Data on small cardamom transcriptome associated with capsule rot disease

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.

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

“…Transcriptomic studies on leaves, stems, flowers, flower buds, capsule rot disease ( Nadiya et al, 2017 ; Mathew et al, 2019 ), mosaic virus disease ( Khan et al, 2020 ) of small cardamom, and Chirke disease ( Mathew et al, 2020 ) of large cardamom are reported. In turmeric species ( C. longa ), inter-cultivar differential gene expression in rhizomes of Nattu, Erode, Mysore, and Suvarna, along with SNP discovery, has been described ( Annadurai et al, 2013 ; Sahoo et al, 2016 ).…”