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)

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…

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…

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)

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…

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)

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)

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…

Comparazione tra liste faunistiche di Lepidotteri e Coccinellidi in aree protette italiane con diverse caratteristiche biogeografiche

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…

FUNCTIONAL GENOMIC APPROACHES TO ELUCIDATE BIOTIC AND ABIOTIC STRESS RESPONSES IN PLANTS

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…

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…

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 …

Preliminary selection of non-target Lepidoptera species for ecological risk assessment of Bt canola in Sicily

It is essential to assess the environmental risk that Bt canola resistant to Lepidopteran pests may hold and to study its effect on species assemblages that fulfil a variety of ecosystem functions. Environmental risk assessment can be improved through the use of an ecological model which can be applied to a specific environment, so that local species can be classified functionally and prioritized to identify potential test species. Several other Lepidoptera species are also directly exposed to Bt toxin. In this paper an ecological approach was followed for selection of non-target Lepidoptera species for ecological risk assessment of Bt canola in Sicily, using data collected over a one-year …

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

Representative Poales HESO1 alignment. Related to Figure 5.

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

Representative Poales URT1 alignment. Related to Figure 5.

Supplementary_Dataset1_HESO1sequences. from RNA uridylation and decay in plants

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

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

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

Supplementary_Dataset2_URT1sequences. from RNA uridylation and decay in plants

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

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)