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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 commonly regulated genes in sensitive and tolerant genotypes, respectively. Gene enrichment analysis showed that protein modifications, hormone metabolism, cell wall, and secondary metabolism are the most conserved pathways involved in cold tolerance. Upregulation of the abiotic stress (heat and drought/salt) related genes [heat shock N-terminal domain-containing protein, 15.7 kDa class I-related small heat shock protein-like, DNAJ heat shock N-terminal domain-containing protein, and HYP1 (HYPOTHETICAL PROTEIN 1)] in sensitive genotypes and downregulation of the abiotic stress (heat and drought/salt) related genes (zinc ion binding and pollen Ole e 1 allergen and extensin family protein) in tolerant genotypes was observed across the species. Almost all development-related genes were upregulated in tolerant and downregulated in sensitive genotypes. Moreover, protein–protein network analysis identified highly interacting proteins linked to cold tolerance. Mapping of abiotic stress-related genes on analysed species genomes provided information that could be essential to developing molecular markers for breeding and building up genetic improvement strategies using CRISPR/Cas9 technologies.

Drought affects plant growth and development, causing severe yield losses, especially in cereal crops. The identification of genes involved in drought tolerance is crucial for the development of drought-tolerant crops. The aim of this study was to identify genes that are conserved key players for conferring drought tolerance in cereals. By comparing the transcriptomic changes between tolerant and susceptible genotypes in four Gramineae species, we identified 69 conserved drought tolerant-related (CDT) genes that are potentially involved in the drought tolerance of all of the analysed species. The CDT genes are principally involved in stress response, photosynthesis, chlorophyll biogenesis, secondary metabolism, jasmonic acid signalling, and cellular transport. Twenty CDT genes are not yet characterized and can be novel candidates for drought tolerance. The k-means clustering analysis of expression data highlighted the prominent roles of photosynthesis and leaf senescence-related mechanisms in differentiating the drought response between tolerant and sensitive genotypes. In addition, we identified specific transcription factors that could regulate the expression of photosynthesis and leaf senescence-related genes. Our analysis suggests that the balance between the induction of leaf senescence and maintenance of photosynthesis during drought plays a major role in tolerance. Fine-tuning of CDT gene expression modulation by specific transcription factors can be the key to improving drought tolerance in cereals.

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 (DEGs) in fruits of “ON” vs. “OFF” shoots, which are involved primarily in sugar metabolism, plant hormone pathways and transcription factors. The premature bud abscission linked to the phenomenon is attributable to a lack of nutrients (primarily sugar) and the possible competition between the same branches’ sinks (fruits vs. inflorescence buds). Hormone pathways are involved as a response to signals degradation and remobilization of carbon and nutrients due to the strengthening of the developing embryos. Genes of the secondary metabolism and transcription factors are also involved in tailoring the individual branches response to the nutritional stress and sink competition. Crosstalk among sugar and various hormone-related genes, e.g., ethylene, auxin, ABA and cytokinin, were determined. The discovery of putative biomarkers like callose synthase 5, trehalose-6-phosphate synthase, NAD(P)-linked oxidoreductase and MIOX2, Jasmonate, and salicylic acid-related genes can help to design precision farming practices to mitigate the alternate bearing phenomenon to increase farming profitability. The aim of the analysis is to provide insight into the gene expression profiling of the fate of “ON” and “OFF” fruits associated with the alternate bearing in the pistachio.

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 "priming fingerprint". Our results show that similarities in transcriptome reprogramming affect a small group of genes with similar and often low fold change value. Similarities affect, among others, the down-regulation of genes involved in methylerythritol 4-phosphate (MEP) pathway (e.g. DXR), photosynthesis (e.g. PSBQ-2), fatty acid synthesis (e.g. FAD2), and transcription factors (TFs) enabling normal development (e.g. BES1, DAR2, COL9), likely reflecting eventual metabolic costs. In contrast, the up-regulation of genes encoding receptors (e.g. RPM1), MAP kinases (MKK2, MPK6, MPK1), TFs enabling defense (e.g. RAP2.12, EIN3, WRKY18, HSFA4A, HSF3, BZIP17), genes involved in beta-oxidation (ACX1), monoterpene synthesis (GPS1), and negative immune signaling regulators (e.g. PP2C38 and BIR1) highlight a common preparation for a broad-spectrum defense. This study reveals a set of conserved transcriptional changes that mark the priming phase in plants, and aids to decipher the role of the transcriptome within the priming changes.

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 (bud and flower). METHODS: The two objectives were obtained through a meta-analysis on 9 RNA-Sequencing (RNA-Seq) studies. Raw data was downloaded from publicly available resource and re-analyzed to find out the significant differentially expressed genes (DEGs) (p -value

Drought negatively affects plant growth and development. The ability to tolerate abiotic stresses varies among species, and among genotypes within species. Unrevealing the molecular mechanisms behind drought response is essential to identify the genes involved in tolerance. A meta-analysis on RNA-Seq data of four Gramineae species was performed to identify the genes representing common key players in response to drought, as well as the regulatory pathways in which these genes are involved. Four available RNA-Seq datasets were selected, representing the transcriptomic response to drought in the leaf of two contrasting genotypes (tolerant and sensitive) in brachypodium, barley, maize and rice. We re-analysed the transcriptomic data with a unique pipeline and detected the differentially expressed genes (DEGs) in both genotypes of the four experiments. The drought-induced variation in DEG expression was compared between tolerant and susceptible genotypes of each species. We assumed that the genes whose expression regulation differs between the two contrasting genotypes represent key players in the differentiation between the tolerant and the sensitive response to drought. The putative rice orthologues of the selected genes were identified to obtain comparable datasets. We found 69 common genes that are putatively involved in drought tolerance in the four species, and protein-protein interaction were predicted. The DEGs encoding transcription factors that may play a role in drought tolerance were also identified. Gene co-expression networks were constructed to reveal common regulatory pathways that putatively differentiate the response of tolerant and susceptible genotypes in the four Gramineae species.

The alteration of heavy (&ldquo, ON/bearing&rdquo, ) and light (&ldquo, OFF/non-bearing&rdquo, ) yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The analysis provides insights into the transcript changes between inflorescence buds on bearing and non-bearing shoots, that we indicated as &ldquo, ON&rdquo, and &ldquo, OFF&rdquo, and shed light on the molecular mechanisms causing premature inflorescence bud abscission in the pistachio cultivar &ldquo, Bianca&rdquo, which can be related to the alternate bearing behavior. In this study, a transcriptome analysis was performed in inflorescence buds of &ldquo, shoots. A total of 14,330 differentially expressed genes (DEGs), most of which are involved in sugar metabolism, plant hormone pathways, secondary metabolism and oxidative stress pathway, were identified. Our results shed light on the molecular mechanisms underlying inflorescence bud abscission in pistachio and we proposed a hypothetical model behind the molecular mechanism causing this abscission in &ldquo, shoots. Results highlighted how changes in genes expressed in nutrient pathways (carbohydrates and mineral elements) in pistachio &ldquo, vs. &ldquo, inflorescence buds triggers a cascade of events involving trehalose-6-phosphate and target of rapamycin (TOR) signaling, SnRK1 complex, hormones, polyamines and ROS which end, through programmed cell death and autophagy phenomena, with the abscission of inflorescence buds. This is the first study reporting gene expression profiling of the fate of &ldquo, inflorescence buds associated with the alternate bearing in the pistachio.

The alteration of heavy (“ON/bearing”) and light (“OFF/non-bearing”) yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of inflorescence buds on high yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The analysis provides insights into the transcript changes between inflorescence buds on bearing and non-bearing shoots, that we indicated as “ON” and “OFF”, and shed light on the molecular mechanisms causing premature inflorescence bud abscission in the pistachio cultivar “Bianca” which can be related to the alternate bearing behavior. In this study, a transcriptome analysis was performed in inflorescence buds of “ON” and “OFF” shoots. A total of 14,330 differentially expressed genes (DEGs), most of which are involved in sugar metabolism, plant hormone pathways, secondary metabolism and oxidative stress pathway, were identified. Our results shed light on the molecular mechanisms underlying inflorescence bud abscission in pistachio and we proposed a hypothetical model behind the molecular mechanism causing this abscission in “ON” shoots. Results highlighted how changes in genes expressed in nutrient pathways (carbohydrates and mineral elements) in pistachio “ON” vs. “OFF” inflorescence buds triggers a cascade of events involving trehalose-6-phosphate and target of rapamycin (TOR) signaling, SnRK1 complex, hormones, polyamines and ROS which end, through programmed cell death and autophagy phenomena, with the abscission of inflorescence buds. This is the first study reporting gene expression profiling of the fate of “ON” and “OFF” inflorescence buds associated with the alternate bearing in the pistachio.

Background:Recent advances in next-generation sequencing technology allow highthroughput RNA-Sequencing to be widely applied in studying coding and non-coding RNA profiling in cells. RNA-Seq data usually contains functional transcriptomic and other small and larger non-coding (nc) RNA sequences. Objective: MicroRNAs (miRNAs), a small nc-RNA act as epigenetic markers and the expression of their target genes and pathways that regulate Hepatocellular Carcinoma (HCC), a primary malignancy of the liver. The unreported potential novel miRNAs targeting HCC pathways can be identified from the sequenced data.Methods:In this study, we performed a computational identification of novel putative miRNAs and their targets from publicly available high-throughput sequencing Fastq data of human HCC cells HepG2, NorHep and SKHep1, retrieved from NCBI-SRA.Results:Totally, 572 unique known precursor miRNAs and 1062 unique novel miRNAs were identified from HepG2, Nor and SKHep1 HCC cell lines. Interestingly, 140 novel miRNAs were predicted to be extensively involved in targeting genes of HCC related pathways such as apoptosis, cell signaling, cell division, cell-cycle arrest, GPCR, MAPK cascade, TOR signaling, TNFSF11 signaling and liver development.Conclusion:The predicted novel miRNAs reported in the paper might have a vital role in regulating the molecular mechanism of HCC and thus, further studies on these miRNAs will provide significant clues for researchers into the complex biological process of liver cancer.

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 at the clinical level, this technique is highly promising for the early diagnosis and therapeutics of diseases caused by AGEs. Protocols are available for high-resolution mass spectrometry of glycated proteins although they are characterized by complex machine management. Simpler procedures are available although much less precise than mass spectrometry. Among them, immunochemical tests are very common since they are able to detect AGEs in a simple and immediate way. In these years, new methodologies have been developed using an in vivo novel and noninvasive spectroscopic methods. These methods are based on the measurement of autofluorescence of AGEs. Another method consists of detecting AGEs in the human skin to detect chronic exposure, without the inconvenience of invasive methods. The aim of this review is to compare the different approaches of measuring AGEs at a clinical perspective due to their strict association with oxidative stress and inflammation.

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, Visualisation and Integrated Discovery) was used for metabolic process enrichment analysis. We identified of a total of 5122 differentially expressed genes when considering all abiotic stresses (3895 were upregulated and 1227 were downregulated). Jasmonate-related genes were more commonly upregulated by drought, whereas gibberellin downregulation was a key signal for drought and heat. In contrast, cold stress clearly upregulated genes involved in ABA (abscisic acid), cytokinin and gibberellins. A gene (non-phototrophic hypocotyl) involved in IAA (indoleacetic acid) response was induced by heat. Regarding secondary metabolism, as expected, MVA pathway (mevalonate pathway), terpenoids and alkaloids were generally upregulated by all different stresses. However, flavonoids, lignin and lignans were more repressed by heat (cinnamoyl coA reductase 1 and isopentenyl pyrophosphatase). Cold stress drastically modulated genes involved in terpenoid and alkaloids. Relating to transcription factors, AP2-EREBP, MADS-box, WRKY22, MYB, homoebox genes members were significantly modulated by drought stress whereas cold stress enhanced AP2-EREBPs, bZIP members, MYB7, BELL 1 and one bHLH member. C2C2-CO-LIKE, MADS-box and a homeobox (HOMEOBOX3) were mostly repressed in response to heat. Gene set enrichment analysis showed that ubiquitin-mediated protein degradation was enhanced by heat, which unexpectedly repressed glutaredoxin genes. Cold stress mostly upregulated MAP kinases (mitogen-activated protein kinase). Findings of this work will allow the identification of new molecular markers conserved across crops linked to major genes involved in quantitative agronomic traits affected by different abiotic stress.

Using Illumina Miseq based 16S rRNA amplicon sequencing approach, the present study evaluated the influence of chromite mining on soil bacterial diversity and community structure in two in situ mine sites along with one chromite mine overburden soil and a forest soil adjacent to Sukinda chromite mines area of Odisha, India exhibiting different heavy metals (Cr, Pb, Mn etc.) concentration gradient. The soil bacterial communities at four study sites harbour a distinct set of phyla types which varies among the sites in relation to soil physico-chemical properties. Among the four locations, the overburden site (medium level of contamination) was distributed with higher bacterial operational taxonomic units (OTUs) abundance clustered at 97% sequence identity, whereas nearby forest soil sample with least contamination was reported with lesser number of bacterial OTUs. Principal component analysis plot indicated that in situ sites were distributed with closely related or most common species than other two samples. The dataset comprises more than 20000 OTUs that are affiliated to seven major bacterial phyla: Actinobacteria and Proteobacteria followed by Firmicutes, Acidobacteria, Chloriflexi, Bacteroidetes and unclassified phylum in all four samples. There is a shift in phylum level bacterial population (Actinobacteria, Proteobacteria and Acidobacteria) from contaminated sites to control sites and suggests that these bacterial groups may be the most metal tolerant organisms found in the contaminated sites. At species level, in situ sites were enriched with most common abundant microbes such as Shigella sp., Bacteroides sp., Propionibacterium acnes, Pantoea sp., Aciditerrimonas sp., Reyranella sp., Alphaproteobacterium sp., Burkholderiaceae sp. Soil pH and concentration of heavy metal such as chromium play a key role in affecting the structure and diversity of microbial communities in this study. This work demonstrates first-ever study in revealing bacterial diversity and presents background information of bacterial communities of Sukinda chromite mine area and shed light on possible bioremediation promoted by bacterial communities.

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 studies. Across all kind of leaves, the drought repressed gene-ontologies were related to the cell wall and membrane re-structuring such as wax biosynthesis, cell wall organization, fatty acid biosynthesis. On the other hand, drought-up-regulated biological processes were related to responses to osmotic stress, abscisic acid, water deprivation, abscisic-activated signalling pathway, salt stress, hydrogen peroxide treatment. A common metabolic feature linked to drought response in leaves is the repression of terpenoid pathways. There was an induction of AL1 (alfin-like), UGKYAH (trihelix), WRKY20, homeobox genes and members of the SET domain family in 6 of 9 studies. Several genes involved in detoxifying and antioxidant reactions, signalling pathways and cell protection were commonly modulated by drought across the 7 species. The chromosome (Chr) mapping of these key abiotic stress genes highlighted that Chr 4 in Arabidopsis thaliana, Chr 1 in Zea mays, Chr 2 and Chr 5 in Triticum aestivum contained a higher presence of drought-related genes compared to the other remaining chromosomes. In seedling studies, it is worth notice the up-regulation of ERF4 and ESE3 (ethylene), HVA22 (abscisic acid), TIR1 (auxin) and some transcription factors (MYB3, MYB94, MYB1, WRKY53 and WRKY20). In mature leaves, ERF1 and Alfin-like 1 were induced by drought while other transcription factors (YABBY5, ARR2, TRFL2) and genes involved phospholipid biosynthesis were repressed. Conclusions The identified and mapped genes might be potential targets of molecular breeding activities to develop cultivars with enhanced drought resistance and tolerance across different crops. Electronic supplementary material The online version of this article (10.1186/s12870-019-1794-y) contains supplementary material, which is available to authorized users.

In Northeast India, widely practiced shifting cultivation practice created various land uses associated with altered soil biochemical and microbial attributes. The present study aimed to analyze soil biochemical and microbial characteristics in rhizosphere using Illumina paired-end sequencing in five dominant land uses (Oil Palm Plantation, OPP; Bamboo Forest, BF; Rubber Plantation, RP; Fallow Land, FL and Natural Forest, NF) of Mizoram, Northeast India. The soils of different land uses were strongly acidic (pH ranged from 4.4–5.3) in nature reflecting the dominance of acidophilic soil microbes (e.g. Acidobacteria, Proteobacteria and Verrucomicrobia) and majority of unassigned bacteria accounting >50% of all sequences. NF soil showed high organic carbon and total nitrogen (TN), however, levels of available phosphorous (Pavail), microbial biomass carbon, ammonium and nitrate nitrogen, and rates of N-mineralization (N-min) were considerably high in BF. Basal soil respiration significantly (p