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Author: Baldodiya, Gajendra Mohan × End date: 2018 × Type: Thesis ×
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    ThesisItemOpen Access
    Study and characterization of the DNA virus diseases in few important crops of Assam
    (AAU, Jorhat, 2018-01) Baldodiya, Gajendra Mohan; DebNath, Palash
    Plant viruses cause many devastating diseases and are responsible for the huge loss in crop production and quality. The Infected plants may show a range of symptoms like leaf yellowing, leaf distortion, growth abnormalities and yield reduction. Although the majority of the plant viruses are RNA viruses, in the recent years, DNA viruses have emerged as a serious problem for vegetables and fiber crops, more specifically in tropical and subtropical regions of the world. In India, Begomoviruses are known for major yield loss in a variety of crops. So far, very few reports on DNA virus diseases are available from the northeastern region, including Assam. In the present study, three important single-stranded DNA viruses, banana bunchy top virus (BBTV), squash leaf curl China virus (SLCCNV) and tobacco curly shoot virus (TbCSV) were identified from Assam infecting banana, pumpkin, and chilli crops respectively. The crop cultivating areas were surveyed and 89 plant samples showing symptoms of geminivirus and BBTV infections were collected from 16 different crops. The broad-spectrum antibody combination, tomato yellow leaf curl virus (TYLCV) in DAS-ELISA (double antibody sandwich ELISA) assay revealed the all possible Begomovirus infections. The molecular detection method by using universal and gene-specific primers confirmed the presence of viral genome in positively screen samples through DAS-ELISA. The full-length genome amplification of detected viruses was achieved by designing walking primers from both ends of the partial genome and rolling circle amplification (RCA) followed by cloning process. The in silico analysis (genomic feature analysis, multiple sequence alignment and phylogenetic grouping) revealed the molecular properties of identified viruses. The BBTV-As-JOR was found closely related with BBTV-Lucknow isolate, although it stands out for few genomic features. Each genomic segment of the BBTV-As-JOR isolate was comprised of an ORF in sense orientation, encoding specific protein like other BBTV isolates. The common region major (CR-M) of DNA-R shows 26nt deletion like BBTV Lucknow but deletion of 36nt in DNA-U3 was found different. The BBTV-As-JOR clustered with PIO (Pacific Indian Ocean) isolates in the phylogenetic analysis based on the R-segment. Similarly, the clustering of other BBTV segments was also found with previously reported BBTV isolates of PIO group. The genome of SLCCNV-As-JOR-G8 pumpkin shared high nucleotide sequences and proteins similarity with SLCCNV-pumpkin-Varanasi DNA-A. The phylogenetic clustering also conferred these findings. The sequence analysis confirmed the presence of seven ORFs viz, AC1, AC2, AC3, AC4, AC5, AV1/CP and AV2 in SLCCNV-As-JOR-G8 pumpkin. The ORFs showed the typical begomoviral genome organization; however, they displayed similarity to different begomoviruses. The TbCSV-As was identified as a close relative of TbCSV)-[SC118] sharing the similarity of two major proteins, AL2 and AL3. The occurrence of TbCSV in chilli (Capsicum frutescens) host plant and causing upward curling of leaves is the first report from India in our knowledge. This study presents the first report of identification and characterization of BBTV, SLCCNV, and TbCSV from Assam which may open up a new insight into the understanding of DNA viruses infecting important crops of the state.