scholarly journals Integrated analyses of rice dark response and leaf color control reveal links with porphyrin and chlorophyll metabolism

2020 ◽  
Author(s):  
Tianxingzi Wang ◽  
Yue Chen ◽  
Zheng Zhu ◽  
Yuqing Liu ◽  
Gaowei Yan ◽  
...  
Keyword(s):  
Stress Response ◽  
Differentially Expressed Genes ◽  
Chlorophyll Biosynthesis ◽  
Light Signal ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Leaf Color ◽  
Chlorophyll Metabolism ◽  
Color Control ◽  
Dark Stress

Abstract Background: Light is a key regulatory signal for rice growth and development. Under dark stress, rice shows leaf yellowing. Whole genome transcriptomic analysis will identify differentially expressed genes (DEG) in dark-treated rice seedlings and DEG-enriched metabolic pathways. Rice leaf color is an essential agronomic trait. Traditional genetic experiments have reported over a hundred of leaf color control (LCC) genes and some of them were also regulated by light signal. Thus, an integrated analysis for the two set of data will be helpful for illustration of the mechanism for both dark-response and leaf color control.Results: Transcriptome changes in response to dark treatment were surveyed by RNA-Seq analysis. About 13,115 differentially expressed genes (DEGs) were identified. One hundred and fifty rice LCC genes were collected. It was found that 102 LCC genes (68.0%) were also dark-response DEGs, which suggests an overlap between dark response and LCC networks. Fifty DEG overlapped LCC genes was associated with chloroplast development. KEGG analysis revealed enrichment of LCC genes in porphyrin and chlorophyll metabolism (PCM) (18/44, 40.9%). Of the 18 LCC genes in the PCM pathway, 15 were dark-response DEGs (83.3%). More interestingly, all of them are involved in a central PCM sub-pathway, chlorophyll biosynthesis.Conclusions: Integrated analysis for dark stress-response and leaf color control identified the correlation between the two processes and mutually supported evidences were obtained. It was found that PCM pathway, particularly chlorophyll biosynthesis process, plays important roles in rice LCC and dark stress-response. This study provides important clues for understanding the mechanisms of dark response and leaf color control and identifying additional LCC genes.

Integrated analyses of rice dark response and leaf color regulation reveal links with porphyrin and chlorophyll metabolism

2020 ◽  
Author(s):  
Tianxingzi Wang ◽  
Yue Chen ◽  
Zheng Zhu ◽  
Yuqing Liu ◽  
Gaowei Yan ◽  
...  
Keyword(s):  
Stress Response ◽  
Chlorophyll Biosynthesis ◽  
Light Signal ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Leaf Color ◽  
Chlorophyll Metabolism ◽  
Leaf Yellowing ◽  
Dark Stress ◽  
Color Regulation

Abstract Background Light is a key regulatory signal for rice growth and development. Under dark stress, rice shows leaf yellowing. Whole genome transcriptomic analysis will identify differentially expressed genes (DEG) in dark-treated rice seedlings and DEG-enriched metabolic pathways. Rice leaf color is an essential agronomic trait. Traditional genetic experiments have reported over a hundred of leaf color-related (LCR) genes and some of them were also regulated by light signal. Thus, an integrated analysis for the two set of data will be helpful for illustration of the mechanism for both dark-response and leaf color regulation. Results Transcriptome changes in response to dark treatment were surveyed by RNA-Seq analysis. About 13,115 DEGs were identified. One hundred and fifty rice LCR genes were collected. It was found that 102 LCR genes (68.0%) were also dark-response DEGs, which suggests an overlap between dark response and LCR networks. Fifty DEG overlapped LCR genes was associated with chloroplast development. KEGG analysis revealed enrichment of LCR genes in porphyrin and chlorophyll metabolism (PCM) (18/44, 40.9%). Of the 18 LCR genes in the PCM pathway, 15 were dark-response DEGs (83.3%). More interestingly, most of them are involved in a central PCM sub-pathway, chlorophyll biosynthesis. Conclusions Integrated analysis for dark stress-response and leaf color regulation identified the correlation between the two processes and mutually supported evidences were obtained. It was found that PCM pathway, particularly chlorophyll biosynthesis process, is a core component of the overlap and plays important roles in rice LCR and dark stress-response. This study provides important clues for identifying additional LCR genes, understanding the mechanisms of dark response and leaf color regulation.

scholarly journals Screening of key genes responsible for Pennisetum setaceum ‘Rubrum’ leaf color using transcriptome sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242618
Author(s):  
Ting Zhu ◽  
Xia Wang ◽  
Zhimin Xu ◽  
Jie Xu ◽  
Rui Li ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Differentially Expressed ◽  
Chlorophyll Degradation ◽  
Anthocyanin Synthesis ◽  
Leaf Color ◽  
Chlorophyll Metabolism ◽  
Pennisetum Setaceum ◽  
Key Genes

Pennisetum setaceum ‘Rubrum’ is an ornamental grass plant that produces purple leaves in high-light environments and light purple or green leaves in low-light environments, the latter of which greatly reduces its aesthetic appeal. Therefore, we aimed to identify the key genes associated with leaf coloration and elucidate the molecular mechanisms involved in the color changes in P. setaceum ‘Rubrum’ leaves. We performed transcriptome sequencing of P. setaceum ‘Rubrum’ leaves before and after shading. A total of 19,043 differentially expressed genes were identified, and the numbers of upregulated and downregulated genes at T1 stage, when compared with their expression at the T0 stage, were 10,761 and 8,642, respectively. The possible pathways that determine P. setaceum ‘Rubrum’ leaf color included flavonoid biosynthesis, flavone and flavonol biosynthesis, and carotenoid biosynthesis. There were 31 differentially expressed genes related to chlorophyll metabolism, of which 21 were related to chlorophyll biosynthesis and 10 to chlorophyll degradation, as well as three transcription factors that may be involved in the regulation of chlorophyll degradation. There were 31 key enzyme genes involved in anthocyanin synthesis and accumulation in P. setaceum ‘Rubrum’ leaves, with four transcription factors that may be involved in the regulation of anthocyanin metabolism. The transcriptome data were verified and confirmed reliable by real-time fluorescence quantitative PCR analysis. These findings provide a genetic basis for improving leaf color in P. setaceum ‘Rubrum.’

scholarly journals De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu-Fu Gao ◽  
Dong-Hui Zhao ◽  
Jia-Qi Zhang ◽  
Jia-Shuo Chen ◽  
Jia-Lin Li ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
De Novo ◽  
Regulatory Genes ◽  
Differentially Expressed ◽  
Anthocyanin Synthesis ◽  
Leaf Color ◽  
Metabolite Analysis ◽  
Color Formation ◽  
Content Change ◽  
Final Color

Abstract Background Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-leaf tree native to Northeastern China, however, there was less knowledge in Acer about anthocyanins biosynthesis and many steps of the pathway remain unknown to date. Results Anthocyanins metabolite and transcript profiling were conducted using HPLC and ESI-MS/MS system and high-throughput RNA sequencing respectively. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside and Cyanidin 3, 5-O-diglucoside were abundant, especially Cyanidin 3, 5-O-diglucoside displayed significant differences in content change at two periods, meaning it may be play an important role for the final color. Transcriptome identification showed that a total of 67.47 Gb of clean data were obtained from our sequencing results. Functional annotation of unigenes, including comparison with COG and GO databases, yielded 35,316 unigene annotations. 16,521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. The genes related to leaf color formation including PAL, ANS, DFR, F3H were selected. Also, we screened out the regulatory genes such as MYB, bHLH and WD40. Combined with the detection of metabolites, the gene pathways related to anthocyanin synthesis were analyzed. Conclusions Cyanidin 3, 5-O-diglucoside played an important role for the final color. The genes related to leaf color formation including PAL, ANS, DFR, F3H and regulatory genes such as MYB, bHLH and WD40 were selected. This study enriched the available transcriptome information for A. pseudosieboldianum and identified a series of differentially expressed genes related to leaf color, which provides valuable information for further study on the genetic mechanism of leaf color expression in A. pseudosieboldianum.

scholarly journals Dark/Light Treatments Followed by γ-Irradiation Increase the Frequency of Leaf-Color Mutants in Cymbidium

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 532 ◽  
Author(s):  
Sang Hoon Kim ◽  
Se Won Kim ◽  
Jaihyunk Ryu ◽  
Si-Yong Kang ◽  
Byoung-Cheorl Kang ◽  
...  
Keyword(s):  
Chlorophyll Biosynthesis ◽  
Flower Color ◽  
Light Treatment ◽  
Leaf Color ◽  
Γ Irradiation ◽  
Dark Light ◽  
Chlorophyll Metabolism ◽  
Anthocyanin Pathway ◽  
Pathway Gene ◽  
Radiation Treatments

Radiation randomly induces chromosomal mutations in plants. However, it was recently found that the frequency of flower-color mutants could be specifically increased by upregulating anthocyanin pathway gene expression before radiation treatments. The mechanisms of chlorophyll biosynthesis and degradation are active areas of plant study because chlorophyll metabolism is closely connected to photosynthesis. In this study, we determined the dark/light treatment conditions that resulted in upregulation of the expression levels of six chlorophyll pathway genes, uroporphyrinogen III synthase (HEMD), uroporphyrinogen III decarboxylase (HEME2), NADPH-protochlorophyllide oxidoreductase (POR) A (PORA), chlorophyll synthase (CHLG), chlorophyllase (CLH2), and red chlorophyll catabolite reductase (RCCR), and measured their effects on the γ-irradiation-induced frequencies of leaf-color mutants in two Cymbidium cultivars. To degrade chlorophyll in rhizomes, 60–75 days of dark treatment were required. To upregulate the expressions of chlorophyll pathway genes, 10 days of light treatment appeared to be optimal. Dark/light treatments followed by γ-irradiation increased chlorophyll-related leaf mutants by 1.4- to 2.0-fold compared with γ-ray treatment alone. Dark/light treatments combined with γ-irradiation increased the frequency of leaf-color mutants in Cymbidium, which supports the wider implementation of a plant breeding methodology that increases the mutation frequency of a target trait by controlling the expression of target trait-related genes.

scholarly journals Physiological and Anatomical Differences and Differentially Expressed Genes Reveal Yellow Leaf Coloration in Shumard Oak

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 169
Author(s):  
Xiaoyun Dong ◽  
Libin Huang ◽  
Qingsheng Chen ◽  
Yunzhou Lv ◽  
Hainan Sun ◽  
...  
Keyword(s):  
Chlorophyll Content ◽  
Differentially Expressed Genes ◽  
Structural Damage ◽  
Chlorophyll Biosynthesis ◽  
Differentially Expressed ◽  
Carotenoid Content ◽  
Yellow Leaf ◽  
Pheophorbide A ◽  
Chlorophyll Fluorescence Parameters ◽  
Leaf Coloration

Shumard oak (Quercus shumardii Buckley) is a traditional foliage plant, but little is known about its regulatory mechanism of yellow leaf coloration. Here, the yellow leaf variety of Q. shumardii named ‘Zhongshan Hongjincai’ (identified as ‘ZH’ throughout this work) and a green leaf variety named ‘Shumard oak No. 23’ (identified as ‘SO’ throughout this work) were compared. ‘ZH’ had lower chlorophyll content and higher carotenoid content; photosynthetic characteristics and chlorophyll fluorescence parameters were also lower. Moreover, the mesophyll cells of ‘ZH’ showed reduced number of chloroplasts and some structural damage. In addition, transcriptomic analysis identified 39,962 differentially expressed genes, and their expression levels were randomly verified. Expressions of chlorophyll biosynthesis-related glumly-tRNA reductase gene and Mg-chelatase gene were decreased, while pheophorbide a oxygenase gene associated with chlorophyll degradation was up-regulated in ‘ZH’. Simultaneously, carotenoid isomerase gene, z-carotene desaturase gene, violaxanthin de-epoxidase gene and zeaxanthin epoxidase gene involved in carotenoid biosynthesis were up-regulated in ‘ZH’. These gene expression changes were accompanied by decreased chlorophyll content and enhanced carotenoid accumulation in ‘ZH’. Consequently, changes in the ratio of carotenoids to chlorophyll could be driving the yellow leaf coloration in Q. shumardii.

scholarly journals Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

2020 ◽  
Author(s):  
Tao Jiang ◽  
Meide Zhang ◽  
Chunxiu Wen ◽  
Xiaoliang Xie ◽  
Wei Tian ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Salvia Miltiorrhiza ◽  
Flower Color ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Anthocyanin Content ◽  
Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

scholarly journals Integrative Analysis for Elucidating Transcriptomics Landscapes of Systemic Lupus Erythematosus

2021 ◽  
Vol 12 ◽  
Author(s):  
Haihong Zhang ◽  
Yanli Wang ◽  
Jinghui Feng ◽  
Shuya Wang ◽  
Yan Wang ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Differentially Expressed Genes ◽  
Lupus Erythematosus ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Potential Candidate ◽  
Systemic Lupus

Systemic lupus erythematosus (SLE) is a complex and heterogeneous autoimmune disease that the immune system attacks healthy cells and tissues. SLE is difficult to get a correct and timely diagnosis, which makes its morbidity and mortality rate very high. The pathogenesis of SLE remains to be elucidated. To clarify the potential pathogenic mechanism of SLE, we performed an integrated analysis of two RNA-seq datasets of SLE. Differential expression analysis revealed that there were 4,713 and 2,473 differentially expressed genes, respectively, most of which were up-regulated. After integrating differentially expressed genes, we identified 790 common differentially expressed genes (DEGs). Gene functional enrichment analysis was performed and found that common differentially expressed genes were significantly enriched in some important immune-related biological processes and pathways. Our analysis provides new insights into a better understanding of the pathogenic mechanisms and potential candidate markers for systemic lupus erythematosus.

scholarly journals Selenium Regulates Gene Expression for Glucosinolate and Carotenoid Biosynthesis in Arabidopsis

2011 ◽  
Vol 136 (1) ◽  
pp. 23-34 ◽  
Author(s):  
Carl E. Sams ◽  
Dilip R. Panthee ◽  
Craig S. Charron ◽  
Dean A. Kopsell ◽  
Joshua S. Yuan
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Plant Species ◽  
Chlorophyll Biosynthesis ◽  
Plant Secondary Metabolites ◽  
Carotenoid Biosynthesis ◽  
Differentially Expressed ◽  
Biosynthesis Pathway ◽  
Tissue Samples ◽  
Expression Of Genes

Glucosinolates (GSs) and carotenoids are important plant secondary metabolites present in several plant species, including arabidopsis (Arabidopsis thaliana). Although genotypic and environmental regulation of GSs and carotenoid compounds has been reported, few studies present data on their regulation at the molecular level. Therefore, the objective of this study was to explore differential expression of genes associated with GSs and carotenoids in arabidopsis in response to selenium fertilization, shown previously to impact accumulations of both classes of metabolites in Brassica species. Arabidopsis was grown under 0.0 or 10.0 μM Na2SeO4 in hydroponic culture. Shoot and root tissue samples were collected before anthesis to measure GSs and carotenoid compounds and conduct gene expression analysis. Gene expression was determined using arabidopsis oligonucleotide chips containing more than 31,000 genes. There were 1274 differentially expressed genes in response to selenium (Se), of which 516 genes were upregulated. Ontology analysis partitioned differentially expressed genes into 20 classes. Biosynthesis pathway analysis using AraCyc revealed that four GSs, one carotenoid, and one chlorophyll biosynthesis pathways were invoked by the differentially expressed genes. Involvement of the same gene in more than one biosynthesis pathway indicated that the same enzyme may be involved in multiple GS biosynthesis pathways. The decrease in carotenoid biosynthesis under Se treatment occurred through the downregulation of phytoene synthase at the beginning of the carotenoid biosynthesis pathway. These findings may be useful to modify the GS and carotenoid levels in arabidopsis and may lead to modification in agriculturally important plant species.

Sign in / Sign up

Export Citation Format

Share Document