Tuesday, October 27, 2020

Gouri, P. R., Jisha, S., and K. K. Sabu. 2020. Dataset on Discovery of MicroRNAs in Centella asiatica (L.) Urb. Data in Brief 106451. Available online 22 October 2020. https://doi.org/10.1016/j.dib.2020.106451

MicroRNAs (miRNAs) are small (21–24 nucleotides), non-coding, riboregulators that regulate gene expression in eukaryotes. Pentacyclic triterpenoid saponins and sapogenins known as centellosides of the plant Centella asiatica (L.) Urb. are known for their broad spectrum medicinal properties. Two C. asiatica accessions viz.,CA301 and CA308 were selected for the miRNAome profiling. Total RNA isolated from fresh young leaves of both accessions along with their replicas was used for library construction. Illumina® sequencing of the four small RNA libraries generated a total of 59,234,923; 58,487,817; 59,520,376; 64,093,228 raw reads. The raw reads were quality filtered and used for the prediction of conserved and novel miRNAs. A total of 227 conserved and 109 novel microRNAs were identified from the libraries. Target gene prediction done using psRNAtarget and PANTHER™GO helped in localization of predicted targets. KEGG (Kyoto Encyclopedia for Genes and Genomes) was used for pathway prediction of the targets of predicted miRNAs. The present study provides first elaborated glimpse of miRNA pool of C. asiatica. The outcome of this research could help understand miRNA dependent regulation of centelloside biosynthesis and to design further metabolic engineering experiments to enhance their content in this important medicinal plant.

Role of miRNAs in biotic and abiotic stress management in crop plants

Anjali N & Sabu K K (2020). Role of miRNAs in biotic and abiotic stress management in crop plants. In: Sustainable Agriculture in the Era of Climate Change. Edited by R. Roychowdhury (Springer New York, USA). Pp. 513-532. https://doi.org/10.1007/978-3-030-45669-6_22

MicroRNAs (miRNAs) are endogenous, 18–25 nucleotide in length, and noncoding RNAs found in animals, plants, and in some viruses. They have been recognized as an important class of gene expression regulators and are involved in a multitude of biological processes in plants, including organ differentiation and development, metabolism, and response to biotic and abiotic stress factors, to mention a few. The method of action of miRNA is by binding to a ribonucleoprotein complex which is incorporated with a protein of Argonaute family. This RNA-induced silencing complex (RISC) targets the mRNA and inhibits its expression by degrading mRNA or by translational repression. It has been reported that posttranscriptional regulation mediated by miRNAs has important roles in adverse stress conditions. Some miRNAs respond to a number of abiotic and biotic stresses, and some others are stress specific. Not only characterization of miRNAs but also identification of their targets is crucial in this field of research. The participation of miRNAs in a species-specific manner to biotic and abiotic stress responses reveals the functional diversification of miRNAs among plant species and highlights the importance of conducting miRNA studies in diverse plant species. MicroRNA-based genetic modification technology is a very powerful technique to develop high-yielding crops which can resist biotic and abiotic stress factors.

Wednesday, March 18, 2020

Data on Large cardamom transcriptome associated with Chirke disease

Mary Mathew K, Renjanan Reshma, M Geethu, Varghese Rithin, Swapna Sasidharan, P P Gouthaman, K K Sabu, F Nadiya, Noushad Muhammad Ali, Dharan S Soumya, R Prakashkumar, A B Remashree. 2019. Data on Large cardamom transcriptome associated with Chirke disease. Data in Brief 29: 10504. https://doi.org/10.1016/j.dib.2019.105047

Abstract
Large cardamom (Amomum subulatum Roxburg), is an ancient spice native to North-Eastern India and Southeast Asia, which belongs to the family Zingiberaceae under the order Scitaminae. Large cardamom is mostly affected by a viral disease termed Chirke caused by Large Cardamom Chirke Virus (LCCV). These disease has spread due to drastic changes in the ecosystem, inadequate rain in dry months and absence of good agricultural practices by the farmers resulting in aphid infestations. In the present study, using HiSeq™ 2000 RNA sequencing technology transcriptome sequencing was performed for both control (disease not expressed) and diseased large cardamom leaf tissues. RNA-seq generated 77260968 (7.72 GB) and 72239708 (7.22 GB) paired raw reads for large cardamom control and diseased samples respectively. The raw data were submitted to the NCBI SRA database under the accession numbers SRX2529373 and SRX2529372 and the assembled transcriptomes were submitted to TSA under the accession numbers GIAV01000000 and GIAW01000000 for the control and diseased samples respectively. The raw reads were quality trimmed and assembled de novo using TRINITY assembler which created 156822 (control) and 148953 (diseased) contigs with N50 values 2107 (control) and 2182 (diseased). The data were used to identify the significantly differentially expressed genes between control and diseased samples.

Data on small cardamom transcriptome associated with capsule rot disease

Mary Mathew K, Renjanan Reshma, M. Geethu, Varghese Rithin, K.K. Sabu, F. Nadiya, Muhammad Ali Noushad, Soumya S. Dharan, Y.S. Rao, A.B. Remashree. 2019. Data on small cardamom transcriptome associated with capsule rot disease. Data in Brief 27: 104625. https://doi.org/10.1016/j.dib.2019.104625

Abstract
Small cardamom (Elettaria cardamomum (L.) Maton, also known as the ‘Queen of Spices’ is a rhizomatous herbaceous monocot from the family Zingiberaceae. In the present study, using HiSeq™ 2000 RNA sequencing technology, transcriptome sequencing was performed for both control and disease stressed small cardamom leaf tissues. RNA-seq generated 46,931,637 (101 base) and 31,682,496 (101 base) raw reads and totally 9.93GB and 6.63GB of sequence data for cardamom control and stressed samples respectively. The raw data were submitted to NCBI SRA database of under the accession numbers SRX2512359 and SRX2512358 for the control and diseased samples respectively. The raw reads were quality filtered and assembled using TRINITY de novo assembler which created 1,11,495 (control) and 91,096 (diseased) contigs with N50 values 3013 (control) and 2729 (stressed). The data was further used to identify significantly differentially expressed unigenes between control and stressed samples. Assembled unigenes were further annotated and evaluated in silico to predict the function using publicly available databases and gene annotation tools.

Thursday, February 27, 2020

Small RNA manipulation in plants: Techniques and recent developments

The term “RNA silencing” refers to the processes that depend on small RNAs (approx. 18–24 nt) to regulate the mRNA expression in eukaryotes. In plants, small RNA regulation plays crucial roles in development, in responses to biotic or abiotic stress, in regulating metabolic pathways, in maintaining genome integrity, and in defense response mechanisms. In the last few years, small RNA manipulation has been used as a research tool to identify and validate gene expression, and studies now extensively focus on applying this technology in commercial applications, especially in medical therapeutics and flower color in ornamental plants. This chapter covers current progress on the application of RNA silencing to produce plants resistant to plant viruses, insects, and fungal pathogens, and also in applying these technologies toward the improvement of agricultural crops and medicinal plants. This chapter will also discuss the challenges, limitations, and biologic safety concerns related to small RNA manipulation in crops.

https://www.sciencedirect.com/science/article/pii/B9780128171127000183

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