جستجوی مقالات مرتبط با کلیدواژه « mirbase » در نشریات گروه « بیوتکنولوژی و ژنتیک گیاهی »

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.

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.