Data on identification of conserved and novel miRNAs in Elettaria cardamomum

Elettaria cardamomum (L.) Maton, or small cardamom referred as ‘queen of spices’, 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.


a b s t r a c t
Elettaria cardamomum (L.) Maton, or small cardamom referred as 'queen of spices', 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.
& The data presented in the article provides information on genome wide conserved and novel miRNA profiling and differential expression analysis of wild and cultivar genotypes of cardamom.
This data identifies miRNAs participating in the negative regulation of significant transcription factors, enzymes and other mRNAs involved in plant development, stress responses and pathogenic resistance.
The identified miRNAs were also compared with other monocots and Arabidopsis to determine the extent of conservation of known miRNAs between cardamom, other monocots and Arabidopsis.
The data allows other researchers to study miRNA regulations in various biosynthetic pathways.

Data
The data shared in this article provides information on conserved and novel miRNAs and differential miRNA expression analysis between wild and cultivar genotypes of cardamom

Plant material
Fresh leaves, stem, flower, flower buds and young fruits were collected from wild and five cultivar (including landraces and released varieties) accessions of cardamom growing in the JNTBGRI cardamom conservatory. The tissues were immediately frozen in liquid nitrogen and kept as such until processing.

Total RNA isolation and small RNA sequencing
Total RNA was isolated from leaves, stem, flower, flower buds and young fruits of cardamom using miRNeasy mini kit combined with modified CTAB method [1]. Quantification and quality analysis were done using 2100 BioAnalyzer (Agilent technologies). The tissues of wild cardamom were pooled as one sample and the tissues from all cultivars were pooled as second sample representing wild and cultivar cardamom. Two sets of total RNA enriched with miRNAs were purified and cDNA library was constructed using Ion total RNA seq Kit V2 according to manufacturer's instructions. The purified libraries were submitted to small RNA sequencing with the Ion Proton Sequencer.

Identification of conserved and novel miRNAs
The raw reads were preprocessed to remove adapter sequences, rRNAs, tRNAs, other small RNAs and sequences below 17 and 27nt. The identical sequences were collapsed and known miRNAs were identified by performing blastn search against plant mature miRNAs from miRBase database. The remaining reads were mapped to the Curcuma longa (Zingiberaceae family) transcriptome sequence (the whole genome or transcriptome sequence of cardamom was not available at the time of the study) to predict putative novel miRNAs using miRDeep-P software [2] satisfying Mayer's criteria [3] of miRNA prediction (Table 1). Using the identified miRNAs we also performed the differential expression analysis, target prediction and Gene Ontology (GO) annotations for wild and cultivar genotypes of cardamom. The information we provided might furnish awareness on genetic resources of wild cardamom, molecular marker development and breeding for developing novel elite cultivars using RNAi technology. The study also provides insight into the genetic variation in wild and domesticated cardamom.

Differential expression analysis and target prediction
Count of each miRNA was normalized to Tags per million (TPM) to compare the abundance of miRNAs in wild and cultivar library. Fold change of each miRNA between the two libraries was calculated employing the formula: log 2 (cultivars/wild) [4]. Unique potential targets were predicted for both novel and conserved miRNAs using psRNA target [5].

Transparency document. Supplementary material
Supplementary data associated with this article can be found in the online version at http://dx.doi. org/10.1016/j.dib.2017.08.037.