Basil interspecific hybridization and transcriptome study indicates altered developmental and metabolic gene expression

Abstract Background In order to understand the developmental modulation of transcriptome and associated gene expression in inter-genomic combinations, a systematic study was planned using two diverse yet closely related species of Ocimum, targeting their hybrid F1 and derived amphidiploid (colchiploid of F1 hybrid). The existing developmental alterations between F1 and amphidiploid through phenotypical and anatomical assessments were analyzed. Results Study of several genes and transcription factors putatively involved in the growth and developmental processes of plants clearly amalgamates the transcriptome data linking the phenotypic differences in F1 and amphidiploid. Additionally, differentially expressed genes of stomatal patterning and development revealed their involvement leading to higher density of stomata in F1 while larger size of stomata in the amphidiploid. Absence of 8,330 transcripts of interspecific hybrid F1 in its amphidiploid and exclusive presence of two detected transcripts in amphidiploid provides a set of genes to analyze the suppressed or activated functions between F1 and amphidiploid. Estimation of chlorophyll, lignin, flavonoid and phenylpropenes (eugenol and methyleugenol) content were correlated with the average FPKM and digital gene expression values in F1 and amphidiploid. Conclusion This is the first investigation which describes the genes and transcription factors influenced by interspecific hybridization leading to developmental changes and alleviation of intergenomic instability in amphidiploid.

Download Full-text

Partitioning of MLX-Family Transcription Factors to Lipid Droplets Regulates Metabolic Gene Expression

Molecular Cell ◽

10.1016/j.molcel.2020.01.014 ◽

2020 ◽

Vol 77 (6) ◽

pp. 1251-1264.e9 ◽

Cited By ~ 10

Author(s):

Niklas Mejhert ◽

Leena Kuruvilla ◽

Katlyn R. Gabriel ◽

Shane D. Elliott ◽

Marie-Aude Guie ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Lipid Droplets ◽

Metabolic Gene ◽

Metabolic Gene Expression

Download Full-text

Faculty Opinions recommendation of Partitioning of MLX-Family Transcription Factors to Lipid Droplets Regulates Metabolic Gene Expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.737324065.793574525 ◽

2020 ◽

Author(s):

Robert Parton

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Lipid Droplets ◽

Metabolic Gene ◽

Metabolic Gene Expression

Download Full-text

Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes

Database ◽

10.1093/database/baz130 ◽

2019 ◽

Vol 2019 ◽

Author(s):

Ganesh Panzade ◽

Indu Gangwar ◽

Supriya Awasthi ◽

Nitesh Sharma ◽

Ravi Shankar

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Histone Modifications ◽

Biological Networks ◽

Transcriptional Control ◽

Digital Gene Expression ◽

Enrichment Analysis ◽

Cell System ◽

A Genome ◽

Spatio Temporal

Abstract Gene regulation is a highly complex and networked phenomenon where multiple tiers of control determine the cell state in a spatio-temporal manner. Among these, the transcription factors, DNA and histone modifications, and post-transcriptional control by small RNAs like miRNAs serve as major regulators. An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a ‘cell system’. Yet, there are limited resources available to this effect. Therefore, we hereby report an integrative information portal (Plant Regulomics Portal; PRP) for plants for the first time. The portal has been developed by integrating a huge amount of curated data from published sources, RNA-, methylome- and sRNA/miRNA sequencing, histone modifications and repeats, gene ontology, digital gene expression and characterized pathways. The key features of the portal include a regulatory search engine for fetching numerous analytical outputs and tracks of the abovementioned regulators and also a genome browser for integrated visualization of the search results. It also has numerous analytical features for analyses of transcription factors (TFs) and sRNA/miRNA, spot-specific methylation, gene expression and interactions and details of pathways for any given genomic element. It can also provide information on potential RdDM regulation, while facilitating enrichment analysis, generation of visually rich plots and downloading of data in a selective manner. Visualization of intricate biological networks is an important feature which utilizes the Neo4j Graph database making analysis of relationships and long-range system viewing possible. Till date, PRP hosts 571-GB processed data for four plant species namely Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays and Glycine max. Database URL: https://scbb.ihbt.res.in/PRP

Download Full-text

Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop (Humulus Lupulus L.)

Viruses ◽

10.3390/v11050419 ◽

2019 ◽

Vol 11 (5) ◽

pp. 419 ◽

Cited By ~ 6

Author(s):

Vishnu Sukumari Nath ◽

Ajay Kumar Mishra ◽

Atul Kumar ◽

Jaroslav Matoušek ◽

Jernej Jakše

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Regulatory Networks ◽

Evolutionary History ◽

Digital Gene Expression ◽

Defense Responses ◽

Integrated Analysis ◽

Systematic Analysis ◽

Viroid Infection ◽

External Stimuli

Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.

Download Full-text

TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth

Genes & Development ◽

10.1101/gad.320127.118 ◽

2019 ◽

Vol 33 (7-8) ◽

pp. 388-402 ◽

Cited By ~ 4

Author(s):

Anant Shah ◽

Tiffany A. Melhuish ◽

Todd E. Fox ◽

Henry F. Frierson ◽

David Wotton

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Tumor Growth ◽

Intestinal Tumor ◽

Acetyl Coa ◽

Metabolic Gene ◽

Metabolic Gene Expression

Download Full-text

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

Frontiers in Plant Science ◽

10.3389/fpls.2015.00467 ◽

2015 ◽

Vol 6 ◽

Cited By ~ 4

Author(s):

Ying Zhao ◽

Haiying Liang ◽

Lan Li ◽

Sha Tang ◽

Xiao Han ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

High Activity ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Digital Gene Expression ◽

Mads Box ◽

Male And Female ◽

Digital Gene Expression Analysis

Download Full-text

Digital gene expression analysis of the response to Ralstonia solanacearum between resistant and susceptible tobacco varieties

Scientific Reports ◽

10.1038/s41598-021-82576-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

YanYan Li ◽

Lin Wang ◽

GuangWei Sun ◽

XiHong Li ◽

ZhenGuo Chen ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Ralstonia Solanacearum ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Digital Gene Expression ◽

Resistant Cultivar ◽

Glutathione Metabolism ◽

Post Inoculation ◽

Primary Resistance

AbstractTobacco bacterial wilt (TBW) caused by Ralstonia solanacearum is the most serious soil-borne disease of tobacco. However, molecular mechanism information of R. solanacearum resistance is limited to tobacco, hindering better breeding of resistant tobacco. In this study, the expression profiles of the rootstalks of Yunyan87 (susceptible cultivar) and Fandi3 (resistant cultivar) at different stages after R. solanacearum infection were compared to explore molecular mechanisms of tobacco resistance against the bacterium. Findings from gene-expression profiling indicated that the number of upregulated differentially expressed genes (DEGs) at 3 and 7 days post-inoculation (dpi) increased significantly in the resistant cultivar. WRKY6 and WRKY11 family genes in WRKY transcription factors, ERF5 and ERF15 family genes in ERFs transcription factors, and genes encoding PR5 were significantly upregulated in the resistant cultivar response to the infection. For the first time, WRKY11 and ERF15 were found to be possibly involved in disease-resistance. The Kyoto Encyclopedia of Genes and Genomes analysis demonstrated glutathione metabolism and phenylpropane pathways as primary resistance pathways to R. solanacearum infection. In the resistant cultivar, DEGs encoding CYP450, TCM, CCoAOMT, 4CL, PAL, CCR, CSE, and CADH, involved in the synthesis of plant antitoxins such as flavonoids, stilbenoids, and lignins, enriched in the phenylpropane pathway were upregulated at 3 and 7 dpi. Furthermore, a pot experiment was performed to verify the role of flavonoids in controlling TBW. This study will strongly contribute to a better understanding of molecular interactions between tobacco plants and R. solanacearum.

Download Full-text