@article {890, title = {Identification and characterization of drought responsive microRNAs and their target genes in cardamom (Elettaria cardamomum Maton) [Next Gen Genomics Facility]}, journal = {Plant Growth Regulation}, year = {2018}, month = {Dec}, abstract = {

Plant miRNAs are found to be present throughout the genome and they regulate gene expression either by cleaving mRNA or inhibiting the translational process at the post transcriptional level. Drought is one of the major limiting factors that negatively affect productivity of plants. Cardamom cultivation is having good production potential but the plants are vulnerable to biotic and abiotic stress factors. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Ion Torrent sequencing of two small RNA libraries prepared from control (C) and treated (T) plants raised under well irrigated and drought stressed treatments respectively created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these miRNAs might have involved in various biological processes to improve plant tolerance to water stress. Several target genes for drought stress regulating miRNAs were identified including miR156l and miR169c which cleave the target mRNA involved in response to water deprivation. miR530b and miR156a target mRNAs which respond to water deprivation and inhibit the translational process. The expression patterns of some of the miRNAs and their targets were validated by qRT-PCR. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.

}, issn = {1573-5087}, doi = {10.1007/s10725-018-0462-9}, url = {https://doi.org/10.1007/s10725-018-0462-9}, author = {Anjali, N. and Nadiya, F. and Thomas, Jinu and Sabu, K. K.} } @article {892, title = {Data on identification of conserved and novel miRNAs in Elettaria cardamomum [Next Gen Genomics Facility]}, journal = {Data Brief}, volume = {14}, year = {2017}, month = {2017 Oct}, pages = {789-792}, abstract = {

(L.) Maton, or small cardamom referred as {\textquoteright}queen of spices{\textquoteright}, is a perennial herbaceous rhizomatous monocot of the family Zingiberaceae. Cardamom seeds and fruits are the economically significant parts and effectively used as a traditional medicine, food additive and flavoring agent. In the present study, using Ion Proton next generation sequencing technology we performed the small RNA sequencing, conserved and novel miRNA predictions of a wild and five cultivar genotypes of cardamom. Small RNA sequencing generated a total of 5,451,328 and 2,756,250 raw reads for wild and cultivar cardamom respectively. The raw data was submitted to SRA database of NCBI under the accession numbers and SRX2273863 (wild) and SRX2273862 (cultivars). The raw reads were quality filtered and predicted conserved and novel miRNAs for wild and cultivar cardamom. The predicted miRNAs, miRNA-targets and functional annotations might provide valuable insights into differences between wild progenitor and cultivated cardamom.

}, issn = {2352-3409}, doi = {10.1016/j.dib.2017.08.037}, author = {Nadiya, F and Anjali, N and Thomas, Jinu and Gangaprasad, A and Sabu, K K} } @article {689, title = {Discovery of MicroRNAs in Cardamom ( Elettaria cardamomum Maton) under Drought Stress}, journal = {Dataset Papers in Science}, volume = {2017}, year = {2017}, month = {07}, pages = {1-4}, author = {Narayanannair, Anjali and Nadiya, F and Thomas, Jinu and Sabu, Kallevettankuzhy} } @article {688, title = {Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom).}, journal = {Genom Data}, volume = {11}, year = {2017}, month = {2017 Mar}, pages = {102-103}, abstract = {

Elettaria cardamomum (L.) Maton, known as {\textquoteright}queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

}, issn = {2213-5960}, doi = {10.1016/j.gdata.2016.12.013}, author = {Nadiya, F and Anjali, N and Thomas, Jinu and Gangaprasad, A and Sabu, K K} }