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Publication Type J
Authors Bansal, J., K. Gupta, M. S. Rajkumar, R. Garg and M. Jain
Title Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors
Source Physiologia Plantarum
Author Keywords DNA methylation abiotic stress salt-stress tolerance gene metabolism expression micrornas discovery chickpea
Abstract Introduction Oryza coarctata is a wild relative of rice that has adapted to diverse ecological environments, including high salinity and submergence. Thus, it can provide an important resource for discovering candidate genes/factors involved in tolerance to these stresses. Here, we report a draft genome assembly of 573 Mb comprised of 8877 scaffolds with N50 length of 205 kb. We predicted a total of 50,562 protein-coding genes, of which a significant fraction was found to be involved in secondary metabolite biosynthesis and hormone signal transduction pathways. Several salinity and submergence stress-responsive protein-coding and long noncoding RNAs involved in diverse biological processes were identified using RNA-sequencing data. Based on small RNA sequencing, we identified 168 unique miRNAs and 3219 target transcripts (coding and noncoding) involved in several biological processes, including abiotic stress responses. Further, whole genome bisulphite sequencing data analysis revealed at least 19%-48% methylcytosines in different sequence contexts and the influence of methylation status on gene expression. The genome assembly along with other datasets have been made publicly available at . Altogether, we provide a comprehensive genomic resource for understanding the regulation of salinity and submergence stress responses and identification of candidate genes/factors involved for functional genomics studies.
Author Address [Bansal, Juhi; Rajkumar, Mohan Singh; Jain, Mukesh] Jawaharlal Nehru Univ, Sch Computat & Integrat Sci, New Delhi 110067, India. [Gupta, Khushboo; Garg, Rohini] Shiv Nadar Univ, Sch Nat Sci, Dept Life Sci, Noida, India. Jain, M (corresponding author), Jawaharlal Nehru Univ, Sch Computat & Integrat Sci, New Delhi 110067, India. mjain@jnu.ac.in
ISSN 0031-9317
ISBN 0031-9317
29-Character Source Abbreviation Physiol. Plant.
Digital Object Identifier (DOI) 10.1111/ppl.13284
Unique Article Identifier WOS:000594395400001

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