Role of Next-Generation RNA-Seq Data in Discovery and Characterization of Long Non-Coding RNA in Plants

The next-generation sequencing (NGS) technologies embrace advance sequencing technologies that can generate high-throughput RNA-seq data to delve into all the possible aspects of the transcriptome. It involves short-read sequencing approaches like 454, illumina, SOLiD and Ion Torrent, and more advance single-molecule long-read sequencing approaches including PacBio and nano-pore sequencing. Together with the help of computational approaches, these technologies are revealing the necessity of complex non-coding part of the genome, once dubbed as “junk DNA.” The ease in availability of high-throughput RNA-seq data has allowed the genome-wide identification of long non-coding RNA (lncRNA). The high-confidence lncRNAs can be filtered from the set of whole RNA-seq data using the computational pipeline. These can be categorized into intergenic, intronic, sense, antisense, and bidirectional lncRNAs with respect to their genomic localization. The transcription of lncRNAs in plants is carried out by plant-specific RNA polymerase IV and V in addition to RNA polymerase II and target the epigenetic regulation through RNA-directed DNA methylation (RdDM). lncRNAs regulate the gene expression through a variety of mechanism including target mimicry, histone modification, chromosome looping, etc. The differential expression pattern of lncRNA during developmental processes and different stress responses indicated their diverse role in plants

ADVANCE REVIEW ON NUTRITIONAL PHYTOCHEMICAL, PHARMACOLOGICAL AND ANTIMICROBIAL PROPERTIES OF CHILI

India is the world's largest producer, consumer and exporter of chili peppers. It is one of the important commercial crops and a major constituent of Indian diet. It has green color and attain red color on ripening. Chili peppers produces alkaloid compound, capsaicinoids, responsible for the hotness. Chili also contain carotenoids, phenols, foliates and oxidative product which show many biological activities in the human body. It is a good source of minerals like iron, magnesium and potassium, vitamins like A, C, B, E and P and dietary fibers. The nutrient values of Chili depend upon the variety and their stages of maturity. Chili has nutritional values, antimicrobial and pharmacological properties. Chili have many biochemical and pharmacological properties like antioxidants, anti-inflammatory, antiallergenic and anti-carcinogenic. Chili is used in the pharmaceutical industry because of its pharmacological properties. Chili plays important role to increase immunity, anti-ulcer, analgesic, anti-inflammatory, and anti-hemorrhoid agent. The extracts of chilli are used to alleviating the pain of arthritis, headaches, burns and neuralgia. It have the power to boost immune system and lower cholesterol, effective in heart disorders. This is the advance study to made a review of chili focusing mainly on its nutritional phytochemical, pharmacological and antimicrobial and clinical uses

Ca2+/cation antiporters (CaCA): Identification, characterization and expression profiling in bread wheat (Triticum aestivum L.)

The Ca2+/cation antiporters (CaCA) superfamily proteins play vital function in Ca2+ ion homeostasis, which is an important event during development and defense response. Molecular characterization of these proteins has been performed in certain plants, but they are still not characterized in Triticum aestivum (bread wheat). Herein, we identified thirty four TaCaCA superfamily proteins, which were classified into TaCAX, TaCCX, TaNCL and TaMHX protein families based on their structural organization and evolutionary relation with earlier reported proteins. Since the T. aestivum comprises an allohexaploid genome, TaCaCA genes were derived from each A, B and D subgenome and homeologous chromosome (HC), except chromosome-group 1. Majority of genes were derived from more than one HCs in each family that were considered as homeologous genes (HGs) due to their high similarity with each other. These HGs showed comparable gene and protein structures in terms of exon/intron organization and domain architecture. Majority of TaCaCA proteins comprised two Na_Ca_ex domains. However, TaNCLs consisted of an additional EF-hand domain with calcium binding motifs. Each TaCaCA protein family consisted of about ten transmembrane and two α-repeat regions with specifically conserved signature motifs except TaNCL, which had single α-repeat. Variable expression of most of the TaCaCA genes during various developmental stages suggested their specified role in development. However, constitutively high expression of a few genes like TaCAX1-A and TaNCL1-B indicated their role throughout the plant growth and development. The modulated expression of certain genes during biotic (fungal infections) and abiotic stresses (heat, drought, salt) suggested their role in stress response. Majority of TaCCX and TaNCL family genes were found highly affected during various abiotic stresses. However the role of individual gene needs to be established. The present study unfolded the opportunity for detail functional characterization of TaCaCA proteins and their utilization in future crop improvement programs

The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat

Rajput R, Tyagi S, Naik J, Pucker B, Stracke R, Pandey A. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. Planta. 2022;256(4): 67.Main conclusion We identified 119 typical CaMYB encoding genes and reveal the major components of the proanthocyanidin regulatory network. CaPARs emerged as promising targets for genetic engineering toward improved agronomic traits in C. arietinum. Chickpea (Cicer arietinum) is among the eight oldest crops and has two main types, i.e., desi and kabuli, whose most obvious difference is the color of their seeds. We show that this color difference is due to differences in proanthocyanidin content of seed coats. Using a targeted approach, we performed in silico analysis, metabolite profiling, molecular, genetic, and biochemical studies to decipher the transcriptional regulatory network involved in proanthocyanidin biosynthesis in the seed coat of C. arietinum. Based on the annotated C. arietinum reference genome sequence, we identified 119 typical CaMYB encoding genes, grouped in 32 distinct clades. Two CaR2R3-MYB transcription factors, named CaPAR1 and CaPAR2, clustering with known proanthocyanidin regulators (PARs) were identified and further analyzed. The expression of CaPAR genes correlated well with the expression of the key structural proanthocyanidin biosynthesis genes CaANR and CaLAR and with proanthocyanidin levels. Protein–protein interaction studies suggest the in vivo interaction of CaPAR1 and CaPAR2 with the bHLH-type transcription factor CaTT8. Co-transfection analyses using Arabidopsis thaliana protoplasts showed that the CaPAR proteins form a MBW complex with CaTT8 and CaTTG1, able to activate the promoters of CaANR and CaLAR in planta. Finally, transgenic expression of CaPARs in the proanthocyanidin-deficient A. thaliana mutant tt2-1 leads to complementation of the transparent testa phenotype. Taken together, our results reveal main components of the proanthocyanidin regulatory network in C. arietinum and suggest that CaPARs are relevant targets of genetic engineering toward improved agronomic traits

Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat

Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, lncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of lncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of lncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few lncRNAs were predicted as precursor (19 lncRNAs), while some as target mimics (1,047 lncRNAs) of known miRNAs involved in various regulatory functions. The results suggested numerous functions of lncRNAs in T. aestivum, and unfolded the opportunities for functional characterization of individual lncRNA in future studies

Flavonols have opposite effects on the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana

Naik J, Tyagi S, Rajput R, et al. Flavonols have opposite effects on the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana. Journal of Experimental Botany. Accepted: erad391.Flavonols are structurally and functionally diverse biomolecules involved in plant biotic and abiotic stress tolerance, pollen development, and inhibition of auxin transport. Despite the ubiquitous nature and multifunctionality of flavonols in land plants, their effects on global gene expression and signaling pathways are unclear. To explore the roles of flavonol metabolites in signaling, we performed comparative transcriptome and targeted metabolite profiling of seedlings from the flavonol-deficient Arabidopsis (Arabidopsis thaliana) loss-of-function mutant flavonol synthase1 (fls1) with and without exogenous supplementation of flavonol derivatives (kaempferol, quercetin, and rutin). Our RNA-seq results indicated that flavanols modulate various biological and metabolic pathways, with significant alteration in camalexin and aliphatic glucosinolate synthesis. Flavonols negatively regulated camalexin biosynthesis but appeared to promote the accumulation of aliphatic glucosinolates via transcription factor–mediated upregulation of biosynthesis genes. Interestingly, upstream amino acid biosynthesis genes involved in methionine and tryptophan synthesis were altered under flavonol deficiency and exogenous supplementation. Quercetin treatment significantly upregulated aliphatic glucosinolate biosynthesis genes compared to kaempferol and rutin. In addition, expression and metabolite analysis of the transparent testa7 mutant, which lacks hydroxylated flavonol derivatives, clarified the role of quercetin in the glucosinolate biosynthesis pathway. This study elucidates the molecular mechanisms by which flavonols interfere with signaling pathways, their molecular targets, and the multiple biological activities of flavonols in plants