Data on large cardamom transcriptome associated with Chirke disease

• Main Authors: K. Mary Mathew, Ranjanan Reshma, M. Geethu, Varghese Rithin, Sasidharan Swapna, P.P. Gouthaman, K.K. Sabu, F. Nadiya, Muhammad Ali Noushad, Soumya S. Dharan, R. Prakashkumar, A.B. Remashree
• Format: Article
• Language: English
• Published: Elsevier 2020-04-01
• Series: Data in Brief
• Online Access: http://www.sciencedirect.com/science/article/pii/S2352340919314039

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. Keywords: Large cardamom, RNA sequencing, Transcriptome, Differential expression