Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.

Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions

Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant's defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.

Understanding the role of miRNAs for improvement of tea quality and stress tolerance

MicroRNAs (miRNAs) are an emerging class of small non-coding RNAs that exhibit important role in regulation of gene expression, mostly through the mechanism of cleavage and/or inhibition of translation of target mRNAs during or after transcription. Although much has been unravelled about the role of miRNAs in diverse biological processes like maintenance of functional integrity of genes and genome, growth and development, metabolism, and adaptive responses towards biotic and abiotic stresses in plants, not much is known on their specific roles in majority of cash crops - an area of investigation with potentially significant and gainful economic implications. Tea (Camellia sinensis) is globally the second most consumed beverage after water and its cultivation has major agro-economic and social ramifications. In recent years, global tea production has been greatly challenged by many biotic and abiotic stress factors and a deeper understanding of molecular processes regulating stress adaptation in this largely under investigated crop stands to significantly facilitate potential crop improvement strategies towards durable stress tolerance. This review endeavours to highlight recent advances in our understanding of the role of miRNAs in regulating stress tolerance traits in tea plant with additional focus on their role in determining tea quality attributes.

Mining of miRNAs from EST data in Dendrobium nobile

Dendrobium nobile is an orchid species highly popular for its therapeutic properties and is often used as a medicinal herb. Documenting miRNA-target associations in D. nobile is an important step to facilitate functional genomics studies in this species. Therefore, it is of interest to identify miRNA sequences from EST data available in public databases using known techniques and tools. We report 14 potential miRNAs from three ESTs of D. nobile. They belong to 3 miRNA families (miR390, miR528 and miR414) linking to transcription factor regulation, signal transduction, DNA and protein binding, and various cellular processes covering 34 different metabolic networks in KEGG. These results help in the understanding of miRNA-mRNAs functional networks in Dendrobium nobile.