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.

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

2020 ◽  
Author(s):  
Yu-fu Gao ◽  
Dong-hui Zhao ◽  
Jia-qi Zhang ◽  
Jia-shuo Chen ◽  
Liping Rong
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. Conclusion 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 Transcriptome sequencing and anthocyanin metabolite analysis determines leaf color of Acer pseudo-sieboldianum in autumn

2019 ◽  
Author(s):  
Donghui Zhao ◽  
Yufu Gao ◽  
Liping Rong
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput Sequencing ◽  
Differentially Expressed ◽  
Leaf Color ◽  
Local Characteristics ◽  
Content Change ◽  
Color Transformation ◽  
Three Stages ◽  
Ornamental Traits ◽  
Key Substances

Abstract Background: Acer pseudo-sieboldianum is an often used color-leafed tree native to northeastern China, whose leaves are gorgeous in autumn and is used to great effect in landscaping. Leaf color is an important index affecting the ornamental traits of color-leafed plants. Thus, it is of great significance to study the mechanism in leaf coloring in Acer pseudo-sieboldianum as the development and application prospects of this research are broad, and further the utilization of local characteristics tree species with colored leaves. Results: In this study, the leaves of Acer pseudo-sieboldianum from three stages in the autumn color-changing period were used as materials. In order to investigate the related differentially expressed genes in the process of color transformation, we determined the anthocyanins in leaves and used high-throughput sequencing to analyze the associated transcriptomes. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside, Cyanidin 3-O-glucoside (Kuromanin) and Cyanidin 3,5-O-diglucoside (Cyanin) have significant differences in their content change in two of the tested periods, meaning these may be the key substances determining the final color of Acer pseudo-sieboldianum. 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. 16521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. We were able to cluster genes related to leaf color formation in Acer pseudo-sieboldianum, including ANS, DFR, F3H, UFGT, and so on, based on the expression at specific times. Conclusions: This study enriched the available transcriptome information for Acer pseudo-sieboldianum 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 Acer pseudo-sieboldianum.

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 Integrative Systems Biology Approaches to Identify Potential Biomarkers and Pathways of Cervical Cancer

2021 ◽  
Vol 11 (5) ◽  
pp. 363
Author(s):  
Arafat Rahman Oany ◽  
Mamun Mia ◽  
Tahmina Pervin ◽  
Salem Ali Alyami ◽  
Mohammad Ali Moni
Keyword(s):  
Cervical Cancer ◽  
Systems Biology ◽  
Differentially Expressed Genes ◽  
Inflammatory Responses ◽  
Profile Analysis ◽  
Target Identification ◽  
Regulatory Genes ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Potential Biomarkers

Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC retains its fatality rate of about half of the infected population globally. The major screening biomarkers and therapeutic target identification have now become a global concern. In the present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4643 differentially expressed genes. The up-regulatory genes mainly concentrate on immune-inflammatory responses, and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment, and we mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC and are verified by expression profile analysis. From our study, we have found that genes LILRB2 and CYBB play crucial roles in CC, as reported here for the first time. Furthermore, the survivability of the hub genes was also assessed, and among them, finally, CXCR4 has been identified as one of the most potential differentially expressed genes that might play a vital role in the survival of CC patients. Thus, CXCR4 could be used as a prognostic and/or diagnostic biomarker and a drug target for CC.

scholarly journals RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

2021 ◽  
Vol 8 ◽  
Author(s):  
Kirsten E. McLoughlin ◽  
Carolina N. Correia ◽  
John A. Browne ◽  
David A. Magee ◽  
Nicolas C. Nalpas ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Mycobacterium Bovis ◽  
Peripheral Blood ◽  
Post Infection ◽  
Time Course ◽  
De Novo ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Infection Time ◽  
Time Point

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

scholarly journals Identification of the Differentially Expressed Genes of Muscle Growth and Intramuscular Fat Metabolism in the Development Stage of Yellow Broilers

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Dongfeng Li ◽  
Zaixu Pan ◽  
Kun Zhang ◽  
Minli Yu ◽  
Debing Yu ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Developmental Stage ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Intramuscular Fat ◽  
Regulatory Genes ◽  
Breast Muscle ◽  
Differentially Expressed ◽  
The Common

High-quality chicken meat is an important source of animal protein for humans. Gene expression profiles in breast muscle tissue were determined, aiming to explore the common regulatory genes relevant to muscle and intramuscular fat (IMF) during the developmental stage in chickens. Results show that breast muscle weight (BMW), breast meat percentage (BMP, %), and IMF (%) continuously increased with development. A total of 256 common differentially expressed genes (DEGs) during the developmental stage were screened. Among them, some genes related to muscle fiber hypertrophy were upregulated (e.g., CSRP3, LMOD2, MUSTN1, MYBPC1), but others (e.g., ACTC1, MYL1, MYL4) were downregulated from Week 3 to Week 18. During this period, expression of some DEGs related to the cells cycle (e.g., CCNB3, CCNE2, CDC20, MCM2) changed in a way that genetically suggests possible inhibitory regulation on cells number. In addition, DEGs associated with energy metabolism (e.g., ACOT9, CETP, LPIN1, DGAT2, RBP7, FBP1, PHKA1) were found to regulate IMF deposition. Our data identified and provide new insights into the common regulatory genes related to muscle growth, cell proliferation, and energy metabolism at the developmental stage in chickens.

scholarly journals Physiological and Transcriptome Analysis of a Yellow-Green Leaf Mutant in Birch (Betula platyphylla × B. Pendula)

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 120 ◽  
Author(s):  
Huixin Gang ◽  
Guifeng Liu ◽  
Su Chen ◽  
Jing Jiang
Keyword(s):  
Differentially Expressed ◽  
Green Leaf ◽  
Pathway Enrichment Analysis ◽  
Leaf Color ◽  
Color Formation ◽  
Leaf Phenotype ◽  
Leaf Mutant ◽  
Antenna Proteins ◽  
And Control ◽  
Chl Biosynthesis

Chlorophyll (Chl)-deficient mutants are ideal materials for the study of Chl biosynthesis, chloroplast development, and photosynthesis. Although the genes encoding key enzymes related to Chl biosynthesis have been well-characterized in herbaceous plants, rice (Oryza sativa L.), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays L.), yellow-green leaf mutants have not yet been fully studied in tree species. In this work, we explored the molecular mechanism of the leaf color formation in a yellow-green leaf mutant (yl). We investigated the differentially expressed genes (DEGs) between yl and control plants (wild type birch (WT) and BpCCR1 overexpression line 11, (C11)) by transcriptome sequencing. Approximately 1163 genes (874 down-regulated and 289 up-regulated) and 930 genes (755 down-regulated and 175 up-regulated) were found to be differentially expressed in yl compared with WT and C11, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs revealed that photosynthesis antenna proteins represent the most significant enriched pathway. The expressions of photosynthesis antenna proteins are crucial to the leaf color formation in yl. We also found that Chl accumulate, leaf anatomical structure, photosynthesis, and growth were affected in yl. Taken together, our results not only provide the difference of phenomenal, physiological, and gene expression characteristics in leaves between yl mutant and control plants, but also provide a new insight into the mutation underlying the chlorotic leaf phenotype in birch.

Sign in / Sign up

Export Citation Format

Share Document