Deep Transcriptome Profiling of Citrus Fruit in Response to Huanglongbing Disease.

Proposal of a Citrus translational genomic approach for early and infield detection of Flavescence dorée in Vitis

Flavescence dore´e (FD) is one of the most widely known grapevine yellows disease and one of the most unabated worldwide in the viticulture sector. In this paper, we outline a strategy for developing an integrated system of technologies to enable rapid, early disease FD detection and diagnosis. We propose the deployment of a newly developed sensor device, the differential mobility spectrometer (DMS), which has shown positive results with a similar vector-borne disease in Citrus. We have previously demonstrated that the gas chromatograph DMS (GC/DMS) can distinguish various citrus diseases, and the system may also allow detection of volatile organic compound (VOC) signals from a tree of othe…

Detection and identification Fabavirus species by one-step RT-PCR and multiplex RT-PCR

The genus Fabavirus of the family Secoviridae comprises a group of poorly characterized viruses. To date, only five species have been described: Broad bean wilt virus 1 (BBWV-1), Broad bean wilt virus 2 (BBWV-2), Lamium mild mosaic virus (LMMV), Gentian mosaic virus (GeMV) and Cucurbit mild mosaic virus (CuMMV). The development is described of two RT-PCR procedures for the detection and identification of Fabavirus species: a one-step RT-PCR using a single pair of conserved primers for the detection of all fabaviruses, and a one-step multiplex RT-PCR using species-specific primers for the simultaneous detection and identification of the above-mentioned species of the genus Fabavirus. These m…

Metabolic profiling and post-harvest behavior of “dottato” fig (Ficus carica L.) fruit covered with an edible coating from O. ficus-indica

Fig fruits are usually highly sensitive to some physiopathological disorders during post-harvest life, such as softening and skin cracking. Indeed, the use of edible coating (EC) has been evaluated in several fruit crops to reduce fruit post-harvest transpiration and to maintain fruit visual quality. The aim of this study was to determine the post-harvest metabolic response of breba figs treated with mucilage extract from O. ficus-indica cladodes, using an untargeted metabolomic approach. Coated and non coated (control) fruit were sealed in plastic bags, and stored at 4 °C for 7 days. The effect of the edible coatings on their quality fruit during cold storage and qualitative attributes wer…

Metabolic profiling of ripe olive fruit in response to moderate water stress

a b s t r a c t The concentrations of different metabolites in olive (Olea europaea (L.)) fruit at harvest can be affected by water availability, with significant consequences on the composition and the quality of the resulting oil. The aim of the present study was to profile the metabolic composition of ripe olives (cv. Cipressino) grown under water-stress and irrigated conditions applied during the last part of the fruit developmental cycle (from pit hardening to commercial harvest). The imposed conditions resulted in a moderate water stress (−3.5 MPa) at the end of the experimental period. Samples (pulp + skin) of fruit collected at the stage of complete epicarp pigmentation were analyze…

Deploying Genome Editing Tools for Dissecting the Biology of Nut Trees

Walnuts are among the most important nut crops grown in temperate regions of the world. Commercial production in California, and increasingly worldwide, relies on only few clonally grafted scion genotypes, particularly “Chandler,” and more recently clonally propagated disease-resistant rootstocks. Diseases, nematodes, insect pests, abiotic stresses, and other nutritional and environmental factors, can reduce walnut productivity and quality, affecting grower profitability. The California Walnut Breeding Program at UC Davis has developed and released scion cultivars and rootstocks to help address some of these problems. Sequencing of the walnut genome is expected to speed walnut breeding by f…

Old apple varieties (Malus domestica Borkh.) found in the Casentino area (Arezzo- Tuscany): morphological, biometrical and molecular (SSR) characterization.

A metabolomic approach to study water stress response in olive.

Identification and characterization of durum wheat microRNAs in leaf and root tissues.

MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs. In addition, seven microRNA homeologous groups were identified in each of the two genomes of the tetraploid durum wheat. Differenti…

Additional file 5: Figure S3. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

A list of commonly regulated proteins by HLB, comparing effects in the two Citrus genotypes. VC = Volkameriana control (healthy), VI = Volkameriana Infected, NC = Navel orange control (healthy), NI = Navel orange infected. Annotation and Citrus ID are indicated. (PDF 121 kb)

Technology generation to dissemination: lessons learned from the tef improvement project

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional- and molecular-breeding techniques to improve tef—an orphan crop important to the food security in the Horn of Africa, a region of the world w…

Genetic variation and evolutionary analysis ofPepino mosaic virusin Sicily: insights into the dispersion and epidemiology

Pepino mosaic virus (PepMV) is a highly infectious potexvirus that causes a severe disease in tomato (Solanum lycopersicum) crops worldwide. In Sicily, the first outbreak was detected in a single greenhouse in 2005 and it was promptly eradicated. However, in 2008, a large number of greenhouses were simultaneously affected, and it was impossible to eradicate or control the virus. This study addressed the dispersion and the genetic diversity of PepMV isolates obtained from the outbreak in Sicily, in comparison with worldwide PepMV isolates, to gain insight into the factors determining the evolution and epidemiology of the virus. A total of 1800 samples from plants with and without symptoms we…

Transcriptome approach to understand the potential mechanisms inhibiting or triggering blossom-end rot development in tomato fruit in response to plant growth regulators.

The objectives of this study were to analyze changes in gene expression and identify candidate genes and gene networks potentially inhibiting or triggering blossom-end rot (BER) in tomatoes treated with plant growth regulators. ?Ace 55 (Vf)? tomato plants were grown in a greenhouse and sprayed with Apogee (300 mg L?1), abscisic acid (ABA) (500 mg L?1), water (control), or gibberellins 4?+?7 (GA4?+?7) (300 mg L?1) weekly after pollination. The BER incidence rate was zero in Apogee- and ABA-, medium in water-, and high in GA4?+?7-treated plants from 26 to 40 days after pollination (DAP). At 26 DAP, healthy blossom-end fruit tissue still not showing visible BER symptoms was used for transcript…

Molecular and metabolic analysis during fruit development and water stress in olive.

Stress responses in citrus peel: Comparative analysis of host responses to Huanglongbing disease and puffing disorder

Abstract A comparison between transcriptomic responses to puffing disorder and Huanglongbing disease was conducted to decipher differences and similarities in gene and pathway regulation induced by abiotic (puffing) and biotic stresses (Huanglongbing) in citrus peel tissues. We functionally analyzed two previously published datasets: the first obtained for the study of puffing disorder using an Affymetrix citrus microarray and the second consisting of a deep sequencing analysis of symptomatic responses to Huanglongbing disease. Transcriptomic data were mined using bioinformatic tools to highlight genes and pathways playing a key role in modulating responses to different types of stress in c…

Identifying Host Molecular Features Strongly Linked With Responses to Huanglongbing Disease in Citrus Leaves

© 2018 Balan, Ibáñez, Dandekar, Caruso and Martinelli. A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46–68 million reads with an alignment percentage of 72.95–86.76%. Only 16 HLB-regulated genes were commonly identified between the three leaf datasets. Among them were key genes encoding proteins involved in cell wall modification such as CESA8, pecti…

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…

Metabolomics Suggests That Soil Inoculation with Arbuscular Mycorrhizal Fungi Decreased Free Amino Acid Content in Roots of Durum Wheat Grown under N-Limited, P-Rich Field Conditions

Arbuscular mycorrhizal fungi (AMF) have a major impact on plant nutrition, defence against pathogens, a plant's reaction to stressful environments, soil fertility, and a plant's relationship with other microorganisms. Such effects imply a broad reprogramming of the plant's metabolic activity. However, little information is available regarding the role of AMF and their relation to other soil plant growth-promoting microorganisms in the plant metabolome, especially under realistic field conditions. In the present experiment, we evaluated the effects of inoculation with AMF, either alone or in combination with plant growth-promoting rhizobacteria (PGPR), on the metabolome and changes in metabo…

Discovery of molecular markers for early detection of Rhynchophorus ferrugineus attacks in Phoenix canariensis.

Water Deficit Affects the Growth and Leaf Metabolite Composition of Young Loquat Plants

Water scarcity in the Mediterranean area is very common and understanding responses to drought is important for loquat management and production. The objective of this study was to evaluate the effect of drought on the growth and metabolism of loquat. Ninety two-year-old plants of &lsquo

Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and…

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 …

Transcript analysis and metabolome profiling of developing olive fruit in relation to different water regimes.

Identifying early host response and countermeasures in citrus to biotic and abiotic stress.

Rhynchophorus ferrugineus attack affects a group of compounds rather than rearranging Phoenix canariensis metabolic pathways

The red palm weevil (RPW; Rhynchophorus ferrugineus) is spreading worldwide and severely harming many palm species. However, most studies on RPW focused on insect biology, and little information is available about the plant response to the attack. In the present experiment, we used metabolomics to study the alteration of the leaf metabolome of Phoenix canariensis at initial (1st stage) or advanced (2nd stage) attack by RPW compared with healthy (unattacked) plants. The leaf metabolome significantly varied among treatments. At the 1st stage of attack, plants showed a reprogramming of carbohydrate and organic acid metabolism; in contrast, peptides and lipid metabolic pathways underwent more c…

Light induces expression of a dehydrin-encoding gene during seedling de-etiolation in sunflower (Helianthus annus L.)

The effects of light quality on the expression of a sunflower dehydrin-encoding gene, HaDhn1, were studied during seedling de-etiolation. Seeds were germinated in the dark and, after 5 days, seedlings were maintained well watered and de-etiolated under different lights for 3, 6, 12, and 24h. Exposure to white light stimulated HaDhn1 transcript accumulation in the cotyledons of these seedlings, contrary to seedlings grown in the dark. HaDhn1 transcripts increased also treating plantlets with monochromatic lights, especially red light. The increase of HaDhn1 transcripts is provoked by the formation of the active form of phytochrome. Further experiments, performed saturating active phytochrome…

RNA-Seq analysis to investigate alternate bearing mechanism in Pistacia vera L

Pistachio (Pistacia vera L.) production suffers a high level of alternate bearing. The mechanism underlying this negative phenomenon is different from other species, such as apple and olive. Pistachio produces a high number of inflorescence buds every year that in heavy cropping trees (“ON”) mostly fall during the kernel development phase, which occurs in July-August. Primary metabolites (i.e., carbohydrates) play a key role in the signaling related to inflorescence bud abscission. In this work, RNA-Seq was used as a tool to investigate transcriptome of inflorescence buds and fruits, sampled from branches with low (“OFF”) and high (“ON”) crop load. Reference based RNA-Seq analysis using Ara…

Characterizing the effects of salt stress in Calendula officinalis L

In this study the effects of salt stress on growth and several stress markers were investigated in the ornamental and medicinal plant Calendula officinalis. One month old plants were submitted to increasing concentrations of salt up to 150mM NaCl for a period of 30 days. Salinity affected growth in terms of stem length and fresh weight of the plants, but water content remained unchanged indicating a certain tolerance to low and mild concentrations of salt. Although Na+ and Cl− increased in parallel to applied salt treatments, the levels of K+ and Ca2+ showed no significant change, while Mg2+ levels recorded a two folds increase upon the application of the highest salt concentration. Other m…

Molecular and agronomic responses to plant-growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal (AM) fungi in durum wheat

Plant-growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake by increasing the availability of nutrients and the root adsorbing surface (Garg et al., 2006; Asghar et al. 2002). The first objective of this study was to determine the effects of these associations on plant total biomass and grain yield in durum wheat (cv. Anco Marzio). Secondly, we aimed to analyze the root transcriptomic and metabolomic changes in response to mychorrizal infections and the expression pattern of key genes involved in nutrient uptake and stress responses. Field analysis were carried out in inner Sicily, a typical Mediterranean area. Four types of biotic a…

Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease.

Background Huanglongbing (HLB) disease is still the greatest threat to citriculture worldwide. Although there is not any resistance source in the Citrus germplasm, a certain level of moderated tolerance is present. A large-scale analysis of proteomic responses of Citrus may help: 1) clarifying physiological and molecular effects of disease progression, 2) validating previous data at transcriptomic level, and 3) identifying biomarkers for development of early diagnostics, short-term therapeutics and long-term genetic resistance. Results In this work we have conducted a proteomic analysis of mature leaves of two Citrus genotypes with well-known differing tolerances to HLB: Navel orange (highl…

Effects of transgenic expression of Brevibacterium linens methionine gamma lyase (MGL) on accumulation of Tylenchulus semipenetrans and key aminoacid contents in Carrizo citrange.

Key message Carrizo transgenic plants overexpressing methionine-gamma-lyase produced dimethyl sulfide. The transgenic plants displayed more resistance to nematode attacks (Tylenculus semipenetrans) and may represent an innovative strategy for nematode control. Abstract Tylenchulus semipenetrans is a nematode pest of many citrus varieties that causes extensive damage to commercial crops worldwide. Carrizo citrange vr. (Citrus sinensis L. Usb × Poncirus trifoliate L. Raf) plants overexpressing Brevibacterium linens methionine-gamma-lyase (BlMGL) produced the sulfur volatile compound dimethyl sulfide (DMS). The aim of this work was to determine if transgenic citrus plants expressing BlMGL show…

Application of the DNA barcoding in the identification of Mediterranean wild plants with ornamental attitude.

Additional file 5: Figure S3. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

A list of commonly regulated proteins by HLB, comparing effects in the two Citrus genotypes. VC = Volkameriana control (healthy), VI = Volkameriana Infected, NC = Navel orange control (healthy), NI = Navel orange infected. Annotation and Citrus ID are indicated. (PDF 121 kb)

A metabolomic approach to study minimally processed peach (Prunus persica) fruits.

Morphological, chemical, and genetic diversity of wild myrtle(Myrtus communis L.) populations in Sicily

Myrtus communis L. İs a shrub widespread in the Mediterranean area. The interest in this species is growing, mainly due to its pharmacological and aromatic properties. The overexploitation of wild populations induced increasing degradation of plant cover with serious risk of loss of genetic diversity. This research explored the morphological, chemical, and genetic diversity of wild myrtle populations in Sicily, with the aim to provide a first characterization of a core collection of 36 accessions from 7 localities for future domestication programs. Amplified fragment length polymorphism fingerprinting generated 152 polymorphic fragments. STRUCTURE analysis identified three genetic clusters …

Analysis of Early Host Responses for Asymptomatic Disease Detection and Management of Specialty Crops

The rapid and unabated spread of vector-borne diseases within US specialty crops threatens our agriculture, our economy, and the livelihood of growers and farm workers. Early detection of vector-borne pathogens is an essential step for the accurate surveillance and management of vector-borne diseases of specialty crops. Currently, we lack the tools that would detect the infectious agent at early (primary) stages of infection with a high degree of sensitivity and specificity. In this paper, we outline a strategy for developing an integrated suite of platform technologies to enable rapid, early disease detection and diagnosis of huanglongbing (HLB), the most destructive citrus disease. The re…

Arbuscular mycorrhizal symbiosis mitigates the negative effects of salinity on durum wheat

Arbuscular mycorrhizal (AM) symbiosis is generally considered to be effective in ameliorating the plant tolerance to salt stress. Unfortunately, the comprehension of the mechanisms implicated in salinity stress alleviation by AM symbiosis is far from being complete. Thus, an experiment was performed by growing durum wheat (Triticum durum Desf.) plants under salt-stress conditions to evaluate the influence of AM symbiosis on both the plant growth and the regulation of a number of genes related to salt stress and nutrient uptake. Durum wheat plants were grown outdoors in pots in absence or in presence of salt stress and with or without AM fungi inoculation. The inoculum consisted of a mixture…

Addition of high C:N crop residues to a P-limited substrate constrains the benefits of arbuscular mycorrhizal symbiosis for wheat P and N nutrition

Many aspects concerning the role of arbuscular mycorrhizal (AM) fungi in plant nutrient uptake from organic sources remain unclear. Here, we investigated the contribution of AM symbiosis to N and P uptake by durum wheat after the addition of a high C:N biomass to a P-limited soil. Plants were grown in pots in the presence or absence of a multispecies AM inoculum, with (Org) or without (Ctr) the addition of 15N-labelled organic matter (OM). A further treatment, in which 15N was applied in mineral form (Ctr+N) in the same amount as that supplied in the Org treatment, was also included. Inoculation with AM had positive effects on plant growth in both control treatments (Ctr and Ctr+N), mainly …

Deep transcriptome profile of early host responses to Huanglongbing in citrus fruit and leaf tissues.

Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance

AbstractThe salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress resp…

Functional genomics in Olea europaea: identification and annotation of differentially expressed transcripts in developing olive fruit.

Additional file 3: Figure S1. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Metabolism oveview of proteomic changes in response to HLB disease, comparing effects in the two Citrus genotypes. (PDF 115Â kb)

Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries.

For certain food products, postharvest controlled stresses or treatments with specific elicitors are applied to induce desired physical/chemical changes and/or to positively affect phytochemical content. This is the case of wine grapes where both strategies, singularly applied or coupled, can be used to modulate berry composition and, as a consequence, affect wine quality traits. Since the knowledge of the effects of these postharvest treatments on berry metabolism and the regulation of gene expression is very limited, a large-scale transcriptome analysis has been carried out, using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries subjected to deh…

New role of sawtooth transcription factors in the shift to photoautotrophic growth in plants

Plant stress biology in epigenomic era.

Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanis…

Application of a portable instrument for rapid and reliable detection of SARS-CoV-2 infection in any environment

Abstract The ongoing outbreak of the novel coronavirus (SARS‐CoV‐2) infection is creating serious challenges for health laboratories that seek to identify viral infections as early as possible, optimally at the earliest appearance of symptom. Indeed, there is urgent need to develop and deploy robust diagnostic methodologies not only to use in health laboratory environments but also directly in places where humans circulate and spread the virus such as airports, trains, boats, and any public aggregation places. The success of a reliable and sensitive asymptomatic diagnosis relies on the identification and measurement of informative biomarkers from human host and virus in a rapid, sensitive, …

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

Transcriptome analysis of Phoenix canariensis Chabaud in response to Rhynchophorus ferrugineus Olivier attacks

Red Palm Weevil (RPW, Rhynchophorus ferrugineus Olivier) threatens most palm species worldwide. Until now, no studies have analyzed the gene regulatory networks of Phoenix canariensis (Chabaud) in response to RPW attacks. The aim of this study was to fill this knowledge gap. Providing this basic knowledge is very important to improve its management.Results: A deep transcriptome analysis was performed on fully expanded leaves of healthy non-infested trees and attacked trees at two symptom stages (middle and late infestation). A total of 54 genes were significantly regulated during middle stage. Pathway enrichment analysis showed that phenylpropanoid-related pathways were induced at this stag…

Additional file 3: Figure S1. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Metabolism oveview of proteomic changes in response to HLB disease, comparing effects in the two Citrus genotypes. (PDF 115Â kb)

Micromorphological, biochemical and genetic characterization of two ancient late bearing apple varieties.

Diagnostic tools to assess citrus health and disease status

Transcriptomic responses to biotic stresses in Malus x domestica: a meta-analysis study.

AbstractRNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. The objective of this work is to identify specific and common molecular responses between different transcriptomic data related to fungi, virus and bacteria attacks in Malus x domestica. We analyzed seven transcriptomic datasets in Malus x domestica divided in responses to fungal pathogens, virus (Apple Stem Grooving Virus) and bacteria (Erwinia amylovora). Data were dissected using an integrated approach of pathway- and gene- set enrichment analysis, Mapman visualization tool, gene ontology analysis and inferred protein-protein interaction network. Our meta-analysis revealed…

Computational annotation of genes differentially espressed during fruit development in olive.

Sicilian Myrtle Diversity: Evaluation of Leaf Total Phenols Content and Antioxidant Properties

Myrtle (Myrtus communis L.) is an aromatic plant spontaneously growing and increasingly cultivated in Mediterranean area. Recently, interest on myrtle plant is growing due to the pharmacological and antioxidant properties since myrtle leaves are important sources of phenolic and antioxidant compounds with health-promoting effects. Plant genotype is the primary factor affecting antioxidant activity and phenol content. For this reason, a core collection of local selected myrtle accessions from Sicily was evaluated with the aim to identify genotypes with high antioxidant value. Thirty-six myrtle individuals belonging to seven populations were studied for leaf total phenols, tannins and antioxi…

Engineering resistance to biotic stress in rootstocks of fruit and nut tree crops.

Agronomic, metabolomic and lipidomic characterization of Sicilian Origanum vulgare (L.) ecotypes

Although Origanum vulgare (L.) has been deeply analysed at phytochemical level, poor knowledge is available regarding non-volatile compounds such as lipids. The aim of this work was to characterise five wild Sicilian Origanum ecotypes from an agronomic, metabolomic and lipidomic perspective. Serradifalco presented higher dry weight and inflorescences/plant than the others while Favara had a significantly higher number of branches per plant and more extensive flowered stratum. Metabolomic analysis, performed with LC-MS-TOF, allowed a preliminary characterisation of the non-volatile metabolome of the five oregano ecotypes Origanum vulgare ssp. hirtum. Twenty-five metabolites were identified b…

Transcriptome profiling of citrus fruit response to huanglongbing disease.

Huanglongbing (HLB) or "citrus greening" is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB- affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of phot…

Study of Biodiversity for Fruit Valorization: the example of Ancient Apple Cultivars (Malus x domestica Borkh.) from Tuscany (Italy)

Molecular Responses to Small Regulating Molecules against Huanglongbing Disease

Huanglongbing (HLB; citrus greening) is the most devastating disease of citrus worldwide. No cure is yet available for this disease and infected trees generally decline after several months. Disease management depends on early detection of symptoms and chemical control of insect vectors. In this work, different combinations of organic compounds were tested for the ability to modulate citrus molecular responses to HLB disease beneficially. Three small-molecule regulating compounds were tested: 1) L-arginine, 2) 6-benzyl-adenine combined with gibberellins, and 3) sucrose combined with atrazine. Each treatment contained K-phite mineral solution and was tested at two different concentrations. T…

Metabolomics approach to studying minimally processed peach (Prunus persica) fruit

Fresh-cut fruit products for both retail and food service applications have increasingly appeared in the market place in recent years. Among different fruit types, peaches can be used and are highly appreciated as fresh-cut product although their commercial success is limited due to their short shelf-life and the quick onset of wounding-related physiological reactions. In this work we analyzed the technological and physiological changes induced by fresh-cut preparation in three different types of peach cultivars: 'Fayette' (melting), 'Wilhelmina' (non-melting) and 'Ghiaccio3' (stony hard). We performed a metabolite targeting profiling to focus on the changes in organic acid levels, importan…

An Epigenetic Alphabet of Crop Adaptation to Climate Change

Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In additi…

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…

Phenology study of Myrtus communis accessions selected from wild populations of Sicily: preliminary results

Myrtus communis is a Mediterranean shrub widely diffused in Sicily. To promote the cultivation of myrtle, seven wild populations were collected from different areas of Sicily, with the aim to select new candidate cultivars in the frame of a selection program. Considering the berries value in the food industry, many efforts need to be done to cultivate myrtle as alternative to harvest from wild plants. To promote cultivation few important phenologic traits have been recorded in candidate cultivar selections from wild populations in Sicily. This study was performed in a repository field under homogeneous environmental conditions. The vegetation activity of the selected accessions begins in Ja…

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…

A microarray analysis highlights the role of tetrapyrrole pathways in grapevine responses to “stolbur” phytoplasma, phloem virus infections and recovered status

Abstract After providing a picture of the global transcriptomic changes of grapevine responses to “stolbur” phytoplasma, the recovery status and molecular responses to the phytoplasma and virus co-presence were analyzed. NimbleGen ® Vitis vinifera genome arrays were used. Lower transcript abundance of the genes involved in photosynthesis, trehalose, phospholipids was observed in response to the presence of “stolbur” phytoplasma. The expression of the genes involved in tetrapyrrole increased. The recovered plants showed that the transcripts involved in ATP synthesis and amino acid metabolism, secondary metabolism and biotic stress-related pathways increased. Recovery was associated with tetr…

Genetic Mechanisms of the Devious Intruder Candidatus Liberibacter in Citrus.

HLB symptom progression may result from three types of dysfunction occurring in Ca.L.-infected citrus: (1) a carbohydrate disorder linked to disruption of the source-sink relationship, (2) perturbation of hormonal crosstalk involved in plant immune responses (JA-SA signaling crosstalk), and (3) changes in the rapid activation of detoxifying pathways (particularly GSTs). The development of innovative short- or long-term biotechnological tools that allow beneficial modulation of these three pathways will help increase Citrus tolerance to this devastating disease.

Flavonoid metabolism and gene expression in developing olive (Olea europaea L.) fruit.

The expression pattern of six genes (phenylalanine-ammonia-lyase, PAL, chalcone synthase, CHS, flavanone 3-hydroxylase, F3H, dihydroflavonol 4-reductase, DFR, anthocyanidin synthase, ANS, UDP-gluco...

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

Identifying key information in transcriptomic data is very important, especially when the “omic” study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrich…

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…

Properties of New Strawberry Lines Compared with Well-Known Cultivars in Winter Planting System Conditions

In Southern Italy and Sicily, strawberry cultivation is dominated by international cultivars such as ‘Candonga Sabrosa’, ‘Florida Fortuna’, ‘Sabrina’ and ‘Sant Andreas’. The primary objective of our study was to compare the field performance of two experimental lines and four established cultivars in a Sicilian representative strawberry production area. The second objective was to compare the fruits physic-chemical nutraceutical characteristics of these genotypes in response to different postharvest fruit storage temperatures. A supporting genetic analysis, via SSR markers, was also performed in order to establish genotype correlations. Our study confirmed the high result of ‘Florida Fortun…

Identification of microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat.

Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal t…

Rhynchophorus ferrugineus attack affects a group of compounds rather than rearranging Phoenix canariensis metabolic pathways.

The red palm weevil (RPW; Rhynchophorus ferrugineus) is spreading worldwide and severely harming many palm species. However, most studies on RPW focused on insect biology, and little information is available about the plant response to the attack. In the present experiment, we used metabolomics to study the alteration of the leaf metabolome of Phoenix canariensis at initial (1st stage) or advanced (2nd stage) attack by RPW compared with healthy (unattacked) plants. The leaf metabolome significantly varied among treatments. At the 1st stage of attack, plants showed a reprogramming of carbohydrate and organic acid metabolism; in contrast, peptides and lipid metabolic pathways underwent more c…

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 (…

Members of the WRKY gene family are upregulated in Canary palms attacked by Red Palm Weevil

The Red Palm Weevil (RPW), Rhynchophorus ferrugineus, is one of the major pests affecting several palm species all around the world. The aim of this work was to identify palm genes that are responsive to RPW infestations as a valuable diagnostic tool to detect the insect attack. We have analysed a total of 15 genes that were divided in two subsets: (1) 7 genes previously linked with RPW attacks, but not involved in biotic stress responses, and (2) 8 genes encoding members of the WRKY family, a class of transcription factors well-known to be linked with both abiotic and biotic stress responses. The analysis was conducted on 4-year-old Canary palms comparing uninfested plants and infested pla…

Molecular and agronomic responses to soil inoculation with plant-growth promoting rhizobacteria and arbuscular mycorrhizae in Triticum durum

Plant-growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake by increasing the availability of nutrients and the root adsorbing surface. However, the molecular mechanisms of plant responses to these associations are still under-investigated. Gene expression analysis could lead to the identification of biomarkers usable to early select genotypes for an increased nutrient uptake efficiency. The main objective of this study was to determine the effects of these associations on plant total biomass and grain yield in durum wheat (cv. Anco Marzio). Secondly, we aimed to analyze the expression pattern of key genes involved in nutrient uptake…

RNA uridylation and decay in plants

RNA uridylation consists of the untemplated addition of uridines at the 3′ extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana . Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include …

Ancient Pomaceae (Malus domestica Borkh. and Pyrus communis L.) cultivars in “Appenino Toscano”(Tuscany, Italy): molecular (SSR) and morphological characterization.

Transcriptome Profiling of Host Responses to Huanglongbing in Mature Citrus Fruit.

Molecular characterization of Sicilian ecotypes of Myrtus communis (L.) using AFLP markers.

Transcriptome and metabolome analysis of citrus fruit to elucidate puffing disorder.

a b s t r a c t A systems-level analysis reveals details of molecular mechanisms underlying puffing disorder in Citrus fruit. Flavedo, albedo and juice sac tissues of normal fruits and fruits displaying symptoms of puffing disorder were studied using metabolomics at three developmental stages. Microarrays were used to compare normal and puffed fruits for each of the three tissues. A protein-protein interaction network inferred from previous work on Arabidopsis identified hub proteins whose transcripts show significant changes in expression. Glycolysis, the backbone of primary metabolism, appeared to be severely affected by the disorder, based on both transcriptomic and metabolomic results. …

Gene regulation in parthenocarpic tomato fruit.

Parthenocarpy is potentially a desirable trait for many commercially grown fruits if undesirable changes to structure, flavour, or nutrition can be avoided. Parthenocarpic transgenic tomato plants (cv MicroTom) were obtained by the regulation of genes for auxin synthesis (iaaM) or responsiveness (rolB) driven by DefH9 or the INNER NO OUTER (INO) promoter from Arabidopsis thaliana. Fruits at a breaker stage were analysed at a transcriptomic and metabolomic level using microarrays, real-time reverse transcription-polymerase chain reaction (RT-PCR) and a Pegasus III TOF (time of flight) mass spectrometer. Although differences were observed in the shape of fully ripe fruits, no clear correlatio…

Effects of irrigation on fruit ripening behavior and metabolic changes in olive

Olive (Olea europaea, cv Leccino) fruits grown under different water regimes were analyzed by metabolomics and specific transcript accumulation analyses. The fruit from non-irrigated (rain-fed) and irrigated trees cultivated under field conditions, with a seasonal water amount equivalent to the calculated crop evapotranspiration (ETc) was compared in the last developmental phase and, in particular, at commercial harvest. Metabolomics (GC-MS) analysis identified several hundred metabolites in ripe mesocarp, 46 of which showed significantly different contents in the rain-fed and irrigated samples. Some compounds involved in primary metabolism (carbohydrates, amino acids, organic acids) and se…

Molecular characterization of Sicilian lentil ecotypes using ISSR.

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…

Caratterizzazione micromorfologica di antiche varieta’ di melo

Development of an efficient regeneration protocol for pear rootstock Pyrodwarf and assessment of somaclonal variability using SSR analysis.

Gene regulatory networks elucidating Huanglongbing disease mechanisms

Next-generation sequencing was exploited to gain deeper insight into the response to infection by Candidatus liberibacter asiaticus (CaLas), especially the immune disregulation and metabolic dysfunction caused by source-sink disruption. Previous fruit transcriptome data were compared with additional RNA-Seq data in three tissues: immature fruit, and young and mature leaves. Four categories of orchard trees were studied: symptomatic, asymptomatic, apparently healthy, and healthy. Principal component analysis found distinct expression patterns between immature and mature fruits and leaf samples for all four categories of trees. A predicted protein - protein interaction network identified HLB-…

In-Field and Early Detection of Xylella fastidiosa Infections in Olive Using a Portable Instrument

Xylella fastidiosa subsp. pauca (Xfp) is a gram-negative pathogenic bacteria responsible for serious diseases (Purcell, 2013) that inflicts considerable economic loss (Li et al., 2007; Luvisi et al., 2017). The pathogen has been linked to olive quick decline syndrome (OQDS). This devastating olive disease was first observed in Salento (Apulia, southeastern Italy) in 2009. Infected trees respond to Xfp infection with scattered desiccation of twigs and small branches in the upper crown, which extend to the rest of the canopy, showing the characteristic blight effect. The disease causes tree death within a few years from the onset of symptoms (Martelli, 2016). The primary agronomic procedure f…

Old pear varieties (Pyrus communis L.) found in the Casentino area (Arezzo-Tuscany): morphological, biometrical and molecular (SSR) characterization.

MOLECULAR AND METABOLIC ANALYSES IN DEVELOPING OLIVE FRUIT IN RELATION TO DIFFERENT WATER REGIMES

Despite the global economic importance of olive (Olea europaea L.), little is known about the molecular and metabolic changes during fruit development and the modulation of quality-related metabolic pathways during drought stress. In this work, we report the expression pattern of genes involved in important pathways of secondary metabolism (polyphenols, terpenoids) during fruit development in rainfed or fully irrigated olive plants. Phenolic compounds represent a complex mixture in both olive fruits and oil. The interest on these compounds is due to their demonstrated anti-atherogenic and anti-cancerogenic effects providing to the olive oil important nutraceutical properties. Several parame…

A molecular and metabolomic approach to studying minimally processed peac fruit.

The expression pattern of genes involved in secondary metabolic processes is altered in fruit of water-stressed olive trees

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…

Computational annotation of genes differentially expressed along olive fruit development

Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) a…

Advanced methods of plant disease detection. A review

International audience; Plant diseases are responsible for major economic losses in the agricultural industry worldwide. Monitoring plant health and detecting pathogen early are essential to reduce disease spread and facilitate effective management practices. DNA-based and serological methods now provide essential tools for accurate plant disease diagnosis, in addition to the traditional visual scouting for symptoms. Although DNA-based and serological methods have revolutionized plant disease detection, they are not very reliable at asymptomatic stage, especially in case of pathogen with systemic diffusion. They need at least 1–2 days for sample harvest, processing, and analysis. Here, we d…

Proposal of a Genome Editing System for Genetic Resistance to Tomato Spotted Wilt Virus

Viruses provoke considerable economical losses in agriculture. New molecular approaches to develop genetic resistance based on translational genomics and precision genetic modifications are highly expected. The type II Clustered, Regularly Interspaced Palindromic Repeats (CRISPR) system including Cas9 nuclease represent a promising and very powerful tool to specifically modulate the expression and activity of genes involved in biotic stress responses. In this study, we describe an approach to develop a platform system based on CRISPR system for genome editing technology in tomato. Tomato is an excellent plant for this approach considering the high-quality genome sequence, the rapid life cyc…

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)

Supplementary_Dataset4_Representative Poales HESO1 alignment. from RNA uridylation and decay in plants

Representative Poales HESO1 alignment. Related to Figure 5.

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)

Supplementary_Dataset5_Representative Poales URT1 alignment. from RNA uridylation and decay in plants

Representative Poales URT1 alignment. Related to Figure 5.

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)

Supplementary_Dataset1_HESO1sequences. from RNA uridylation and decay in plants

HESO1 sequences in FASTA format. Related to Figures 3 and 4.

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: Table S2. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Differentially regulated host proteins in control and infected leaf tissues of Volkameriana (p-valueâ

Additional file 2: Table S2. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Differentially regulated host proteins in control and infected leaf tissues of Volkameriana (p-valueâ

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)

Supplementary_Dataset3_HESO1 and URT1 alignment. from RNA uridylation and decay in plants

Alignment of HESO1 and URT1 sequences. Related to Figures 3 and 4.

Additional file 1: Table S1. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Differentially regulated host proteins in control and infected leaf tissues of Navel orange (p-valueâ

Additional file 1: Table S1. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

Differentially regulated host proteins in control and infected leaf tissues of Navel orange (p-valueâ

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)

Supplementary_Dataset2_URT1sequences. from RNA uridylation and decay in plants

URT1 sequences in FASTA format. Related to Figures 3 and 4.

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)

Additional file 4: Figure S2. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

HLB-differentially regulated proteins involved in secondary metabolism in the two Citrus genotypes. Each colored square represents the expression change (see color key) in a protein associated with the biosynthetic pathway. (TIF 268Â kb)

Additional file 4: Figure S2. of Proteomic analysis highlights the role of detoxification pathways in increased tolerance to Huanglongbing disease

HLB-differentially regulated proteins involved in secondary metabolism in the two Citrus genotypes. Each colored square represents the expression change (see color key) in a protein associated with the biosynthetic pathway. (TIF 268Â kb)