Open AccessPlant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec
Author(s) -
Aamir W. Khan,
Johnson George K,
Rahul Singh Jasrotia,
U. B. Angadi,
M.A. Iqbal,
Sarika Jaiswal,
Anil Rai,
Dinesh Kumar
Publication year - 2020
Publication title -
bhartiya krishi anusandhana patrika
Language(s) - English
Resource type - Journals
eISSN - 0976-4631
pISSN - 0303-3821
DOI - 10.18805/bkap206
Subject(s) - transcriptome , biology , germplasm , gene , small rna , genome , sequence assembly , genetics , disease , computational biology , rna , microbiology and biotechnology , botany , gene expression , medicine , pathology
Small cardamom (Elettaria cardamomum), is one of the costliest spices across the globe. It is grown in limited coastal tropical countries. It is widely exported agri-produce with global turnover of > 10 billion USD. It is majorly affected by the mosaic or marble disease and hence warrants the deep study at molecular level. Till now, there is no availability of whole genome sequence along with any genomic resources. Under such cases, RNA seq approach can be a rapid and economical alternative to gather the information at genomic level. De novo transcriptome assembly was carried out using Illumina Hiseq data. Analysis revealed a total of 5317 differentially expressed genes, 2267 transcription factors, >100 pathways and 175,952 genic region putative markers. Gene regulatory network analysis was performed to see the molecular events playing role in marble disease. We report the first transcriptomic results that shows the disease mechanism mediated by perturbation in auxin homeostasis and ethylene signaling. These events lead to senescence. We also developed the web-genomic resource, SCMVTDb which houses putative molecular markers, candidate genes and transcript information. Such web resource can be used in small cardamom germplasm improvement against mosaic disease in endeavour of its increased productivity.