0000000000312362
AUTHOR
Jubina Benny
Identification of conserved genes linked to responses to abiotic stresses in leaves among different plant species
As a consequence of global climate change, certain stress factors that have a negative impact on crop productivity such as heat, cold, drought and salinity are becoming increasingly prevalent. We conducted a meta-analysis to identify genes conserved across plant species involved in (1) general abiotic stress conditions, and (2) specific and unique abiotic stress factors (drought, salinity, extreme temperature) in leaf tissues. We collected raw data and re-analysed eight RNA-Seq studies using our previously published bioinformatic pipeline. A total of 68 samples were analysed. Gene set enrichment analysis was performed using MapMan and PageMan whereas DAVID (Database for Annotation, Visuali…
Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Background Our study is the first to provide RNA-Seq data analysis related to transcriptomic responses towards drought across different crops. The aim was to identify and map which genes play a key role in drought response on leaves across different crops. Forty-two RNA-seq samples were analyzed from 9 published studies in 7 plant species (Arabidopsis thaliana, Solanum lycopersicum, Zea mays, Vitis vinifera, Malus X domestica, Solanum tuberosum, Triticum aestivum). Results Twenty-seven (16 up-regulated and 11 down-regulated) drought-regulated genes were commonly present in at least 7 of 9 studies, while 351 (147 up-regulated and 204 down-regulated) were commonly drought-regulated in 6 of 9 …
The priming fingerprint on the plant transcriptome investigated through meta-analysis of RNA-Seq data
Plants may enter into a state of alert that allows them to deploy defensive measures in a more effective way upon stress occurrence. This phenomenon is termed defense priming, and it is started in plants with a still enigmatic priming phase in which complex molecular and physiological changes occur. During the priming phase the plant transcriptome is deeply affected, but it remains largely unclear the extent of the transcriptional changes that contribute to prime the plant. In this study, we performed a meta-analysis of publicly available RNA-Seq data obtained during different priming conditions and in different plant species in order to investigate the existence of a transcriptional "primi…
Transcriptome Analysis of Pistacia vera Inflorescence Buds in Bearing and Non-Bearing Shoots Reveals the Molecular Mechanism Causing Premature Flower Bud Abscission
The alteration of heavy (&ldquo
Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops
The present study aimed at identifying and mapping key genes expressed in root tissues involved in drought and salinity tolerance/resistance conserved among different fruit tree species. Twenty-six RNA-Seq samples were analyzed from six published studies in five plant species (Olea europaea, Vitis riparia Michx, Prunus mahaleb, Prunus persica, Phoenix dactylifera). This meta-analysis used a bioinformatic pipeline identifying 750 genes that were commonly modulated in three salinity studies and 683 genes that were commonly regulated among three drought studies, implying their conserved role in resistance/tolerance/response to these environmental stresses. A comparison was done on the genes th…
Transcriptome Response of Metallicolous and a Non-Metallicolous Ecotypes of Noccaea goesingensis to Nickel Excess
Root transcriptomic profile was comparatively studied in a serpentine (TM) and a non-metallicolous (NTM) population of Noccaea goesingensis in order to investigate possible features of Ni hyperaccumulation. Both populations were characterised by contrasting Ni tolerance and accumulation capacity. The growth of the TM population was unaffected by metal excess, while the shoot biomass production in the NTM population was significantly lower in the presence of Ni in the culture medium. Nickel concentration was nearly six- and two-fold higher in the shoots than in the roots of the TM and NTM population, respectively. The comparison of root transcriptomes using the RNA-seq method indicated disti…
Transcriptomic Analysis of the Pistacia vera (L.) Fruits Enable the Identification of Genes and Hormone-Related Gene Linked to Inflorescence Bud Abscission
Pistacia vera (L.) is an alternate bearing species. The tree produces axillary inflorescence buds every year. Still, they abscise in “ON” overloaded shoots, causing a limited production in the following “OFF” year, causing a significant and unfavorable production fluctuation. In this work, we carried out de novo discovery and transcriptomic analysis in fruits of “ON” and “OFF” shoots of the cultivar Bianca. We also investigated whether the fruit signaling pathway and hormone biosynthesis directly or indirectly linked to the premature fall of the inflorescence buds causing alternate bearing. We identified 1536 differentially expressed genes (DE…
INVESTIGATION ON THE GENETIC BASIS OF ENVIRONMENTAL STRESS IN FRUIT TREE CROPS
Plant stress can be divided into two major categories: abiotic stress and biotic stress. Abiotic stress happens when plants are exposed to the environment either physically or chemically. There is an emergency in developing crop varieties that are tolerant to abiotic stresses to ensure food security and safety in the coming years. Multiple abiotic stress like drought, heat, frost at flowering and nutrient deficiency can cause an erratic fruiting behavior or following extreme events, the death of the plants. Plants require an optimal level of nutrients and essential minerals for their growth and development that are mainly acquired from soil by their roots. Nutrient deficiency is an environm…
Deciphering transcriptional regulation mechanisms underlining fruit development and ripening in Vitis vinifera
BACKGROUND: Grapes (Vitis vinifera ) are an important woody crop cultivated in a broad range of environmental conditions. Grapefruit development is a physiological process whose molecular regulatory networks are still not sufficiently investigated. OBJECTIVE: The primary aim of the work was to identify which key genes, molecular mechanisms and networks were involved in fruit ripening and development through a comparison of available transcriptomic data at different stages during grape development and ripening. Secondly, we aimed at identifying among these fruit-related genes, which genes play also a functional role in other developmental and physiological processes in reproductive tissues (…
Advanced Glycation End Products (AGEs): Biochemistry, Signaling, Analytical Methods, and Epigenetic Effects
The advanced glycation end products (AGEs) are organic molecules formed in any living organisms with a great variety of structural and functional properties. They are considered organic markers of the glycation process. Due to their great heterogeneity, there is no specific test for their operational measurement. In this review, we have updated the most common chromatographic, colorimetric, spectroscopic, mass spectrometric, and serological methods, typically used for the determination of AGEs in biological samples. We have described their signaling and signal transduction mechanisms and cell epigenetic effects. Although mass spectrometric analysis is not widespread in the detection of AGEs…
Identifying conserved genes involved in crop tolerance to cold stress
Low temperature is a limiting factor for crop productivity in tropical and subtropical climates. Cold stress response in plants involves perceiving and relaying the signal through a transcriptional cascade composed of different transduction components, resulting in altered gene activity. We performed a meta-analysis of four previously published datasets of cold-tolerant and cold-sensitive crops to better understand the gene regulatory networks and identify key genes involved in cold stress tolerance conserved across phylogenetically distant species. Re-analysing the raw data with the same bioinformatics pipeline, we identified common cold tolerance-related genes. We found 236 and 242 common…
Additional file 10: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S4. Genes involved in the leaf developmental stage that are commonly drought-regulated were shown. Common in seedling studies and common in mature studies were given in separate sheets. GeneID, description, expression pattern and binname were indicated. (XLSX 14 kb)
Additional file 8: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S6. The 27 key genes that were drought-regulated in at least 7 of 9 studies were mapped in the respective chromosomes of the 7 crops. (TIF 536 kb)
Additional file 11: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S6. Genes involved in drought response corresponding to each of the study were shown. TAIR ID, description and log2FC were indicated. (XLSX 321 kb)
Additional file 12: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S5. Genes involved in drought response at different leaf developmental stages (unique for seedling, unique for mature and common for seedling and mature) were shown. TAIR ID, log2FC and expression pattern were indicated. (XLSX 56 kb)
Additional file 3: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S2. MapMan overview showing transcriptomic effects of drought in key categories selected such as secondary metabolism, cellular responses and signaling. Genes were identified as Arabidopsis orthologs of each genes of the analyzed plant species. Red means up-regulated and green means down-regulated. (TIF 226 kb)
Additional file 9: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S3. Genes mapped in the chromosome which are involved in atleast 7 of 9 studies. Arabidopsis ortholog, description and corresponding gene IDs were indicated. (XLSX 12 kb)
Additional file 2: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S1. Clustering heatmap showing the hierarchical relationship among the studies selected for the analysis. Resulted log2FC values of the analysis for generating the tree was indicated. (TIF 163 kb)
Additional file 6: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S5. Key genes encoding transcription factors, hormone metabolism and abiotic stress responses obtained from DAVID software were mapped in the respective chromosomes of the 7 crops. (TIF 536 kb)
Additional file 5: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S4. Protein-protein interaction network analysis predicted for genes commonly regulated in five mature leaf studies performed in Vitis vinifera, Solanum tuberosum, Triticum aestivum, Zea mays (study1) and Zea mays (study 2)based on Arabidopsis knowledgebase. (TIF 185 kb)
Additional file 4: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Figure S3. Protein-protein interaction network analysis predicted for genes commonly regulated in three seedling leaf studies performed in Arabidopsis thaliana, Malus X domestica and Solanum lycopersicum based on Arabidopsis knowledgebase. (TIF 332 kb)
Additional file 1: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S1. The table consists of gene_ID, corresponding arabidopsis orthologs and log2 fold change values for significantly regulated genes (FDRâ
Additional file 7: of Identification of key genes and its chromosome regions linked to drought responses in leaves across different crops through meta-analysis of RNA-Seq data
Table S2. Genes mapped in the chromosome which are involved in transcription factors, abiotic stress response and hormone metabolism. Arabidopsis ortholog, description and corresponding gene IDs were indicated. (XLSX 17 kb)