Bioinformatics
Aboozar Soorni; Sepehr Meratian Esfahani; Badraldin Ebrahim Sayed-Tabatabaei
Abstract
Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental ...
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Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental factors are changed to produce the most effective substance in medicinal plants, but in newer approaches that are based on plant genetics, higher yields are observed. One of these approaches is the use of miRNAs. These miRNAs control gene expression after transcription by mRNA analysis or inhibition of their translation, and play different roles in biological and metabolic processes in plants and animals. One of the simplest and least expensive methods for identifying miRNAs is the use of bioinformatics tools and methods. To identify distinct miRNA in different species of thyme, a study based on homology search was conducted using transcriptomic data of thyme. First, this information was refined and then aligament performed against all known miRNAs in the miRBase database. After screening of results based on factors such as length and e-value level, the secondary structure of miRNAs was analyzed with UNAfold tool. Target genes were identified using psRNATARGET tool and phylogenetic relationships were investigated using maximum likelihood method and RaxML tool. In total 64 distinct candidate’s miRNAs were identified in different species of thymus and 14 miRNAs included miR172 and miR396 played an important role in terpenes synthesis and it has been proven in previous studies. The phylogenetic tree was able to show the relationship between miRNAs in different species.
Plant Disease and Biotechnology
Fatemeh Mohammadi; Aboozar Soorni; Rahim Mehrabi
Abstract
Two-spotted spider mite (Tetranychus urticae Koch) is one of the most important pests of beans (Phaseolus vulgaris L.). Since, complex gene networks are involved in creating sensitivity or resistance against the two-spotted spider mite; therefore, in this research we used biological system methods to ...
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Two-spotted spider mite (Tetranychus urticae Koch) is one of the most important pests of beans (Phaseolus vulgaris L.). Since, complex gene networks are involved in creating sensitivity or resistance against the two-spotted spider mite; therefore, in this research we used biological system methods to identify key networks. For this purpose, we used the RNA-Seq data related to the two-spotted spider mite stress on common bean plant. After providing the gene expression matrix, molecular networks were analyzed using weighted co-expression network analysis (WGCNA). After the modules identification, the gene functions in each module were investigated and analyzed. According to the results, a total of 699 genes were identified with differential expression in response to two-spotted spider mite stress, which were placed in 7 co-expression modules through hierarchical clustering. Gene ontology and interaction analysis of key genes using the String database showed that the response of common bean transcriptome to two-spotted spider mite infestation includes genes encoding protein kinases, catalysts, transcription factors, and metabolite production and pathways of hormonal message transmission. It is notable that among the most important genes that showed co-expression, WRKY and lipoxygenase were highlighted. The turquoise module had the higher number of genes involved in resistance, and this module and the yellow module had the highest correlation with the resistant variety after five and one day of contamination, respectively. Also, the black module had the highest correlation with the sensitive variety after five days of contamination. In conclusion, this study increases our knowledge of the molecular mechanisms involved in resistance to the two-spotted spider mite. Also, the genes examined in this research can be introduced as breeding targets to create resistance.
Bioinformatics
Aboozar Soorni; Parnian Karimzadeh; Samira Dehghani
Abstract
Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed ...
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Thyme species are very important due to the production of secondary metabolites such as terpenoids. Since the identification of key genes such as genes related to terpenoids biosyntesis pathway can play an effective role in plant breeding programs, especially thyme species, the present study was aimed to investigate the transcriptomes of T. daenensis, T. vulgaris, T. lancifolius, T. persicus, T. pubescens to identify key genes in the biosynthesis of monoterpenoids, chloroplast genes sequence and evaluation of similarities and differences among these species. For this purpose, total RNAs extracted from vegetative growth were sent to Macrogene of Korea for sequencing with theIllumina HiSeq 2500 platform. After assembling the sequences using various tools, the best results was selected and transcripts were documented in different databases. Then, according to the documented results, key genes responsible in the synthesis of terpenoids and chloroplast gene sequence were identified, and then phylogenetic relationships among species was investigated. According to the evaluation indicators, the best assembly was a product of Binpacker tools. Based on the results, the sequence of 10 genes involved in the synthesis of terpenoids was obtained. Interestingly, among the identified TPSs, most of the contigs were classified into the TPSb and TPSa classes of terpenoids. The sequence of 73 chloroplast genes was extracted from the transcriptome data and finally the phylogenetic relationship was evaluated according to 400, 70 bp of cpDNA. The study of phylogenetic relationships showed a close genetic relationship between T. daenensi and T.vulgaris which can introduce T. daenensis as an appropriate replacement for T. vulgaris in different purpose, especially in pharmacological applications. The results show that Z. multiflora can most probably be as one of the ancestors of Thymus, which is significantly different from Thymus species in terms of its genetic structure, especially the key genes of the terpene biosynthesis pathway.
