Journal of Plant Bioinformatics and Biotechnology

Introduction to NGS platforms and their role in plant genetic modification

Maryam Shariat; Saeid Neysi

Volume 2, Issue 1 , April 2022, , Pages 18-32

http://dx.doi.org/10.22034/JPBB.2022.322974.1017

Abstract

DNA sequencing is one of the most important techniques in the field of molecular biology, according to which the order of nucleotides can be determined in a piece of DNA. There are ... Read More

A Review of RNA Motifs, Identification Algorithms and their Function on Plants

Davoud Naderi; Raheba Jami; Fazal UR Rehman

Volume 1, Issue 1 , June 2021, , Pages 28-40

http://dx.doi.org/10.22034/jpbb.2021.271442.1001

Abstract

Recent Genomic research has significantly developed human knowledge on structural non-coding RNAs (ncRNAs) which folds into characteristic secondary structures and performs specific-structure ... Read More Recent Genomic research has significantly developed human knowledge on structural non-coding RNAs (ncRNAs) which folds into characteristic secondary structures and performs specific-structure dependent biological functions. Hence, RNA secondary structure prediction is among the most commonly evaluated issues in computational RNA biology. The aim of the present study is to introduce the key role of RNA motifs in biological processes. Such motifs are specifically effective in regulating gene expression, maintaining structure and strength of RNA molecule, splicing the early mRNA, and providing the most appropriate recognition site for protein binding. Doing research and analyzing RNA motifs requires using several methods and algorithms which can provide the structure and properties of these building blocks in organisms. Generally, the most successful computational methods used in organizing RNA include the QRNA, RNAz, and CMfinder algorithms, which correlate nucleotides and other features of RNA structure formation and maintenance. In plants, RNA Recognition Motif (RRM), an 80- amino acid protected motif, is one of the most abundant protein motifs in eukaryotes. This motif has various important roles like participating in growth processes and responding to stresses in plants, and accelerating different metabolic processes. In addition, further analysis of ORRM family members represented presence of ORRM2, ORRM3 and ORRM4 acting as RNA editing factors in mitochondria as well as ORRM6 which is a chloroplast RNA editing factor. Among the construction motifs, the Pseudoknot motif which contributes to several biological activities such as altering expression of pathogenic genes in some viruses and formation of telomerase and self-truncating introns is of great significance, since these are important breeding factors in biotechnology. Based on the results of the study, it can be proposed that further studies on bioinformatics analysis of plant motifs are required to be implemented to open new windows on controlling pathogens in plants.

In Silico Genome-Wide Identification and Characterization of Glutathione Peroxidase Gene Family in Wild Cherries (Prunus avium L)

Zahra Shirazi; Fatemeh Khakdan

Volume 1, Issue 1 , June 2021, , Pages 60-72

http://dx.doi.org/10.22034/jpbb.2021.289018.1008

Abstract

Biotic and abiotic stresses are the main problems affecting the quantity and quality losses of antioxidants in wild cherry (Prunus avium L), which provide health benefits to humans, ... Read More Biotic and abiotic stresses are the main problems affecting the quantity and quality losses of antioxidants in wild cherry (Prunus avium L), which provide health benefits to humans, such as anti-allergic, anti-inflammatory, antimicrobial, and anti-cancer benefits. Glutathione peroxidase (GPX) isoenzymes act a major role in responding to oxidative stresses through the multiple metabolic pathways. Protein sequences of GPXs family form Arabidopsis thaliana and Oryza sativa were used to identify homologous proteins by the BlastP in the sweet cherry’s genome. After the alignment, the existence of the specific domain, phylogenetic relationships, subcellular localization analysis, as well as exon-intron structures and conserved motives were evaluated in this study. MicroRNA target site and codon usage bias were also investigated. Furthermore, the existence of cis-regulatory element and SSR markers were identified. The three-dimensional structure of the GPXs protein prediction and the accuracy of the predicted model was also investigated. Regarding molecular docking, the best pose for considering the accuracy of binding site was evaluated. Finally, by analyzing biological process and molecular function, gene ontology of the predicted protein was considered. We identified the five GPX genes in P. avium that classified into 3 separate groups based on their phylogenetic relationships. The predicted subcellular localization showed the GPX proteins that localized both chloroplast and mitochondria. Also, results showed ENC values were ranked 45.92 to 59.21 in PavGPX3 and PavGPX2. The results of cis‐regulatory elements showed PavGPX8 contained ten cis‐regulatory elements which was the lowest number among PavGPXs. The best pose and protein interaction in the verified 3D model were the first pose with the -28.5 minimization energy in docking process. It was concluded that the precise information on putative roles of P. avium GPXs genes could be helpful in determining their functional characterizations. The presence of several developmental process, stresses, light and hormones- responsive elements in the upstream of these genes, and GPXs‐targeted miRNAs suggested that GPX family members may play various roles in different biological responses. Finally, the GPXs gene was proposed as a good candidate for genetic engineering and breeding programs in order to introduce an abiotic stress- tolerant cultivar.

Journal of Plant Bioinformatics and Biotechnology

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Current Issue

Volume 2 (2022)

Volume 1 (2021)

Main Subjects = Bioinformatics

Introduction to NGS platforms and their role in plant genetic modification

Abstract

A Review of RNA Motifs, Identification Algorithms and their Function on Plants

Abstract

In Silico Genome-Wide Identification and Characterization of Glutathione Peroxidase Gene Family in Wild Cherries (Prunus avium L)

Abstract