scholarly journals NetREx – Network-based Rice Expression Analysis Server for Abiotic Stress Conditions

2021 ◽  
Author(s):  
Nita Parekh ◽  
Mayank Musaddi ◽  
Sanchari Sircar
Keyword(s):  
Expression Analysis ◽  
Biological Process ◽  
Research Community ◽  
Stress Conditions ◽  
Orthologous Genes ◽  
Experimental Conditions ◽  
Tissue Specific ◽  
Gene Annotations ◽  
Complex Phenotypes ◽  
Transcriptomic Studies

Recent focus on transcriptomic studies in food crops like rice, wheat and maize provide new opportunities to address issues related to agriculture and climate change. Re-analysis of such data available in public domain supplemented with annotations across molecular hierarchy can be of immense help to the plant research community, particularly co-expression networks representing transcriptionally coordinated genes that are often part of the same biological process. With this objective we have developed NetREx, a Network based Rice Expression Analysis Server, that hosts ranked co-expression networks of Oryza sativa using publicly available mRNA-seq data across uniform experimental conditions. It provides a range of interactable data viewers and modules for analysing user queried genes across different stress conditions (drought, flood, cold and osmosis) and hormonal treatments (abscisic and jasmonic acid) and tissues (root and shoot). Subnetworks of user-defined genes can be queried in preconstructed tissue-specific networks, allowing users to view the fold-change, module memberships, gene annotations and analysis of their neighborhood genes and associated pathways. The webserver also allows querying of orthologous genes from Arabidopsis, wheat, maize, barley, and sorghum. Here we demonstrate that NetREx can be used to identify novel candidate genes and tissue-specific interactions under stress conditions and can aid in the analysis and understanding of complex phenotypes linked to stress response in rice. Available at: https://bioinf.iiit.ac.in/netrex/index.html

scholarly journals Reference Gene Selection for Normalizing Gene Expression in Ips Sexdentatus (Coleoptera: Curculionidae: Scolytinae) Under Different Experimental Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Gothandapani Sellamuthu ◽  
Shan Amin ◽  
Jan Bílý ◽  
Jirí Synek ◽  
Roman Modlinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Expression Analysis ◽  
Reference Genes ◽  
Gene Expression Analysis ◽  
Gene Selection ◽  
Experimental Conditions ◽  
Tissue Specific ◽  
Reference Gene Selection ◽  
Ips Sexdentatus

Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae) is one of the most destructive and economically important forest pests. A better understanding of molecular mechanisms underlying its adaptation to toxic host compounds may unleash the potential for future management of this pest. Gene expression studies could be considered as one of the key experimental approaches for such purposes. A suitable reference gene selection is fundamental for quantitative gene expression analysis and functional genomics studies in I. sexdentatus. Twelve commonly used reference genes in Coleopterans were screened under different experimental conditions to obtain accurate and reliable normalization of gene expression data. The majority of the 12 reference genes showed a relatively stable expression pattern among developmental stages, tissue-specific, and sex-specific stages; however, some variabilities were observed during varied temperature incubation. Under developmental conditions, the Tubulin beta-1 chain (β-Tubulin) was the most stable reference gene, followed by translation elongation factor (eEF2) and ribosomal protein S3 (RPS3). In sex-specific conditions, RPS3, β-Tubulin, and eEF2 were the most stable reference genes. In contrast, different sets of genes were shown higher stability in terms of expression under tissue-specific conditions, i.e., RPS3 and eEF2 in head tissue, V-ATPase-A and eEF2 in the fat body, V-ATPase-A and eEF2 in the gut. Under varied temperatures, β-Tubulin and V-ATPase-A were most stable, whereas ubiquitin (UbiQ) and V-ATPase-A displayed the highest expression stability after Juvenile Hormone III treatment. The findings were validated further using real-time quantitative reverse transcription PCR (RT-qPCR)-based target gene expression analysis. Nevertheless, the present study delivers a catalog of reference genes under varied experimental conditions for the coleopteran forest pest I. sexdentatus and paves the way for future gene expression and functional genomic studies on this species.

scholarly journals Transmembrane START domain proteins:in silicoidentification, characterization and expression analysis under stress conditions in chickpea (Cicer arietinumL.)

2015 ◽  
Vol 11 (2) ◽  
pp. e992698 ◽  
Author(s):  
Viswanathan Satheesh ◽  
Parameswaran Chidambaranathan ◽  
Prasanth Tejkumar Jagannadham ◽  
Vajinder Kumar ◽  
Pradeep K. Jain ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Stress Conditions ◽  
Start Domain

scholarly journals Enzyme activity in the micropylar region of Melanoxylon brauna Schott seeds during germination under heat stress conditions

2020 ◽  
Vol 42 ◽  
Author(s):  
Marcone Moreira Santos ◽  
Eduardo Euclydes de Lima e Borges ◽  
Glauciana da Mata Ataíde ◽  
Raquel Maria de Oliveira Pires ◽  
Debora Kelli Rocha
Keyword(s):  
Enzyme Activity ◽  
Heat Stress ◽  
Seed Germination ◽  
Pectin Methylesterase ◽  
Stress Conditions ◽  
Southeastern Brazil ◽  
Experimental Conditions ◽  
Mannanase Activity ◽  
Ecological Importance ◽  
The Many

Abstract: Recent studies indicate that global temperatures will rise substantially in the 21st century, leading to the extinction of several plant species, as plant metabolism and germination are greatly affected by temperature. Melanoxylon brauna, a tree species native to the Atlantic Forest that occurs from northeastern to southeastern Brazil, is one of the many species threatened by global warming. Despite the economic and ecological importance of M. brauna, studies investigating the influence of heat stress on seed germination and biochemical responses are still incipient. This study aimed to evaluate enzyme activity in the micropylar region of M. brauna seeds during germination under heat stress conditions. Endo-β-mannanase, α-galactosidase, polygalacturonase, pectin methylesterase, pectin lyase, total cellulase, 1,3-β-glucosidase, and 1,4-β-glucosidase activities were determined in micropyles of seeds imbibed for 24, 48 and 72 h at 25, 35 and 45 °C. Seed germination was highest at 25 °C. Endo-β-mannanase activity was not detected under any of the experimental conditions, but imbibition temperature had a significant effect on the activity of all other enzymes.

scholarly journals Validation of Internal Control Genes for Quantitative Real-Time PCR Gene Expression Analysis in Morchella

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2331 ◽  
Author(s):  
Qianqian Zhang ◽  
Wei Liu ◽  
Yingli Cai ◽  
A-Feng Lan ◽  
Yinbing Bian
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Expression Analysis ◽  
Internal Control ◽  
Reference Genes ◽  
Gene Expression Analysis ◽  
Stable Gene ◽  
Experimental Conditions ◽  
The Stability ◽  
Vacuolar Protein

The reliability of qRT-PCR results depend on the stability of reference genes used for normalization, suggesting the necessity of identification of reference genes before gene expression analysis. Morels are edible mushrooms well-known across the world and highly prized by many culinary kitchens. Here, several candidate genes were selected and designed according to the Morchella importuna transcriptome data. The stability of the candidate genes was evaluated with geNorm and NormFinder under three different experimental conditions, and several genes with excellent stability were selected. The extensive adaptability of the selected genes was tested in ten Morchella species. Results from the three experimental conditions revealed that ACT1 and INTF7 were the most prominent genes in Morchella, CYC3 was the most stable gene in different development stages, INTF4/AEF3 were the top-ranked genes across carbon sources, while INTF3/CYC3 pair showed the robust stability for temperature stress treatment. We suggest using ACT1, AEF3, CYC3, INTF3, INTF4 and INTF7 as reference genes for gene expression analysis studies for any of the 10 Morchella strains tested in this study. The stability and practicality of the gene, vacuolar protein sorting (INTF3), vacuolar ATP synthase (INTF4) and14-3-3 protein (INTF7) involving the basic biological processes were validated for the first time as the candidate reference genes for quantitative PCR. Furthermore, the stability of the reference genes was found to vary under the three different experimental conditions, indicating the importance of identifying specific reference genes for particular conditions.

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