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Shyamli PS, Pradhan S, Panda M, Parida A. De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance. Front Plant Sci 2021; 12:766999. [PMID: 34970282 PMCID: PMC8712769 DOI: 10.3389/fpls.2021.766999] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Abiotic stresses, especially drought stress, are responsible for heavy losses in productivity, which in turn poses an imminent threat for future food security. Understanding plants' response to abiotic stress at the molecular level is crucially important for mitigating the impacts of climate change. Moringa oleifera is an important multipurpose plant with medicinal and nutritional properties and with an ability to grow in low water conditions, which makes the species an ideal candidate to study the regulatory mechanisms that modulate drought tolerance and its possible use in agroforestry system. In the present communication, we report whole-genome sequencing (WGS) of this species and assemble about 90% of the genome of M. oleifera var. Bhagya into 915 contigs with a N50 value of 4.7 Mb and predicted 32,062 putative protein-coding genes. After annotating the genome, we have chosen to study the heat shock transcription factor (HSF) family of genes to analyze their role in drought tolerance in M. oleifera. We predicted a total of 21 HSFs in the M. oleifera genome and carried out phylogenetic analyses, motif identification, analysis of gene duplication events, and differential expression of the HSF-coding genes in M. oleifera. Our analysis reveals that members of the HSF family have an important role in the plant's response to abiotic stress and are viable candidates for further characterization.
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Affiliation(s)
- P Sushree Shyamli
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Seema Pradhan
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
| | - Mitrabinda Panda
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Ajay Parida
- Institute of Life Sciences, An Autonomous Institute Under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, India
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Sushree Shyamli P, Rana S, Suranjika S, Muthamilarasan M, Parida A, Prasad M. Genetic determinants of micronutrient traits in graminaceous crops to combat hidden hunger. Theor Appl Genet 2021; 134:3147-3165. [PMID: 34091694 DOI: 10.1007/s00122-021-03878-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Improving the nutritional content of graminaceous crops is imperative to ensure nutritional security, wherein omics approaches play pivotal roles in dissecting this complex trait and contributing to trait improvement. Micronutrients regulate the metabolic processes to ensure the normal functioning of the biological system in all living organisms. Micronutrient deficiency, thereby, can be detrimental that can result in serious health issues. Grains of graminaceous crops serve as an important source of micronutrients to the human population; however, the rise in hidden hunger and malnutrition indicates an insufficiency in meeting the nutritional requirements. Improving the elemental composition and nutritional value of the graminaceous crops using conventional and biotechnological approaches is imperative to address this issue. Identifying the genetic determinants underlying the micronutrient biosynthesis and accumulation is the first step toward achieving this goal. Genetic and genomic dissection of this complex trait has been accomplished in major cereals, and several genes, alleles, and QTLs underlying grain micronutrient content were identified and characterized. However, no comprehensive study has been reported on minor cereals such as small millets, which are rich in micronutrients and other bioactive compounds. A comparative narrative on the reports available in major and minor Graminaceae species will illustrate the knowledge gained from studying the micronutrient traits in major cereals and provides a roadmap for dissecting this trait in other minor species, including millets. In this context, this review explains the progress made in studying micronutrient traits in major cereals and millets using omics approaches. Moreover, it provides insights into deploying integrated omics approaches and strategies for genetic improvement in micronutrient traits in graminaceous crops.
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Affiliation(s)
- P Sushree Shyamli
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, Haryana (NCR Delhi), 121001, India
| | - Sumi Rana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Sandhya Suranjika
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, 751024, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Raghav S, Ghosh A, Turuk J, Kumar S, Jha A, Madhulika S, Priyadarshini M, Biswas VK, Shyamli PS, Singh B, Singh N, Singh D, Datey A, Avula K, Smita S, Sabat J, Bhattacharya D, Kshatri JS, Vasudevan D, Suryawanshi A, Dash R, Senapati S, Beuria TK, Swain R, Chattopadhyay S, Syed GH, Dixit A, Prasad P, Pati S, Parida A. Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Front Microbiol 2020; 11:594928. [PMID: 33329480 PMCID: PMC7732478 DOI: 10.3389/fmicb.2020.594928] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/21/2020] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers-based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assemblies identified the presence of all the five reported clades 19A, 19B, 20A, 20B, and 20C in the population. The analyses revealed Europe and Southeast Asia as two major routes for introduction of the disease in India followed by local transmission. Interestingly, the19B clade was found to be more prevalent in our sequenced genomes (17%) compared to other genomes reported so far from India. Haplotype network analysis showed evolution of 19A and 19B clades in parallel from predominantly Gujarat state in India, suggesting it to be one of the major routes of disease transmission in India during the months of March and April, whereas 20B and 20C appeared to evolve from 20A. At the same time, 20A and 20B clades depicted prevalence of four common mutations 241 C > T in 5' UTR, P4715L, F942F along with D614G in the Spike protein. D614G mutation has been reported to increase virus shedding and infectivity. Our molecular modeling and docking analysis identified that D614G mutation resulted in enhanced affinity of Spike S1-S2 hinge region with TMPRSS2 protease, possibly the reason for increased shedding of S1 domain in G614 as compared to D614. Moreover, we also observed an increased concordance of G614 mutation with the viral load, as evident from decreased Ct value of Spike and the ORF1ab gene.
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Affiliation(s)
- Sunil Raghav
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Arup Ghosh
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | - Sugandh Kumar
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Atimukta Jha
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | | | | | | | - Bharati Singh
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Neha Singh
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Deepika Singh
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Ankita Datey
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Kiran Avula
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | - Shuchi Smita
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | | | | | | | | | - Rupesh Dash
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | | | - Rajeeb Swain
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | | | | | - Punit Prasad
- Institute of Life Sciences (ILS), Bhubaneswar, India
| | | | | | | | - Ajay Parida
- Institute of Life Sciences (ILS), Bhubaneswar, India
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