, proteome, metabolome) is now opening new doors to simultaneously uncover the molecular basis of their synthesis and their evolution across diverse plant lineages. Drawing upon the recent literature, this perspective discusses these aspects and, where known, their ecological and evolutionary relevance. A primer on omics-guided approaches to discover the genetic and biochemical basis of functional specialized metabolites is also provided.

Integrative Analysis of Metabolomic and Transcriptomic Data Reveals the Mechanism of Color Formation in Corms of Pinellia ternata

Pinellia ternata (Thunb.) Breit. (P. ternata) is a very important plant that is commonly used in traditional Chinese medicine. Its corms can be used as medicine and function to alleviate cough, headache, and phlegm. The epidermis of P. ternata corms is often light yellow to yellow in color; however, within the range of P. ternata found in JingZhou City in Hubei Province, China, there is a form of P. ternata in which the epidermis of the corm is red. We found that the total flavonoid content of red P. ternata corms is significantly higher than that of yellow P. ternata corms. The objective of this study was to understand the molecular mechanisms behind the difference in epidermal color between the two forms of P. ternata. The results showed that a high content of anthocyanidin was responsible for the red epidermal color in P. ternata, and 15 metabolites, including cyanidin-3-O-rutinoside-5-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside, were screened as potential color markers in P. ternata through metabolomic analysis. Based on an analysis of the transcriptome, seven genes, including PtCHS1, PtCHS2, PtCHI1, PtDFR5, PtANS, PtUPD-GT2, and PtUPD-GT3, were found to have important effects on the biosynthesis of anthocyanins in the P. ternata corm epidermis. Furthermore, two transcription factors (TFs), bHLH1 and bHLH2, may have regulatory functions in the biosynthesis of anthocyanins in red P. ternata corms. Using an integrative analysis of the metabolomic and transcriptomic data, we identified five genes, PtCHI, PtDFR2, PtUPD-GT1, PtUPD-GT2, and PtUPD-GT3, that may play important roles in the presence of the red epidermis color in P. ternata corms.

Analysis of coloration characteristics of Tunisian soft-seed pomegranate arils based on transcriptome and metabolome

In this study, combining metabolome and transcriptome, color related attributes and phenolic compositions of Tunisian pomegranate arils from 7 Chinese regions at same developing stage were studied. The total anthocyanin (TAC), flavonoids, and percent polymeric color (PPC) were ranged at 8.93-28.41 mg/100 g arils, 37.55-69.72 mg/100 g arils, and 3.38-21.96%, respectively. In total, 51 phenolic compounds were characterized, most of which were markedly higher in reddish-purple pomegranate arils than those levels in reddish pomegranate arils. In contrast, the accumulation of tannins was significantly higher in reddish pomegranate arils. Among the 49 differentially expressed genes, 8 and 5 genes were matched to β-glucosidase and peroxidase, respectively. Correlation analysis showed that PPC was negatively correlated with 10 phenolic metabolites and TAC, positively correlated with L*, polymeric color, and 1 gene (|r| > 0.7, p < 0.01). Our results provide new insights for understanding the difference in coloration of pomegranate arils.

Beyond Purple Tomatoes: Combined Strategies Targeting Anthocyanins to Generate Crimson, Magenta, and Indigo Fruit

The range of colours of many flowers and fruits is largely due to variations in the types of anthocyanins produced. The degree of hydroxylation on the B-ring affects the hue of these pigments, causing a shift from the orange end of the visible spectrum to the blue end. Besides colour, this modification can also affect other properties of anthocyanins, including the ability to protect the plant against different stresses or, when included in the human diet, to provide benefits for disease prevention. The level of hydroxylation of the B-ring is determined by the activity of two key hydroxylases, F3′H and F3′5′H, and by the substrate preference of DFR, an enzyme acting downstream in the biosynthetic pathway. We show that, in tomato, a strategy based on fruit-specific engineering of three regulatory genes (AmDel, AmRos1, AtMYB12) and a single biosynthetic gene (AmDFR), together with the availability of a specific mutation (f3′5′h), results in the generation of three different varieties producing high levels of anthocyanins with different levels of hydroxylation. These tomatoes show distinctive colours and mimic the classes of anthocyanins found in natural berries, thus providing unique near-isogenic material for different studies.

Chromosome numbers for the Italian flora: 11

In this contribution, new chromosome data obtained on material collected in Italy are presented. It includes counts for Centaurea aegusae, Hieracium racemosum subsp. lucanum, H. australe subsp. australe, Lysimachia arvensis subsp. arvensis, Micromeria graeca subsp. graeca, and M. graeca subsp. consentina.

Interactions with Microbial Proteins Driving the Antibacterial Activity of Flavonoids

Flavonoids are among the most abundant natural bioactive compounds produced by plants. Many different activities have been reported for these secondary metabolites against numerous cells and systems. One of the most interesting is certainly the antimicrobial, which is stimulated through various molecular mechanisms. In fact, flavonoids are effective both in directly damaging the envelope of Gram-negative and Gram-positive bacteria but also by acting toward specific molecular targets essential for the survival of these microorganisms. The purpose of this paper is to present an overview of the most interesting results obtained in the research focused on the study of the interactions between flavonoids and bacterial proteins. Despite the great structural heterogeneity of these plant metabolites, it is interesting to observe that many flavonoids affect the same cellular pathways. Furthermore, it is evident that some of these compounds interact with more than one target, producing multiple effects. Taken together, the reported data demonstrate the great potential of flavonoids in developing innovative systems, which can help address the increasingly serious problem of antibiotic resistance.