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Showing 4 results for Subject: Bioinformatics
Atefeh Khakpour, Maryam Zolfaghari, Karim Sorkheh,
Volume 6, Issue 1 (9-2019)
Abstract
Glycyrrhiza is one of the important medicinal plants that is in danger of extinction. Search for finding accessions that have a higher glycyrrhizic acid is very important in breeding programs. Functional genomics methods such as EST sequencing prepare the ability to identify consensus gene families among studied species and interpretation of the genome. In this research, 55960 EST sequences of two different species of this plant along with the protein sequences were analyzed in order to identify the molecular aspects and functional analysis of the genome and the gene network involved in the biosynthesis of glycyrrhizin. Also, in order to validation of results, relative expression of four important genes in the pathway of glycyrrhizin biosynthesis including squalene synthase (SQS), β-amyrin synthase (BAS), β –amyrin 11-oxidase (CYP88D6) and UDP-glucuronyl transferase (UGT) were evaluated. After trimming and qualitative evaluation the sequences, 6427 contig sequences and 30895 singleton (37322 unigene) were generated, which covered a total of 26884666 bp (7.06%) of the licorice genome. Genome functional activity showed that most genes play a role in the catalytic activity and cellular and metabolic processes in which these genes interact within cells and intracellular organels. Locating this group of genes showed that the genes involved in glycyrrhizin biosynthesis pathway were localized in endoplasmic reticulum. Results of validation using qRT-PCR showed that in the autumn and in the rhizome tissue, the genes of BAS, CYP88D6, UGT and SQS were up-regulated. The results of this study can be valuable for genomic sequencing, functional groups, genetic diversity and functional genomics of this plant.
Hossein Zeinalzadeh-Tabrizi, Sadollah Mansouri, Abbas Fallah-Toosi,
Volume 8, Issue 1 (8-2021)
Abstract
Analysis of genotype by environment interaction using different statistical methods is very important in plant breeding. In order to evaluate the seed yield stability of promising sesame lines using different parametric and non-parametric statistics, an experiment was conducted using 13 promising sesame lines with check variety Oltan at three locations of Karaj, Mashhad, and Moghan (Iran) in a randomized complete block design with four replications over two years (2016 and 2017). Combined analysis of variance for seed yield of promising sesame lines showed that the effect of genotype and the three-way interaction of genotype × year × location at the level of 0.01% probability were statistically significant. Karaj-96 environment with 1346 kg/ha and Mashhad-96 environment with 1001 kg/ha had the highest and lowest mean yield, respectively. The highest and lowest mean seed yield among genotypes in all test environments were related to G6 line with 1444 kg/ha and G12 line with 762 kg/ha, respectively. Heatmap along with cluster analysis divided both genotypes and stability parameters into three groups. Based on cluster analysis, genotype G12 was clustered into the first group, genotypes G1, G3, G7, G8, and G13 were clustered into the second group and the rest of the genotypes along with the check cultivar Oltan were clustered into the third group. The genotypes of the second group with the highest rank in most criteria of stability stasistics were stable compared to other genotypes and among them, the genotypes G8, G1 and G3 (with mean yields 1417, 1398 and 1291 Kg/ha, repectively) were selected and recommended in the test locations due to their average yield above the average yield of all genotypes.
Razieh Khadivar, Ahmad Ismaili, Seyed Sajad Sohrabi, Hasan Torabi Podeh,
Volume 9, Issue 2 (3-2023)
Abstract
Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. In the course of evolution evolution, crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged in plant in response to drought and other abiotic stresses. In the present study, after identifying lncRNAs within the expression profile of lentil, RNA-seq data and real-time PCR analyses were employed to examine the expression pattern of some of the identified lncRNAs under drought stress. Additionally, psych R package was used to generate the lncRNAs-DEGs co-expression network. A total of 3590 lncRNA sequences were identified in lentils transcriptome. Numerous lncRNAs were co-expressed with genes involved in circadian rhythm regulation, zinc ion response, photosynthetic photoreaction, and ion homeostasis. The LCUL_evgLocus_104392, LCUL_evgLocus_99066 and LCUL_evgLocus_61876 sequences were differentially expressed in response to drought stress. Examining the co-expression of these sequences with differentially expressed genes in response to drought stress, led to the identification of metabolic pathways associated with these sequences. In this study, lncRNA sequences were identified for the first time in lentil, and provided useful insights into the function of lncRNA in plant resistance to drought stress. The lncRNAs-DEGs co-expression network can lead to a better understanding of drought response mechanisms in lentil.
Forough Joudaki, Ahmad Ismaili, Seyed Sajad Sohrabi, Seyedeh Zahra Hosseini, Hadi Ahmadi,
Volume 10, Issue 2 (2-2024)
Abstract
Gall oak (Quercus infectoria) is one of the extraordinary tree species with functional medicinal properties within the oak family. Various studies have confirmed the presence of numerous secondary metabolites with therapeutic properties in this plant. Despite the significance of gall oak, its genetic structure remains elusive. Therefore, unraveling the genetic structure of gall ok may provide valuable insights into its potential applications across diverse industries. MicroRNAs emerge as pivotal genetic elements implicated in the biosynthesis of crucial metabolites across a wide range of different plant species. Despite the significant role of miRNAs in plants, as of yet, no miRNAs have been reported in Q. infectoria.. Therefore, in the present study, after assembling the transcriptome of Q. infectoria, the conserved microRNAs were identified. Leaf and root samples of Q. infectoria were collected from trees in the Shineh region, and 2-year-old seedlings were grown from mature oaks in Khorramabad (Lorestan Province, Iran). Total RNA was extracted from roots and leaves using the Djami-Tchatchou method. After sequencing by the Illumina HiSeq 2500 platform and checking the quality of all the generated reads, the adapter sequences were removed, and the high-quality reads were assembled using Trinity package. To identify miRNAs and their target genes, all plant miRNAs sequences were downloaded from the miRbase database. The BLASTn algorithm was employed to identify the highest similarity between unigenes and mature plant miRNAs. Furthermore, BLASTx was used to search against the non-redundant proteins (NR) database to remove protein-coding unigenes. The investigation of miRNA second-structure prediction involved assessing the similarity between potential unigenes and mature miRNA sequences using the mfold web tool. Identification of miRNA target genes and gene ontology (GO) was performed using the psRNAtarget web-tool and OmicsBox software, respectively. Following a range of strict filtering criteria, four miRNAs belonging to conserved miRNAs families were identified, including qin-miR156, qin-miR399, qin-miR160, and qin-miR172. KEGG pathway analysis showed the target genes were involved in the citrate cycle pathway. Examining miRNA target genes in Q. infectoria and analyzing their interaction network, finally led to the identification of three hub genes. Identified miRNA target genes were associated with the biosynthesis of various enzyme groups, suggesting that most of miRNAs regulating hydrolases, transferases, and oxidoreductases. Given the role of microRNAs in regulating transcription factors and their impact on genes involved in secondary metabolite biosynthesis, future breeding programs in Q. infectoria may benefit from the potential of such regulatory elements as a guide and key.
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