scholarly journals Transcriptomic profiling of purple broccoli reveals light-induced anthocyanin biosynthetic signaling and structural genes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8870 ◽  
Author(s):  
Chunqing Liu ◽  
Xueqin Yao ◽  
Guangqing Li ◽  
Lei Huang ◽  
Zhujie Xie
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Anthocyanin Biosynthesis ◽  
Digital Gene Expression ◽  
Flower Head ◽  
Anthocyanin Accumulation ◽  
Rna Seq ◽  
Light Conditions ◽  
Structural Genes ◽  
Rna Sequences

Purple Broccoli (Brassica oleracea L. var italica) attracts growing attention as a functional food. Its purple coloration is due to high anthocyanin amounts. Light represents a critical parameter affecting anthocyanins biosynthesis. In this study, ‘Purple Broccoli’, a light-responding pigmentation cultivar, was assessed for exploring the mechanism underlying light-induced anthocyanin biosynthesis by RNA-Seq. Cyanidin, delphinidin and malvidin derivatives were detected in broccoli head samples. Shading assays and RNA-seq analysis identified the flower head as more critical organ compared with leaves. Anthocyanin levels were assessed at 0, 7 and 11 days, respectively, with further valuation by RNA-seq under head-shading and light conditions. RNA sequences were de novo assembled into 50,329 unigenes, of which 38,701 were annotated against four public protein databases. Cluster analysis demonstrated that anthocyanin/phenylpropanoid biosynthesis, photosynthesis, and flavonoid biosynthesis in cluster 8 were the main metabolic pathways regulated by light and had showed associations with flower head growth. A total of 2,400 unigenes showed differential expression between the light and head-shading groups in cluster 8, including 650 co-expressed, 373 specifically expressed under shading conditions and 1,377 specifically expressed under normal light. Digital gene expression (DGE) analysis demonstrated that light perception and the signal transducers CRY3 and HY5 may control anthocyanin accumulation. Following shading, 15 structural genes involved in anthocyanin biosynthesis were downregulated, including PAL, C4H, 4CL, CHS, CHI, F3H and DFR. Moreover, six BoMYB genes (BoMYB6-1, BoMYB6-2, BoMYB6-3, BoMYB6-4, BoMYBL2-1 and BoMYBL2-2) and three BobHLH genes (BoTT8_5-1, BoTT8_5-2 and BoEGL5-3) were critical transcription factors controlling anthocyanin accumulation under light conditions. Based on these data, a light-associated anthocyanin biosynthesis pathway in Broccoli was proposed. This information could help improve broccoli properties, providing novel insights into the molecular mechanisms underpinning light-associated anthocyanin production in purple vegetables.

scholarly journals Transcriptome profiling of anthocyanin-related genes reveals effects of light intensity on anthocyanin biosynthesis in red leaf lettuce

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4607 ◽  
Author(s):  
Yanzhao Zhang ◽  
Shuzhen Xu ◽  
Yanwei Cheng ◽  
Zhengfeng Peng ◽  
Jianming Han
Keyword(s):  
Light Intensity ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Anthocyanin Biosynthesis ◽  
Gene Annotation ◽  
High Irradiance ◽  
High Light ◽  
Anthocyanin Content ◽  
Structural Genes ◽  
Leaf Lettuce

Red leaf lettuce (Lactuca sativaL.) is popular due to its high anthocyanin content, but poor leaf coloring often occurs under low light intensity. In order to reveal the mechanisms of anthocyanins affected by light intensity, we compared the transcriptome ofL. sativaL. var.capitataunder light intensities of 40 and 100 μmol m−2s−1. A total of 62,111 unigenes were de novo assembled with an N50 of 1,681 bp, and 48,435 unigenes were functionally annotated in public databases. A total of 3,899 differentially expressed genes (DEGs) were detected, of which 1,377 unigenes were up-regulated and 2,552 unigenes were down-regulated in the high light samples. By Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the DEGs were significantly enriched in 14 pathways. Using gene annotation and phylogenetic analysis, we identified seven anthocyanin structural genes, includingCHS,CHI,F3H,F3′H,DFR,ANS, and3GT, and two anthocyanin transport genes,GSTandMATE. In terms of anthocyanin regulatory genes, five MYBs and one bHLH gene were identified. AnHY5gene was discovered, which may respond to light-signaling and regulate anthocyanin structural genes. These genes showed a log2FC of 2.7–9.0 under high irradiance, and were validated using quantitative real-time-PCR. In conclusion, our results indicated transcriptome variance in red leaf lettuce under low and high light intensity, and observed a anthocyanin biosynthesis and regulation pattern. The data should further help to unravel the molecular mechanisms of anthocyanins influenced by light intensity.

scholarly journals Metabolome and Transcriptome Sequencing Analysis Reveals Anthocyanin Metabolism in Pink Flowers of Anthocyanin-Rich Tea (Camellia sinensis)

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1064 ◽  
Author(s):  
Dylan Rothenberg ◽  
Haijun Yang ◽  
Meiban Chen ◽  
Wenting Zhang ◽  
Lingyun Zhang
Keyword(s):  
Camellia Sinensis ◽  
Flower Development ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Functional Enrichment ◽  
Anthocyanin Synthesis ◽  
Sequencing Analysis ◽  
Anthocyanin Accumulation ◽  
Structural Genes ◽  
Anthocyanin Pathway

Almost all flowers of the tea plant (Camellia sinensis) are white, which has caused few researchers to pay attention to anthocyanin accumulation and color changing in tea flowers. A new purple-leaf cultivar, Baitang purple tea (BTP) was discovered in the Baitang Mountains of Guangdong, whose flowers are naturally pink, and can provide an opportunity to understand anthocyanin metabolic networks and flower color development in tea flowers. In the present study, twelve anthocyanin components were identified in the pink tea flowers, namely cyanidin O-syringic acid, petunidin 3-O-glucoside, pelargonidin 3-O-beta-d-glucoside, which marks the first time these compounds have been found in the tea flowers. The presence of these anthocyanins seem most likely to be the reason for the pink coloration of the flowers. Twenty-one differentially expressed genes (DEGs) involved in anthocyanin pathway were identified using KEGG pathway functional enrichment, and ten of these DEG’s screened using venn and KEGG functional enrichment analysis during five subsequent stages of flower development. By comparing DEGs and their expression levels across multiple flower development stages, we found that anthocyanin biosynthesis and accumulation in BTP flowers mainly occurred between the third and fourth stages (BTP3 to BTP4). Particularly, during the period of peak anthocyanin synthesis 17 structural genes were upregulated, and four structural genes were downregulated only. Ultimately, eight critical genes were identified using weighted gene co-expression network analysis (WGCNA), which were found to have direct impact on biosynthesis and accumulation of three flavonoid compounds, namely cyanidin 3-O-glucoside, petunidin 3-O-glucoside and epicatechin gallate. These results provide useful information about the molecular mechanisms of coloration in rare pink tea flower of anthocyanin-rich tea, enriching the gene resource and guiding further research on anthocyanin accumulation in purple tea.

scholarly journals Transcriptomic Profiling of Apple Calli With a Focus on the Key Genes for ALA-Induced Anthocyanin Accumulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Jie Zheng ◽  
Longbo Liu ◽  
Huihui Tao ◽  
Yuyan An ◽  
Liangju Wang
Keyword(s):  
Molecular Mechanisms ◽  
Aminolevulinic Acid ◽  
Anthocyanin Biosynthesis ◽  
Transcript Level ◽  
Flavonoid Biosynthesis ◽  
Anthocyanin Accumulation ◽  
Structural Genes ◽  
Metabolism Regulation ◽  
Positive Regulators ◽  
R2r3 Myb

The red color is an attractive trait of fruit and determines its market acceptance. 5-Aminolevulinic acid (ALA), an eco-friendly plant growth regulator, has played a universal role in plant secondary metabolism regulation, particularly in flavonoid biosynthesis. It has been widely reported that ALA can up-regulate expression levels of several structural genes related to flavonoid metabolism and anthocyanin accumulation. However, the molecular mechanisms behind ALA-induced expression of these genes are complicated and still far from being completely understood. In this study, transcriptome analysis identified the differentially expressed genes (DEGs) associated with ALA-induced anthocyanin accumulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the flavonoid biosynthesis (ko00941) pathway was significantly enhanced in the ALA-treated apple calli at 24, 48, and 72 h after the treatment. Expression pattern revealed that ALA up-regulated the expression of the structural genes related to not only anthocyanin biosynthesis (MdCHS, MdCHI, MdF3’H, MdDFR, MdANS, and MdUFGT) but also anthocyanin transport (MdGST and MdMATE). Two R2R3-MYB transcription factors (MdMYB10 and MdMYB9), which are the known positive regulators of anthocyanin biosynthesis, were significantly induced by ALA. Gene overexpression and RNA interference assays demonstrated that MdMYB10 and MdMYB9 were involved in ALA-induced anthocyanin biosynthesis. Moreover, MdMYB10 and MdMYB9 might positively regulate the transcription of MdMATE8 by binding to the promoter region. These results indicate that MdMYB10 and MdMYB9 modulated structural gene expression of anthocyanin biosynthesis and transport in response to ALA-mediated apple calli coloration at the transcript level. We herein provide new details regarding transcriptional regulation of ALA-induced color development.

scholarly journals Combined Transcriptome and Metabolome Integrated Analysis of Acer mandshuricum to Reveal Candidate Genes Involved in Anthocyanin Accumulation

2021 ◽  
Author(s):  
Shikai Zhang ◽  
Wang Zhan ◽  
Anran Sun ◽  
Ying Xie ◽  
Zhiming Han ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Integrated Analysis ◽  
Anthocyanin Accumulation ◽  
Structural Genes ◽  
Leaf Color ◽  
Accumulation Pattern ◽  
Color Formation ◽  
Red Color

Abstract The red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in leaf color change periods in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin bio-synthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.

scholarly journals Didelphis albiventris: an overview of an unprecedented transcriptome sequencing of the white-eared opossum

2019 ◽  
Author(s):  
Íria Gabriela Dias dos Santos ◽  
Tiago Antônio de Oliveira Mendes ◽  
Gerluza Aparecida Borges Silva ◽  
Amanda Maria Sena Reis ◽  
Cláudia Barros Monteiro Vitorello ◽  
...  
Keyword(s):  
Limb Development ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Mammalian Species ◽  
Rna Seq ◽  
Go Annotation ◽  
Development And Differentiation ◽  
Marsupial Species ◽  
Didelphis Albiventris

Abstract Background The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. They have been used as animal models to study different aspects in science, from the restoration of degraded green areas to medical aspects of the Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also aid the comprehension of the molecular mechanisms that govern the different stages of organogenesis, as their joeys are born after only 13 days, depending on placentation, and the final stages of organogenesis occurs when the neonates are inside the pouch, depending on lactation. As the genome of this opossum species, and/or its transcriptome, had not been completely sequenced yet, the use of D. albiventris as an animal model is limited. In this work, we have sequenced the D. albiventris transcriptome, by RNA-seq, to obtain the first catalogue of differentially expressed genes (DE) and gene ontology (GO) annotation during the neonatal stages of the marsupial development. Results The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at five days old (P5) and ten days old (P10). The de novo assembly of these transcripts allowed us to obtain 85,338 transcripts. Only ~30% of these transcripts could be mapped against M. domestica genome, the closest phylogenetic relative with available nucleotide sequences. Among the expressed transcripts, 2,077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1,453 between P5 and P10. Enriched GO terms were mainly related to immune system, blood tissue development and differentiation, vision, hearing, digestion, CNS and limb development. Conclusions The unveiling of opossum transcriptomes provides an out-group to better understand the distinct characteristics associated with the evolution of mammalian species. Nevertheless, this is the first transcriptome sequencing and available catalogue of genes of a marsupial species at different neonatal stages, allowing the study of mechanisms involved in the organogenesis.

scholarly journals Didelphis albiventris: an overview of an unprecedented transcriptome sequencing of the white-eared opossum

2019 ◽  
Author(s):  
Íria Gabriela Dias dos Santos ◽  
Tiago Antônio de Oliveira Mendes ◽  
Gerluza Aparecida Borges Silva ◽  
Amanda Maria Sena Reis ◽  
Cláudia Barros Monteiro Vitorello ◽  
...  
Keyword(s):  
Animal Model ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Rna Seq ◽  
Development And Differentiation ◽  
Marsupial Species ◽  
Scientific Questions ◽  
Didelphis Albiventris

Abstract BackgroundThe white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development.ResultsThe D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at five days of age (P5) and at ten days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2,077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1,453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development.ConclusionsThe elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.

scholarly journals Combined transcriptome and metabolome integrated analysis of Acer mandshuricum to reveal candidate genes involved in anthocyanin accumulation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shikai Zhang ◽  
Wang Zhan ◽  
Anran Sun ◽  
Ying Xie ◽  
Zhiming Han ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Integrated Analysis ◽  
Anthocyanin Accumulation ◽  
Structural Genes ◽  
Leaf Color ◽  
Accumulation Pattern ◽  
Color Formation ◽  
Red Color

AbstractThe red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin biosynthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

scholarly journals Methyl Jasmonate- and Light-Induced Glucosinolate and Anthocyanin Biosynthesis in Radish Seedlings

2015 ◽  
Vol 10 (7) ◽  
pp. 1934578X1501000 ◽  
Author(s):  
Naif Abdullah Al-Dhabi ◽  
Mariadhas Valan Arasu ◽  
Sun Ju Kim ◽  
Md. RomijUddin ◽  
Woo Tae Park ◽  
...  
Keyword(s):  
Methyl Jasmonate ◽  
Anthocyanin Biosynthesis ◽  
Anthocyanin Accumulation ◽  
Light Conditions ◽  
Asian Countries ◽  
Low Concentrations ◽  
Meja Treatment ◽  
Radish Sprouts ◽  
Dark Conditions ◽  
Radish Seedlings

Radish sprouts and young seedlings are considered important dietary vegetables in Asian countries. In this study, we investigated the levels of glucosinolate and anthocyanin accumulation in radish seedlings in response to light and methyl jasmonate (MeJA) treatments. MeJA facilitated the accumulation of glucosinolate and anthocyanins under light conditions. The glucosinolate and anthocyanin contents in the radish seedlings that were exposed to light after MeJA treatment were higher than those of the seedlings that were grown in the dark without MeJA. At a concentration of 100 μM, MeJA led to the greatest accumulation of the most glucosinolates under both light and dark conditions. Under light conditions, the levels of glucoraphenin, glucoerucin, and glucotropaeolin accumulation were 1.53-, 1.60-, and 1.30-fold higher, respectively, than those of the control. Remarkable accumulations of glucobrassicin were observed under light conditions (4.4-, 6.7-, and 7.8-fold higher than that of the control following the application of 100, 300, and 500 μM MeJA, respectively). The level of cyanidin in the 300μM MeJA-treated seedlings was double of that in the control without MeJA treatment. The highest level of pelargonidin was observed after treatment with 500 μMMeJA under light conditions; this level was 1.73times higher than that in the control. A similar trend of anthocyaninaccumulation was observed in the radish seedlings following MeJA treatment under dark conditions, but the levels of anthocyanins were considerably lower in the seedlings that were grown in the dark. Our findings suggest that light and low concentrations of MeJA enhance the accumulations of glucosinolates and anthocyanins during the development of radish seedlings.

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