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.
Highlights
Small cardamom (Elettaria cardamomum (L.) Maton, known as the ‘Queen of Spices’ is a rhizomatous herbaceous monocot from the family Zingiberaceae
In the present study, using HiSeqTM 2000 RNA sequencing technology, transcriptome sequencing was performed for both control and disease stressed small cardamom leaf tissues
Agricultural and Biological Sciences Plant Science Text (FASTQ sequence files), table Data were generated using RNA HiSeqTM 2000 RNA sequencing technology Raw data in FASTQ format Freshly collected leaf samples was used for RNA isolation RNA seq libraries representing control and capsule rot disease stressed small cardamom were prepared and transcriptome sequencing was performed and de novo assembled to generate unigenes Plant growth and treatments were given under controlled conditions at ICRI, Idukki, Kerala, India
Summary
Agricultural and Biological Sciences Plant Science Text (FASTQ sequence files), table Data were generated using RNA HiSeqTM 2000 RNA sequencing technology Raw data in FASTQ format Freshly collected leaf samples (from both control and infected small cardamom plants) was used for RNA isolation RNA seq libraries representing control and capsule rot disease stressed small cardamom were prepared and transcriptome sequencing was performed and de novo assembled to generate unigenes Plant growth and treatments were given under controlled conditions at ICRI, Idukki, Kerala, India. Transcriptome data generated from leaves of plants grown under specific conditions could provide information on molecular mechanism underlying disease tolerance. Data shared in this article includes RNA-seq generated paired end strand specific 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
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
