Molecular Plant Breeding
Leila Farhadi; Ali Arminian; sajad Rashidi Monfared
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific ...
Read More
MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific name (Camelina Sativa L.) is an oil-medicinal plant belonging to the Brassicaceae family. First the RNA was extracted from C. sativa leaf and sent to the Beijing genome institute for RNA-sequencing. Then the data were assembled denovo with Trinity software after removing the reads with lower quality than the threshold level and trimming them. Detection of miRNAs was then performed by miRDeep2 software. Accordingly, we identified 33 miRNAs from the leaf dataset, and their secondary structures were evaluated. The target genes of the detected miRNAs were identified by the psRNAtarget website. Examining the target genes showed that a total of 1415 genes are regulated by these microRNAs, which belong to several gene families with different biological functions, including the genes of proteins that bind to the Squamusa promoter, the protein kinase family, etc. Comparing the expression of microRNA carrying genes (TPM) in the two studied doubled haploid lines, showed that except for miR296 and miR474 which were more expressed in line number 1, the other miRNAs had higher expression in line number 2. Considering the lower amount of oil production in line number 1 compared to line number 2, this indicates the relationship of these two microRNAs with oil production. miR483 was not expressed in any of the lines. miR113 and miR206 had the highest expression levels among all microRNAs. The higher expression of micro RNAs in line 2 probably indicates the higher activity of the silencing mechanism at the transcription level for the target genes in this line compared to line number 1.
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 ...
Read More
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
Seyyed Mohsen Sohrabi; Ali Akbarabadi; Kamran Samiei; Anahita Panji
Abstract
Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present ...
Read More
Tomato (Solanum lycopersicum) is an annual, self-pollinated and diploid plant belonging to the potato family (Solanaceae). Different types of this plant form an important part of the world's diet. Bacterial diseases are one of the most important factors limiting tomato production worldwide. In the present study, by using transcriptome (RNA-seq) analysis followed by gene network analysis, the key genes involved in response to bacterial diseases were identified and their various characteristics were investigated. The results of the transcriptome analysis showed that bacterial pathogens have different effects on the transcriptome of tomato. Further analysis revealed 913 common differentially expressed genes among different bacterial treatments. Network analysis identified five key genes named large guanine nucleotide binding protein, mitogen-activated protein kinase 5, mitogen-activated protein kinase 7, heat shock protein 90 kDa and hop-interacting protein. Further analysis of identified key genes showed that all of them contain biotic stress related regulatory elements (w-box, WRE3 and WUN-motif) in their promoter region and have an important role in responding to biotic stresses. The key genes identified in this research can be used in classic breeding programs or in production of disease-resistant transgenic plants after a more detailed examination.
Keywords: Gene networks, Plant breeding, Plant diseases, Tomato, Transcriptome
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 ...
Read More
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.
Bioinformatics
Hadis Boroun; Amir Siahpoosh; Seyyed Mohsen Sohrabi; Mohammad Reza Nikbakht; Javad Ghasemian Yadegari; Mohsen Mohammadi; Seyed Sajad Sohrabi
Abstract
Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin ...
Read More
Antimicrobial peptides (AMPs) are one of the most important defense barriers of plants against a wide range of pathogens. The snakins attract special attention because they are one of the most important and main cysteine-rich peptides among plant anti-microbial peptides. In the present study, some snakin gene family members were identified and characterized from onion (Allium cepa L.) using bioinformatics and experimental methods. All snakin protein sequences were retrieved from NCBI database. The snakin consensus sequence was obtained from alignment of retrieved sequences. Then, the consensus sequence was aligned against the onion transcriptome using tBLASTn tool. The resulting sequences were analyzed to determine the full-ORF, and to prediction of functional domains, signal peptides, subcellular localization, physicochemical properties, amino acid frequency and anti-microbial activity. The complete coding sequence of snakin genes were amplified by PCR. Finally, the presence of seven snakin genes, with an average ORF length of 332 bp, were confirmed in onion. The high similarity of the onion snakin genes with homologous snakin genes belonging to other plant species in terms of nucleotide and protein sequences as well as structural was revealed by bioinformatics analysis. The results also showed that all identified onion snakins had the potential antimicrobial activity. Due to the potential antimicrobial activity of identified peptides, by producing these peptides in different expression systems, they can be used as new antimicrobial agents against human, animal and plant pathogens.
Bioinformatics
Zahra Aminfar; Babak Rabiei; Masoud Tohidfar; Mohammad Hossein Mirjalili
Abstract
Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol ...
Read More
Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol phosphate (MEP) pathway in plastids. To perform a meta-analysis of two pathways of MVA and MEP, expression data of the microarray experiments in different tissues, developmental stages, biotic and abiotic stresses were used in Arabidopsis thaliana as a model plant. The transcriptom meta-analysis was carried out using Genevestigator as a large database containing transcriptomics data of GEO in NCBI and ArrayExpress in EBI. The results of the meta-analysis showed that the transcription of genes encoding the enzymes of MVA and MEP pathway did not coordinate and they had different expression patterns in developmental stages, various tissues and conditions. MVA pathway genes show the highest expression in the roots and reproductive organs, while the MEP pathway genes are expressed in photosynthetic tissues. The results obtained here can help to understand how the underlying pathway gene networks are organized and regulated in different conditions, tissues and developmental stages.
Bioinformatics
Reza Mir Drikvand; Seyyed sajad Sohrabi; Seyyed Mohsen ُSohrabi; Kamran Samiei
Abstract
MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation ...
Read More
MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation and response to stresses in plants. Coriander or Coriandrum sativum L. is a plant of Apiaceae family with different nutritional and pharmaceutical applications. Up to now, the genome of this plant has not been sequenced and there is no report of miRNAs identification has been recorded for it. The present study was performed to identify the conserved miRNAs and their target genes in transcriptome of coriander plant. Firstly, Transcriptome of seed and leaf tissues was assembled and non-coding transcripts were identified and considered as miRNA precursor. Finally, among candidate sequences, three miRNAs named csa-miR162, csa-miR169 and csa-miR399 belong to three conserved families were identified after strict filtering. Identified miRNAs showed differential expression between seed and leaf tissues and also role of their target genes in different biological processes was confirmed. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of coriander plant in the present study, these miRNAs can be used as candidate genes to improve qualitative and quantitative yield and resistance to different stresses in this plant.
Molecular Plant Breeding
Parvaneh Mahmodi; Ahmad Moeini; Seyed Mojtaba Khayam Nekoie; Mohsen Mardi; Ghasem Hosseini Salekdeh
Volume 4, Issue 6 , October 2014, , Pages 35-46
Abstract
Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing ...
Read More
Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing has risen as a cost-effective and powerful method for transcriptome study. De novo assembly of transcripts provides main solution to transcriptome analysis for organisms without reference genome. Precise sequencing and assembly of transcriptome reliable data are necessary for the downstream analysis. Accordingly, this work was analyzed by two of the most popular software's Trinity and SOAPdenovo for saffron stigma transcriptome to study the effective programs for transcriptome assembly. The results showed that the mean sequence length and the number of unigenes obtained by Trinity were more than SOAPdenovo (Trinity: 689, SOAPdenovo: 624). Translation of the better results produced by the appropriate assembler to protein led to a significant increase in the number of its records obtained at databases. Furthermore, these unigenes might help to identify more metabolite pathways. Assembled unigenes by Trinity had no lacking distance and were about twice the unigenes assembled by SOAPdenovo. As a general conclusion, it seems that selection of an appropriate software and its parameters is not easy without comprehension understanding of different software operation and their setting. Thus, comparison of the different softwares efficiency on the different organisms could provide some practical suggestions and choose an appropriate software.
