Comprehensive molecular insights into the stress response dynamics of rice ( Oryza sativa L.) during rice tungro disease
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Comprehensive molecular insights into the stress response dynamics of rice (Oryza sativa L.) during rice tungro disease by RNA-seq-based comparative whole transcriptome analysis GAURAV KUMAR and INDRANIL DASGUPTA* Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India *Corresponding author (Email, [email protected], [email protected]) MS received 26 June 2019; accepted 30 December 2019 Rice tungro is a serious viral disease of rice resulting from infection by two viruses, Rice tungro bacilliform virus and Rice tungro spherical virus. To gain molecular insights into the global gene expression changes in rice during tungro, a comparative whole genome transcriptome study was performed on healthy and tungroaffected rice plants using Illumina Hiseq 2500. About 10 GB of sequenced data comprising about 50 million paired end reads per sample were then aligned on to the rice genome. Gene expression analysis revealed around 959 transcripts, related to various cellular pathways concerning stress response and hormonal homeostasis to be differentially expressed. The data was validated through qRT-PCR. Gene ontology and pathway analyses revealed enrichment of transcripts and processes similar to the differentially expressed genes categories. In short, the present study is a comprehensive coverage of the differential gene expression landscape and provides molecular insights into the infection dynamics of the rice-tungro virus system. Keywords.
Differentially expressed genes; pathway analysis; rice tungro disease; RNA-Seq; transcriptome
1. Introduction Rice Tungro Disease (RTD) is one of the most important viral diseases of rice prevailing in South and Southeast Asian countries, causing an annual loss of approximately US $1.5 billion in rice production (Bunawan et al. 2014). RTD is caused by the simultaneous infection with two viral species; Rice tungro bacilliform virus (RTBV, a pararetrovirus, having a double-stranded DNA genome, Genus: Tungrovirus, Family: Caulimoviridae) and Rice tungro spherical virus (RTSV, a plant picornavirus having a single-stranded positive-sense RNA genome, Genus: Waikavirus, Family: Secoviridae (Hibino et al. 1978; Hay et al. 1991; Jones et al. 1991; Shen et al. 1993; Thompson et al. 2017). The vector Green Leaf Hopper (GLH), Nephotettix virescens, jointly transmits RTBV and RTSV in a semi-persistent manner. RTBV alone causes severe disease symptoms in the host,
but is incapable of independent transmission through GLH. RTSV, on the other hand, can be transmitted independently by GLH, but causes only mild stunting symptoms in most rice varieties (Hibino et al. 1978; Hibino et al. 1979; Cabauatan and Hibino 1985). Attempts have been made earlier to elucidate the physiological and biochemical changes in rice plants affected with RTD. For example, several studies indicate a decrease in photosynthetic and accessory pigments, enzymes and substrates along with altered growth hormo
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