Omics-driven bioinformatics for plant lectins discovery and functional annotation - A comprehensive review.

Lectins are known for their specific and reversible binding capacity to carbohydrates. These molecules have been particularly explored in plants due to their reported properties, highlighting antimicrobial, antiviral, anticancer, antiparasitic, insecticidal, and immunoregulatory actions. The increasing availability of lectin and lectin-like sequences in omics data banks provides an opportunity to identify important candidates, inferring their roles in essential signaling pathways and processes in plants.

From Genes to Stress Response: Genomic and Transcriptomic Data Suggest the Significance of the Inositol and Raffinose Family Oligosaccharide Pathways in , Adaptation to the Caatinga Environment.

is an important forage and extremophilic plant native to the Brazilian Caatinga semiarid region. It has only recently been subjected to omics-based investigations, and the generated datasets offer insights into biotechnologically significant candidates yet to be thoroughly examined. INSs (inositol and its derivatives) and RFO (raffinose oligosaccharide family) pathways emerge as pivotal candidates, given their critical roles in plant physiology.

DEAD-Box RNA Helicase Family in Physic Nut ( L.): Structural Characterization and Response to Salinity.

Helicases, motor proteins present in both prokaryotes and eukaryotes, play a direct role in various steps of RNA metabolism. Specifically, SF2 RNA helicases, a subset of the DEAD-box family, are essential players in plant developmental processes and responses to biotic and abiotic stresses. Despite this, information on this family in the physic nut ( L.

Bridging the Gap: Combining Genomics and Transcriptomics Approaches to Understand , an Orphan Legume from the Brazilian Caatinga.

is a scientifically orphaned legume found in the Brazilian Caatinga biome (a semi-arid environment). This work utilized omics approaches to investigate some ecophysiological aspects of stress tolerance/resistance in , study its genomic landscape, and predict potential metabolic pathways. Considering its high-confidence conceptual proteome, 1694 (~2.

Unlocking Cowpea's Defense Responses: Conserved Transcriptional Signatures in the Battle against CABMV and CPSMV Viruses.

(CABMV) and (CPSMV) threaten cowpea commercial production. This study aimed to analyze Conserved Transcriptional Signatures (CTS) in cowpea's genotypes that are resistant to these viruses. CTS covered up- (UR) or down-regulated (DR) cowpea transcripts in response to CABMV and CPSMV mechanical inoculations.

From Gene to Transcript and Peptide: A Deep Overview on Non-Specific Lipid Transfer Proteins (nsLTPs).

Non-specific lipid transfer proteins (nsLTPs) stand out among plant-specific peptide superfamilies due to their multifaceted roles in plant molecular physiology and development, including their protective functions against pathogens. These antimicrobial agents have demonstrated remarkable efficacy against bacterial and fungal pathogens. The discovery of plant-originated, cysteine-rich antimicrobial peptides such as nsLTPs has paved the way for exploring the mentioned organisms as potential biofactories for synthesizing antimicrobial compounds.

Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations.

Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized.

The WRKY transcription factor family in cowpea: Genomic characterization and transcriptomic profiling under root dehydration.

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most tolerant legume crops to drought and salt stresses.

Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity.

Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts.

The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses.

The present work represents a pioneering effort, being the first to analyze genomic and transcriptomic data from (cowpea) kinases. We evaluated the cowpea kinome considering its genome-wide distribution and structural characteristics (at the gene and protein levels), sequence evolution, conservation among Viridiplantae species, and gene expression in three cowpea genotypes under different stress situations, including biotic (injury followed by virus inoculation-CABMV or CPSMV) and abiotic (root dehydration). The structural features of cowpea kinases (VuPKs) indicated that 1,293 VuPKs covered 20 groups and 118 different families.

Reference genes for quantitative real-time PCR normalization of Cenostigma pyramidale roots under salt stress and mycorrhizal association.

Cenostigma pyramidale is a native legume of the Brazilian semiarid region which performs symbiotic association with arbuscular mycorrhizal fungi (AMF), being an excellent model for studying genes associated with tolerance against abiotic and biotic stresses. In RT-qPCR approach, the use of reference genes is mandatory to avoid incorrect interpretation of the relative expression. This study evaluated the stability of ten candidate reference genes (CRGs) from C.

Transcriptome of Cenostigma pyramidale roots, a woody legume, under different salt stress times.

Salinity stress has a significant impact on the gain of plant biomass. Our study provides the first root transcriptome of Cenostigma pyramidale, a tolerant woody legume from a tropical dry forest, under three different salt stress times (30 min, 2 h, and 11 days). The transcriptome was assembled using the RNA sequencing (RNA-Seq) de novo pipeline from GenPipes.

Salt tolerance of begins with immediate regulation of aquaporin activity in the root system.

Unlabelled: The ability to respond quickly to salt stress can determine the tolerance level of a species. Here, we test how rapidly the roots of react to high salinity conditions. In the first 24 h after saline exposure, the plants reduced stomatal conductance, increased CO assimilation, and water use efficiency.

Importance of inositols and their derivatives in cowpea under root dehydration: An omics perspective.

This work presents a robust analysis of the inositols (INSs) and raffinose family oligosaccharides (RFOs) pathways, using genomic and transcriptomic tools in cowpea under root dehydration. Nineteen (~70%) of the 26 scrutinized enzymes presented transcriptional up-regulation in at least one treatment time. The transcriptional orchestration allowed categorization of the analyzed enzymes as time-independent (those showing the same regulation throughout the assay) and time-dependent (those showing different transcriptional regulation over time).

Reference genes selection for Calotropis procera under different salt stress conditions.

Calotropis procera is a perennial Asian shrub with significant adaptation to adverse climate conditions and poor soils. Given its increased salt and drought stress tolerance, C. procera stands out as a powerful candidate to provide alternative genetic resources for biotechnological approaches.

Plant Thaumatin-like Proteins: Function, Evolution and Biotechnological Applications.

Thaumatin-like proteins (TLPs) are a highly complex protein family associated with host defense and developmental processes in plants, animals, and fungi. They are highly diverse in angiosperms, for which they are classified as the PR-5 (Pathogenesis-Related-5) protein family. In plants, TLPs have a variety of properties associated with their structural diversity.

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications.

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles.

Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR.

Background: Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM).

Genotype-dependent regulation of drought-responsive genes in tolerant and sensitive sugarcane cultivars.

Drought is the most damaging among the major abiotic stresses. Transcriptomic studies allow a global overview of expressed genes, providing the basis for molecular markers development. Here, the HT-SuperSAGE technique allowed the evaluation of four drought-tolerant cultivars and four-sensitive cultivars, after 24h of irrigation suppression.

Validation of novel reference genes for reverse transcription quantitative real-time PCR in drought-stressed sugarcane.

One of the most challenging aspects of RT-qPCR data analysis is the identification of reliable reference genes. Ideally, they should be neither induced nor repressed under different experimental conditions. To date, few reference genes have been adequately studied for sugarcane (Saccharum spp.

Early transcriptional response of soybean contrasting accessions to root dehydration.

Drought is a significant constraint to yield increase in soybean. The early perception of water deprivation is critical for recruitment of genes that promote plant tolerance. DeepSuperSAGE libraries, including one control and a bulk of six stress times imposed (from 25 to 150 min of root dehydration) for drought-tolerant and sensitive soybean accessions, allowed to identify new molecular targets for drought tolerance.

Natural antisense transcripts in plants: a review and identification in soybean infected with Phakopsora pachyrhizi SuperSAGE library.

Natural antisense ranscripts (NAT) are RNA molecules complementary to other endogenous RNAs. They are capable of regulating the expression of target genes at different levels (transcription, mRNA stability, translation, etc.).

Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress.

Background: Despite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.

Methods: A curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants.