Current Genomics - Volume 23, Issue 1, 2022

MicroRNAs, short single-stranded noncoding RNAs ranging in length from 18 ~ 24 bp, are found in all kingdoms of eukaryotes and even viruses. It was found that miRNAs are involved in a variety of biological processes, and their intracellular aberrant expression is related to diseases and abnormalities in the immune system. Since then, it has been considered essential to develop an efficient miRNA detection system. In this review, the limitations of traditional scheme-based miRNA detection methods are compared and analyzed. In particular, nucleic acid amplification-based miRNA detection methods and nanomaterial-based miRNA detection methods, which are widely used as a biosensing platform because of various features and advantages, such as high sensitivity, specificity, and simplicity, are analyzed. Based on this analysis, the latest examples of a combination of the advantages of nucleic acid amplification and those of nanomaterials are examined to suggest the characteristics of the next-generation miRNA biosensing.

Background: Seed abortion is a common phenomenon in Chinese jujube that seriously hinders the process of cross-breeding. However, the molecular mechanisms of seed abortion remain unclear in jujube. Methods: Here, we performed transcriptome sequencing using eight flower and fruit tissues at different developmental stages in Ziziphus jujuba Mill. ‘Zhongqiusucui’ to identify key genes related to seed abortion. Histological analysis revealed a critical developmental process of embryo abortion after fertilization. Results: Comparisons of gene expression revealed a total of 14,012 differentially expressed genes. Functional enrichment analyses of differentially expressed genes between various sample types uncovered several important biological processes, such as embryo development, cellular metabolism, and stress response, that were potentially involved in the regulation of seed abortion. Furthermore, gene co-expression network analysis revealed a suite of potential key genes related to ovule and seed development. We focused on three types of candidate genes, agamous subfamily genes, plant ATP-binding cassette subfamily G transporters, and metacaspase enzymes, and showed that the expression profiles of some members were associated with embryo abortion. Conclusion: This work generates a comprehensive gene expression data source for unraveling the molecular mechanisms of seed abortion and aids future cross-breeding efforts in jujube.

Background: Even though miRNAs play vital roles in developmental biology by regulating the translation of mRNAs, they are poorly studied in oomycetes, especially in the plant pathogen Phytophthora. Objective: The study aimed to predict and identify the putative miRNAs and their targets in Phytophthora infestans and Phytophthora cinnamomi. Methods: The homology-based comparative method was used to identify the unique miRNA sequences in P. infestans and P. cinnamomi with 148,689 EST and TSA sequences of these species. Secondary structure prediction of sRNAs for the 76 resultant sequences has been performed with the MFOLD tool, and their targets were predicted using psRNATarget. Results: Novel miRNAs, miR-8210 and miR-4968, were predicted from P. infestans and P. cinnamomi, respectively, along with their structural features. The newly identified miRNAs were identified to play important roles in gene regulation, with few of their target genes predicted as transcription factors, tumor suppressor genes, stress-responsive genes, DNA repair genes, etc. Conclusion: The miRNAs and their targets identified have opened new interference and editing targets for the development of Phytophthora resistant crop varieties.

Background: Chickpea is one of Turkey's most significant legumes, and because of its high nutritional value, it is frequently preferred in human nourishment.Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants. Objective: Current study aimed at revealing complete chloroplast genome sequence of one of the wild type Cicer species, Cicer bijugum, and comparing its genome with cultivated Cicer species, Cicer arietinum, by using bioinformatics analysis tools. Except for Cicer arietinum, there has been no study on the chloroplast genome sequence of Cicer species.Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type Cicer species, Cicer bijugum, and compare the chloroplast genome of Cicer bijugum with the cultivated one Cicer arietinum. Methods: In this study, we sequenced the whole chloroplast genome of Cicer bijugum, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, Cicer arietinum, by using online bioinformatics analysis tools. Results: We determined the size of the chloroplast genome of C. bijugum as 124,804 bp and found that C. bijugum did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the C. bijugum chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15, and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that C. bijugum was phylogenetically closer to cultivated chickpea as compared to the other species. Conclusion: It is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary, and genetic engineering studies with chickpea species.

Background: Flower senescence is the last stage of flower development and affects the ornamental and economic value of flower plants. There is still less known on flower senescence of the ornamental plant Camellia lutchuensis, a precious species of Camellia with significant commercial application value. Methods: Transcriptome sequencing was used to investigate the flower senescence in five developmental stages of C. lutchuensis. Results: By Illumina HiSeq sequencing, we generated approximately 101.16 Gb clean data and 46649 differentially expressed unigenes. Based on the different expression pattern, differentially expressed unigenes were classified into 10 Sub Class. And Sub Class 9 including 8252 unigenes, was highly expressed in the flower senescent stage, suggesting it had a potential regulatory relationship of flower senescence. First, we found that ethylene biosynthesis genes ACSs, ACOs, receptor ETR genes and signaling genes EINs, ERFs all upregulated during flower senescence, suggesting ethylene might play a key role in the flower senescence of C. lutchuensis. Furthermore, reactive oxygen species (ROS) production related genes peroxidase (POD), lipase (LIP), polyphenoloxidase (PPO), and ROS scavenging related genes glutathione S-transferase (GST), glutathione reductase (GR) and superoxide dismutase (SOD) were induced in senescent stage, suggesting ROS might be involved in the flower senescence. Besides, the expression of monoterpenoid and isoflavonoid biosynthesis genes, transcription factors (WRKY, NAC, MYB and C2H2), senescence-associated gene SAG20 also were increased during flower senescence. Conclusion: In C. lutchuensis, ethylene pathway might be the key to regulate flower senescence, and ROS signal might play a role in the flower senescence.