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Flower morphology of Michelia maudiae. (a) “White” flower of M. maudiae Dunn. (b) “Rubellis” flower mutation of M. maudiae Dunn var. rubicund. (c) Different developmental stages of the two types of M. maudiae. (d) Definition and characterization of experimental materials for transcriptome and metabolome data. WE: “white flower” at an early stage (stage 3); WL: “white flower” at a later stage (stage 6); RE: “Rubellis flower” at an early stage (stage 3); RL: “Rubellis flower” at a later stage (stage 6).
Source publication
Michelia maudiae Dunn is one of the important ornamental plants in the Magnoliaceae family, and the color of its flowers usually appears naturally pure white. The discovery of a rubellis flower named M. maudiae Dunn var. rubicunda provides an opportunity to reveal the metabolism of the flavonoids and anthocyanins of this "early angiosperm" plant. C...
Citations
... In recent years, metabolomics, in combination with transcriptomics, has provided a powerful tool for the study and characterization of the molecular basis of mechanisms in many plants [22]. For example, Lang et al., through the transcriptome and metabolomic analysis of a Rubellis flower, described the metabolism of flavonoids and anthocyanins in this early angiosperm plant [23]. ...
Mikania micrantha is a highly invasive vine, and its ability to sexually reproduce is a major obstacle to its eradication. The long-distance dissemination of M. micrantha depends on the distribution of seeds; therefore, inhibiting M. micrantha flowering and seed production is an effective control strategy. The number of blooms of M. micrantha differs at different altitudes (200, 900, and 1300 m). In this study, we used a combination of metabolomics and transcriptomics methods to study the patterns of metabolite accumulation in the flower buds of M. micrantha. Using LC-MS/MS, 658 metabolites were found in the flower buds of M. micrantha at three different altitudes (200, 900, and 1300 m). Flavonoids and phenolic acids were found to be the main differential metabolites, and their concentrations were lower at 900 m than at 200 m and 1300 m, with the concentrations of benzoic acid, ferulic acid, and caffeic acid being the lowest. The biosynthesis pathways for flavonoids and phenolic compounds were significantly enriched for differentially expressed genes (DEGs), according to the results of transcriptome analysis. The production of flavonoid and phenolic acids was strongly linked with the expressions of phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and 4-coumarate-CoA ligase (4CL), according to the results of the combined transcriptome and metabolome analysis. These genes’ roles in the regulation of distinct phenolic acids and flavonoids during M. micrantha bud differentiation are still unknown. This study adds to our understanding of how phenolic acids and flavonoids are regulated in M. micrantha flower buds at various altitudes and identifies regulatory networks that may be involved in this phenomenon, offering a new approach for the prevention and management of M. micrantha.
... For example, transcript levels of LAR and ANR genes were higher in white than red fruits in strawberry (Salvatierra et al., 2013). The transcript accumulation of MmANR gene leads to the abundant catechin and epicatechin in white flowers in Michelia maudiae (Lang et al., 2019). ...
Modern anthuriums, Anthurium andraeanum (Hort.) are among the most popular flowering plants and widely used for interior decoration. Their popularity is largely attributed to the exotic spathes with different colors. Previous studies have reported color development in red spathe cultivars, but limited information is available on key genes regulating white and green colored spathes. This study analyzed anthocyanin, chlorophyll, and carotenoid contents as well as transcript differences in spathes of eight cultivars that differed in spathe colors ranging from red to white and green. Results showed that increased expression of a transcription factor AaMYB2 was associated with elevated levels of anthocyanin in spathes, but decreased expression of AaMYB2 and increased expression of AaLAR (leucoanthocyanidin reductase) and AaANR (anthocyanidin reductase) were accompanied with the accumulation of colorless proanthocyanidin, thus the white spathe. As to the green colored spathe, chlorophyll content in the green spathe cultivar was substantially higher than the other cultivars. Correspondingly, transcripts of chlorophyll biosynthesis-related genes AaHemB (porphobilinogen synthase) and AaPor (protochlorophyllide oxidoreductase) were highly upregulated but almost undetectable in white and red spathes. The increased expression of AaHemB and AaPor was correlated with the expression of transcription factor AaMYB124. Subsequently, qRT-PCR analysis confirmed their expression levels in nine additional cultivars with red, white, and green spathes. A working model for the formation of white and green spathes was proposed. White colored spathes are likely due to the decreased expression of AaMYB2 which results in increased expression of AaLAR and AaANR, and the green spathes are attributed to AaMYB124 enhanced expression of AaHemB and AaPor. Further research is warranted to test this working model.
... The four studies generated RNA-Seq data sets for the analysis of genetic factors underlying differences in pigmentation. The analyzed species were Michelia maudiae [67], Rhododendron obtusum [68], Trifolium repens [69], and Hosta plantaginea [70] (Additional file 3). The selection of each dataset was based on the following criteria: (I) paired-end RNA-Seq data, (II) study has biological replicates, and (III) the authors have not identified the specific gene responsible for the color difference. ...
... A study about the flower color variation in Michelia maudiae [67] generated RNA-Seq data sets (Table S2) of plants of an anthocyanin-pigmented accession (red flower) and of plants of an unpigmented accession (white flower). Flower samples were taken at an early and a late developmental stage to compare not only accessions, but also developmental stages. ...
... M. maudiae is a perennial tree belonging to the family Magnoliaceae. Lang et al. [67] conducted an RNA-Seq experiment to investigate the flower color variation in M. maudiae. Early and late developmental stages of the white and red flowers were sampled. ...
Background
Anthocyanins represent one of the most abundant coloration factors found in plants. Biological functions of anthocyanins range from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins.
Results
A systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties across flowering plant species was performed. Literature was screened for cases in which causal genes were previously identified. Transcriptomic data sets were processed to determine the genes most likely to be responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the pigmentation differences was quantified. Gene expression differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are substantially more likely to explain pigmentation differences than bHLH or WD40 genes.
Conclusions
These findings support previous assumptions about the plasticity of transcriptional regulation and its importance for the evolution of novel coloration phenotypes. The particular significance of MYBs and their apparent dominant role in the specificity of the MBW complex are underlined by our findings.
... qRT-PCR was conducted using AceQ qPCR SYBR Green Master mix (Vazyme). Relative expression levels of genes were analysed using the 2 − Ct method, and actin was used as a reference gene (Lang et al. 2019). All samples were examined in (technical) triplicate with three biological replicates. ...
Michelia compressa (Maxim.) Sarg. is one of the important timber trees in Taiwan province, P. R. China. Michelia 'Zhongshanhanxiao' is a group of variants found among the progeny of M. compressa that exhibit higher growth rates compared with normal individuals, with significantly increased stem diameter and height, as well as enlarged leaves and flowers. However, the molecular mechanisms fostering the growth advantage and morphological variations are unknown and deserve further study. Through analyzing the transcriptome, metabolome and physiological processes of leaves, we identified remarkable differences in gene expression and metabolic profiles between Michelia 'Zhongshanhanxiao' and both the maternal M. compressa and its normal progeny. These differences were widely associated with plant-pathogen interaction, phenylpropanoid biosynthesis, cyanoamino acid metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. Additionally, physiological measurements showed that Michelia 'Zhongshanhanxiao' possesses stronger photosynthetic capacity and higher plant hormone contents. These results suggest that the heterosis of Michelia 'Zhongshanhanxiao' is regulated by candidates related to cell division, resistance to pathogens and accumulation of organic compounds. The findings of this study provide crucial information on the molecular mechanisms underlying the growth advantages conferred by heterosis in trees.
... It is a feasible research method, and has been successfully applied to the study of heat resistance and the response of many species, such as Korean fir [32], dove tree [33], and maize [47]. In this study, 104,052 unigenes were assembled, which was close to that of the same genus species, such as M. maudiae (109,729 unigenes) [48]. Abundant DEGs were identified that may respond to the heat stress, which provides the first insights into the transcriptomic data of M. macclurei under heat stress by fire simulation. ...
Heat stress due to external heat sources such as fire is an ecological problem for plants. When forest plants suffer from fire, high temperatures cause an array of morphological, physiological, and biochemical changes, which affect growth and development. Michelia macclurei Dandy is an evergreen broad-leaved tree species with the characteristics of fast growth, strong adaptability, and good fire-resistance. Some studies have improved the understanding of how fire behavior affects physiology, function and mortality, but the extreme heat response genes and mechanisms need improved understanding. In this study, we conducted a fire experiment (slight and severe) and RNA-Seq in M. macclure. The de novo assembly obtained 104,052 unigenes, and 48.46% were annotated in at least one public database. Specifically, 4458 and 4810 differentially expressed genes (DEGs) were identified in slight and severe fire treatment groups, respectively. In two treatment groups, 612 unigenes were differentially expressed, which were enriched in ‘oxidoreductase activity’ in the molecular function (MF) category of Gene Ontology (GO) enrichment analysis, suggesting the core role of oxidoreductase activity in response to extremely high temperatures in M. macclurei. In KEGG enrichment analysis of DEGs, the ‘plant hormone signal transduction’ is overrepresented, suggesting that this process plays an important role during heat response in M. macclurei. In the pathways of cytokinine and salicylic acid, some vital DEGs were enriched, which were related to cell division, shoot initiation, and disease resistance, and the potential interactions during heat stress were discussed. Moreover, the DEGs linked to heat stress response were identified, including heat shock factors, stress enhanced protein, signal transduction, photosystem, and major transcription factors. The qRT-PCR examination of various tissues, expression dynamics, and treatments revealed that the genes coding for the heat shock protein HSF30, stress enhanced protein, and photosystem I reaction center subunit II exhibited particularities in leaf tissue. Genes coding for heat shock proteins displayed a distinct expression pattern between fire treatment and conventional heat stress, which could signify the distinctive function of HSPs and the mechanism of heat responses. Altogether, these may interact to respond to fire stress through alterations in cellular processes, signaling transduction, and the synthesis and degradation of response proteins in M. macclurei. The results of this study provide a crucial transcriptional profile influenced by heat stress in M. macclurei, and could be of great use to explore the fire prevention mechanisms of fire-resistant tree species.
... As mRNAs are devoid of introns, the resulting predictions are likely more accurate than predicting gene models from genomic sequences that are based on ambiguous splice-site predictions. Furthermore, protein-coding gene validation by additional peptide evidence through high-resolution mass spectrometry can strongly improve the annotation as shown in various previous studies investigating individual species (Jaffe et al. 2004;Castellana et al. 2008;Desgagné-Penix et al. 2010;Evans et al. 2012;Volkening et al. 2012;Mohien et al. 2013;Kumar et al. 2016;Chapman and Bellgard 2017;Prasad et al. 2017;Ma et al. 2018;Lang et al. 2019;Ding et al. 2020;Levin et al. 2020;Müller et al. 2021). ...
Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans . Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
... Specific to the type of flavonoids, it was found that the quercetin content in yellow flowers of Gossypium arboreum L. was higher than that of white flowers, while the kaempferol content was lower than that of white flowers [48]. Quercetin content in yellow flowers of Michelia maudiae Dunn was higher than that in white flowers [49]. These results proved that the flavonoid content affects the colour development of most yellow flowers. ...
Rhododendron liliiflorum H. Lév., with white outer edges and yellow inner edges of petals, is an ornamental flower that originated in China. In this study, we analysed the white (W) and yellow (Y) parts of R. liliiflorum flowers by RNA sequencing. Then, unigene assembly, unigene annotation, and classification of Eukaryotic Orthologous Groups (KOGs) were performed. Gene ontology (GO) classification and pathway enrichment analysis for unigenes were also conducted. A total of 219,221 transcripts and 180,677 unigenes of R. liliiflorum were obtained from 48.52 Gb of clean reads. Differentially expressed gene (DEG) analysis indicated that 2310 unigenes were upregulated and 3062 were downregulated in W vs. Y. Thirty-six of these DEGs were involved in the flavonoid biosynthesis pathway. Pathway enrichment analysis showed that DEGs were significantly enriched in phenylpropanoid, flavonoid, and isoflavone biosynthesis. The expression of dihydroflavonol-4-reductase (DFR) and chalcone synthase (CHS) may affect differences in R. liliiflorum flower colour. The findings on flavonoid biosynthesis and other related genes in this study will provide guidance for exploring the mechanism of flower colour formation in Rhododendron.
... We, therefore, hypothesized that the transcript modules correlated with the MetM7 metabolite module would include functional genes most likely associated with the biosynthesis of rutin and associated metabolites. Several studies have highlighted the importance of integrating transcriptome and metabolome datasets in identifying functional genes [29,38,[54][55][56][57][58]. Therefore, using a similar strategy in M. japonicus, we performed a correlation analysis between metabolite and transcript modules and identified the transcript modules TransM9 and TransM4, sharing a high correlation (R 2 > 0.7) with the MetM7 metabolite module. ...
High-throughput RNA sequencing (RNA-seq) analysis of samples from Mallotus japonicus, a traditional medicinal plant, yielded two novel RNA viruses tentatively named Mallotus japonicus virus A (MjVA) and Mallotus japonicus virus B (MjVB). The MjVA and MjVB genomes encode proteins showing amino acid sequence similarities to those of poleroviruses (the genus Polerovirus, the family Solemoviridae) and amalgaviruses (the genus Amalgavirus, the family Amalgaviridae), respectively. The MjVA genome contains seven highly overlapping open reading frames, which are translated to seven proteins through various translational mechanisms, including -1 programmed ribosomal frameshifting (PRF) at the slippery motif GGGAAAC, non-AUG translational initiation, and stop codon readthrough. The MjVB genome encodes two proteins; one of which is translated by +1 PRF mechanism at the slippery motif UUUCGN. The abundance analysis of virus-derived RNA fragments revealed that MjVA is highly concentrated in plant parts with well-developed phloem tissues as previously demonstrated in other poleroviruses, which are transmitted by phloem feeders, such as aphids. MjVB, an amalgavirus generally transmitted by seeds, is distributed in all samples at low concentrations. Thus, this study demonstrates the effectiveness and usefulness of RNA-seq analysis of plant samples for the identification of novel RNA viruses and analysis of their tissue distribution. Keywords: Polerovirus; Amalgavirus; Mallotus japonicus; RNA virus; viral genome; programmed ribosomal frameshifting.
... In general, anthocyanin accumulation is closely related to flower development and color changes. Flower coloration is mainly determined by the type and content of six different anthocyanidins, including cyanidin, peonidin, and pelargonidin which confer plant with pink and red pigmentation, and delphinidin, malvidin, and petunidin that confer plant with blue and purple pigmentation (Lang et al., 2019;Wang et al., 2021b). In addition, the flower color of ornamental plants also depends on cell structure (Zhao and Tao, 2015), plant hormones (Roepke et al., 2013), pH (Stewart et al., 1975;Pina, 2014), and environmental factors (Lai et al., 2011;Zhang et al., 2015;Shao et al., 2022b). ...
Cotton is one of the most important multiple-usage crops, including fiber, oil, protein, and even ornament. Anthocyanins are the main chromogenic substances in plants, giving the floral organs of ornamental plants their bright colors. Here, we characterized a cotton accession (Gossypium hirsutum L.) showing pink petals with red spot at the base of petal. The pink flower (PF) accession is thought to be derived from interspecific cross between G. hirsutum and a diploid wild cotton species G. bickii native to Australia. We mapped the genetic region underlying the PF trait using bulked segregant RNA sequencing (BSR-Seq) and demonstrated introgression of a genomic region from G. bickii based on re-sequencing of the PF accession and comparative genomic analyses. The introgression fragment contains an R2R3-MYB gene (GH_A07G0851 or GhPF) homologous to GbBM regulating the formation of the red spots at the base of petals in G. barbadense. The coding region of GH_A07G0851 from the PF accession has a 15-bp deletion found only in Australian diploid wild cotton species, G. bickii, and G. australe, which possess light pink flowers with red spots at the base of petals. The temporal expression pattern of GH_A07G0851 tightly correlates with coloration of pink flowers during their development. The results demonstrate the importance of MYB gene in regulation of biosynthesis and accumulation of anthocyanins in cotton flowers and provide candidate gene for manipulating flower color, an important attribute that can facilitate the production of hybrid seeds through attracting pollinators for efficient pollen transfer so to enhance utilization of heterosis in cotton.
... This variation can be used as important material for the development and cultivation of new varieties for D. delavayi. In recent years, the metabolome and transcriptome have been widely used to breed various plants by combining the gene data in the transcriptome with the phenotypic profiles in the metabolome as well as to enrich metabolic pathways and molecular interactions to screen for key metabolic pathways or genes and to carry out indepth analyses and validation on metabolites [27,28]. ...
... This variation can be used as important material for the development and cultivation of new varieties for D. delavayi. In recent years, the metabolome and transcriptome have been widely used to breed various plants by combining the gene data in the transcriptome with the phenotypic profiles in the metabolome as well as to enrich metabolic pathways and molecular interactions to screen for key metabolic pathways or genes and to carry out in-depth analyses and validation on metabolites [27,28]. ...
The metabolome and transcriptome profiles of three different variations of mature Docynia delavayi fruit were synthesized to reveal their fruit color formation mechanism. A total of 787 secondary metabolites containing 149 flavonoid metabolites, most of which were flavonoids and flavonols, were identified in the three variations using ultra performance liquid chromatography- tandem mass spectrometry (UPLC-MS/MS), and we found that the secondary metabolites cyanidin-3-O-galactoside and cyanidin-3-O-glucoside were the major coloring substances in D. delavayi. This was associated with the significant upregulation of the structural genes F3H and F3′H in the anthocyanin synthesis pathway and the control genes WRKY, MYB, bZIP, bHLH, and NAC in RP. F3′H expression may play a significant role in the selection of components for anthocyanin synthesis. Our results contribute to breeding and nutritional research in D. delavayi and provide insight into metabolite studies of the anthocyanin biosynthetic pathway.
