BRIC-National Institute of Plant Genome Research

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BRIC-National Institute of Plant Genome Research

An Autonomous Institute of Biotechnology Research and Innovation Council
Deptartment of Biotechnology, Ministry of Science and Technology
Government of India

Sowing seeds for a better tomorrow

Dr. Debasis Chattopadhyay

Scientist VII

Ph.D. – Calcutta University
Post-Doctoral Fellow – The Cleveland Clinic Foundation, Ohio

Profile

Research Interests

Our program focuses on two major areas of research, namely, improvement of tolerance to abiotic stresses (i.e. drought and salt) in higher plants by improving root traits, and genome sequencing and analyses.

Abiotic Stress Tolerance

Water and nutrient availability limits plant growth and ultimately the yield in all agricultural ecosystems. While the breeders in the past decades have made huge improvements by manipulating тАШshoot-based traitsтАЩ, especially the reproductive qualities, the root, an important ecological topic has received less attention. There is still an immense potential to increase yields because the wide genetic variation trapped in roots has not been exploited properly so far. About one-third of earthтАЩs aerable land is arid, and there are very few areas that are not subject to periodic drought. Our group focuses on mechanism of root growth under abiotic stress and thereby improving stress tolerance in plant. We have identified genes encoding transcription factors and kinases and demonstrated their role in root development during abiotic stresses. Our long-term goal is to use genetic engineering to improve root biomass and tolerance to abiotic stresses of important crops particularly, chickpea.

Genome Sequencing

Our laboratory is one of the three Indian centers that sequenced chromosome 5 of tomato genome. Chickpea is the third most important food legume crop. We have published an advanced draft genome assembly and analysis of a desi-type chickpea. We have also reported a draft genome assembly of the wild progenitor of chickpea,┬аCicer reticulatum. These genome assemblies are being utilized in our laboratory to map the quantitative trait loci responsible in chickpea for root development under water deficit using mapping populations in order to improve chickpea yield with less water.

Awards & Honors

Year

Honors

2018

Fellow of Indian National Science Academy

2013

Fellow of The Indian Academy of Sciences

2013

Fellow of West Bengal Academy of Science and Technology

2009

Fellow of The National Academy of Sciences, India

Year

Awards

2020

J C Bose National Fellowship, SERB-DST

2017

NASI-Reliance Industries Platinum Jubliee Award

2015

TATA Innovation Fellowship by the Department of Biotechnology, Govt. of India.

2010

National Bioscience Award for Career Development, DBT, Govt. of India

2006

Prof. Umakant Sinha Memorial Award, Indian Science Congress Association

Publications

Vishwakarma NK, Yadav S, Sardar A, Choudhary M, Chattopadhyay D (2026) CBL1/9-CIPK6 complex negatively regulates Respiratory burst oxidase homolog D in Arabidopsis thaliana. Plant Journal 125, e70700, doi:10.1111/tpj.70700

Singh S, Pal L, Rajput R, Chhatwal H, Singh N, Chattopadhyay D*, Pandey A* (2024) CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum. Planta 260:38┬аhttps://doi.org/10.1007/s00425-024-04470-7┬а(Joint Corresponding author)

Gupta SK, Dwivedi V, Kute NS, Francis P, Parida SK, Chattopadhyay D (2024) Identification of a stable drought-tolerant hig-yielding line for chickpea crop improvement. Plant Molecular Biology Research.┬аhttps://doi.org/10.1007/s11105-024-01471-4

Sharma NK, Yadav S, Gupta SK, Irulappan V, Francis A, Senthil-Kumar M and Chattopadhyay D (2023) MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root.┬аPlant, Cell & Environment. ┬аhttps://onlinelibrary.wiley.com/doi/10.1111/pce.14666

Francis A, Singh NP, Singh M, Sharma P, Gayacharan, Kumar Durgesh, Basu U, Bajaj D, Varshney N, Joshi DC, Semwal DP, Tyagi V, Wankhede D, Bharadwaj R, Singh AK, Parida SK,┬аChattopadhyay D┬а(2023) The ricebean genome provides insight into Vigna genome evolution and facilitates genetic enhancement.┬аPlant Biotechnology Journal┬аhttps://onlinelibrary.wiley.com/doi/10.1111/pbi.14075

Dwivedi V, Pal L, Singh S, Singh NP, Parida SK and┬аChattopadhyay D┬а(2023) The chickpea WIP2 gene underlying a major QTL contributes to lateral root development.┬аJournal of Experimental Botany┬аhttps://doi.org/10.1093/jxb/erad171

Gupta SK, Vishwakarma NK, Malakar P, Vanaspati P, Sharma NK,┬аChattopadhyay D┬а(2023) Development of an Agrobacterium-derived codon-optimized CRISPR/Cas9 system for chickpea genome editing.┬аProtoplasma┬аhttps://doi.ord/10.1007/s00709-023-01856-4

Francis A, Ghosh S, Tyagi K, Prakasham V, Rani M, Singh NP, Pradhan A, Sundaram RM, Priyanka C, Laha GS, Kannan C, Prasad MS,┬аChattopadhyay D*, Jha G* (2023) Evolution of pathogenicity-associated genes in Rhizoctonia solani AG1-IA by genome duplication and transposon-mediated gene function alterations.┬аBMC Biology┬аdoi:┬аhttps://doi.org/10.1186/s12915-023-01526-0┬а(* co-corresponding author)

Saxena S, Pal L, Naik J, Singh Y, Verma PK,┬аChattopadhyay D, Pandey A (2023) The R2R3-MYB-SG7 transcription factor CaMYB39 orchestrates surface phenylpropanoid metabolism and pathogen resistance in chickpea.┬аNew Phytologist┬аdoi:10.1111/nph.18758

Sharma P, Goudar G, Kumar AC, Ananthan R, Subhash K, Chauhan A, Longvah T, Singh M, Bhardwaj R, Parida SK, Singh AK, Gayacharan,┬аChattopadhyay D┬а(2023) Assessment of diversity in anti-nutrient profile, resistant starch, minerals and carbohydrate components in different ricebean (Vigna umbellata) accessions.┬аFood Chemistry┬а405 (Pt A):134835 doi:10.1016/j.foodchem.2022.134835

Pal L, Dwivedi V, Gupta SK, Saxena S, Pandey A,┬аChattopadhyay D┬а(2023) Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat clours.┬аJour. Exp. Botany┬а74 (1):130-148

Varshney RK, Roorkiwal M,……Francis A,……Chattopadhyay D,……Xu X, Liu X (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes.┬аNature┬а559: 622-627

Sharma NK, Gupta SK, Dwivedi V,┬аChattopadhyay D┬а(2020) Lignin deposition in chickpea root xylem under drought.┬аPlant Signal. Behav.┬а15(6):e1754621

Khandal H, Gupta SK, Dwivedi V, Mandal D, Sharma NK, Vishwakarma NK, Pal L, Choudhary M, Francis A, Malakar P, Singh NP, Sharma K, Sinharoy S, Singh NP, Sharma R,┬аChattopadhyay D. (2020) Root-specific expression of chickpea cytokinin oxidase/dehydrogenase 6 leads to enhanced root growth, drought tolerance and yield without compromising nodulation.┬аPlant Biotechnology Journal┬аdoi:10.1111/pbi.13378

Khandal H, Singh AP,┬аChattopadhyay D┬а(2020) The MicroRNA397b-LACCASE2 module regulates root lignification under water and phosphate deficiency.┬аPlant Physiology┬а182:1387-1403

Meena MK, Vishwakarma NK, Tripathi V,┬аChattopadhyay D┬а(2019) CBL-interacting protein kinase 25 contributes to root meristem development.┬аJour. Exp. Bot.┬а70(1):133-147

Dwivedi V, Parida SK,┬аChattopadhyay┬аD┬а(2017) A repeat length variation in myo-inositol monophosphatase gene contributes to seed size trait in chickpea.┬аScientific Reports.┬а┬а7:4764

Khandal H, Parween S, Roy R, Meena MK,┬аChattopadhyay D. (2017) MicroRNA profiling provides insights into post-transcriptional regulation of gene expression in chickpea root apex under salinity and water deficiency.┬аScientific Reports. 7:4632

Sahu KK,┬аChattopadhyay D┬а(2017) Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping.┬аBMC Genomics┬а18:430

Sardar A, Nandi AK,┬аChattopadhyay D┬а(2017) CBL-interacting protein kinase 6 negatively regulates immune response to Pseudomonas syringae in Arabidopsis.┬аJ. Exp. Bot.┬аdoi:10.1093/jxb/erx170

Gupta S, Nawaz K, Parween S, Roy R, Sahu KK, Pole AK, Khandal H, Srivastava R, Parida SK,┬аChattopadhyay D┬а(2017) Draft genome sequence of┬аCicer reticulatum┬аL., the wild progenitor of chickpea provides a resource for agronomic trait improvement.┬аDNA Res.┬а24(1), 1-10

Verma S, Gazara R, Nizam S, Parween S,┬аChattopadhyay D, Verma PK (2016) Draft genome sequencing and secretome analysis of fungal pathogen Ascochyta rabei provides insight into the necrotrophic effector repertoire.┬аScientific Reports. 6:24638

Jain D, Khandal H, Khurana JP,┬аChattopadhyay D┬а(2016) Pathogenesis related-10 protein CaARP functions as aldo/keto reductase to scavenge cytotoxic aldehydes.┬аPlant Mol. Biol.┬а90: 171-187

Meena MK, Ghawana S, Dwivedi V, Roy A,┬аChattopadhyay D┬а(2015) Expression of chickpea CIPK25 enhances root growth and tolerance to dehydration and salt stress in transgenic tobacco.┬аFront. Plant Sci. 6:683

Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M,┬аChattopadhyay D, Bhatia S (2015) High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.┬аScientific Reports┬а5:13387

Parween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S,┬аChattopadhyay D┬а(2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum┬аL.).┬аScientific Reports┬аDoi: 10.1038/srep12806.

Meena MK, Ghawana S, Sardar A, Dwivedi V, Khandal H, Roy R,┬аChattopadhyay D┬а(2015)┬аInvestigation of genes encoding Calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum┬аL.)┬аPLoS ONE┬а(In Press)

Misra G, Priya P, Bandhiwal N, Bareja N, Jain M, Bhatia S,┬аChattopadhyay D, Tyagi AK and Yadav G (2014) The Chickpea Genomic Web Resource: Visualization and Analysis of the Desi-type Cicer arietinum Nuclear Genome for Comparative Exploration of Legumes.┬аBMC Plant Biology 14:┬а315

Yadav RK and┬аChattopadhyay D┬а(2014) Differential soybean gene expression during early phase of infection with Mungbean yellow mosaic India virus.┬аMol Biol Rep. 41(8):┬а5123 – 5134.

Suresh BV, Roy R, Sahu K, Misra G,┬аChattopadhyay D┬а(2014) Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research.┬аPLoS ONE 9(1):┬аe86387 ┬а┬аDatabase: Click Here

Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Kant C, Sharma P, Yadav G, Bhatia S, Tyagi AK,┬аChattopadhyay D┬а(2013) A draft genome sequence of the pulse crop chickpea (Cicer arietinum┬аL.).┬аPlant Journal.┬аDOI: 10.1111/tpj.12173

Jain D and┬аChattopadhyay D┬а(2013) Promoter of CaZF a chickpea gene that positively regulates growth and stress tolerance is activated by an AP2-family transcription factor CAP2.┬аPLoS ONE┬а8(2): e56737

Pandey G, Misra G, Kumari K, Gupta S, Parida SK,┬аChattopadhyay D┬аand Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L)].┬аDNA Res.┬аDoi:10.1093/dnares/dst002

Gaur R, Azam S, Jeena G, Khan AW, Choudhury S, Jain M, Yadav G, Tyagi AK,┬аChattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum┬аL.).┬аDNA Res.┬а19(5): 357-373

The Tomato Genome Consortium (2012)┬аThe tomato genome sequence provides insights into fleshy fruit evolution.┬аNature┬а485: 635-641

Yadav RK and Chattopadhyay D (2011) Enhanced viral intergenic region specific siRNA accumulation and DNA methylation correlates with resistance against a geminivirus.┬аMol. Plant Microbe Interactions 24:┬а1189-1197.

Jain D and Chattopadhyay D (2010) Analysis of gene expression in response to water deficit of chickpea (Cicer arietinum┬аL.) varieties differing in drought tolerance.┬аBMC Plant Biology 10:┬а24

Sahu PP, Rai NK, Chakraborty S, Singh M, Prasanna HC, Ramesh B, Chattopadhyay D, Prasad M (2010) Tomato cultivar tolerant to Tomato leaf curl New Delhi virus infection induces virus-specific siRNA accumulation and defence associated host gene expression.┬аMolecular Plant Pathology 11(4):┬а531-544

Tripathi V, Parasuraman B, Laxmi A and┬аChattopadhyay D┬а(2009) CIPK6, a CBL-interacting protein kinase is required for development and salt tolerance in plant.┬аPlant Journal 58:778-790

Shukla RK, Raha S, Tripathi V and┬аChattopadhyay D┬а(2006) Expression of CAP2, an AP2-family transcription factor from Chickpea enhances growth and tolerance to dehydration and salt tress in transgenic tobacco.┬аPlant Physiology 142: 113-123.

Boominathan P, Shukla RK, Kumar A, Manna D, Negi D, Verma PK and┬аChattopadhyay D┬а(2004) Long term transcript accumulation during the development of dehydration adaptation in┬аCicer arietinum┬аL.┬аPlant Physiology 135(3):1608-1620.

Jain D, Roy N and┬аChattopadhyay D┬а(2009) CaZF, a plant transcription factor functions independent of Hog1p and Calcineurin in┬аSaccharomyces cerevisiae┬аto provide osmotolerance.┬аPLoS ONE┬а4(4):e5154

Shukla RK, Vripathi V, Jain D, Yadav RK and┬аChattopadhyay D┬а(2009) CAP2 enhances germination of transgenic tobacco seeds at high temperature and promotes heat stress tolerance in yeast.┬аFEBS Journal┬а(doi:10.1111/j.1742-4658.2009.07219.x)

Yadav RK, Shukla RK and┬аChattopadhyay D┬а(2009) Soybean cultivar resistant to Mungbean Yellow Mosaic India Virus infection induces viral RNA degradation earlier than the susceptible cultivar.┬аVirus Research 144: 89-95 (doi:10.1016/j.virusres.2009.04.011).

Tripathi V, Syed N, Laxmi A and┬аChattopadhyay D┬а(2009) Role of CIPK6 in root growth and auxin transport.┬аPlant Signaling and Behavior 4(7):663-665.

Shridhar S,┬аChattopadhyay D┬аand Yadav G (2009) PLecDom: A Program for identification and Analysis of Plant Lectin Domains.┬аNucleic Acid Research Jul 1; 37: W452-8. Epub 2009 May 27

Kaur H, Shukla RK, Yadav G,┬аChattopadhyay D┬аand Majee M (2008) Two divergent genes encoding L-myo-inositol 1-phosphate synthase1 (CaMIPS1) and 2 (CaMIPS2) are differentially expressed in chickpea.┬аPlant Cell Environ 31:1701-1716

Yadav V, Kundu S,┬аChattopadhyay D, Negi P, Wei N, Deng XW and Chattopadhyay S (2002) Light regulated modulation of Z- box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5 in┬аArabidopsis.┬аPlant Journal 31(6): 731-753.

The Tomato Genome Sequencing Consortium (2009) A snapshot of the emerging tomato genome sequence.┬аThe Plant genome 2(1): 78-92

Mueller LA, Tanksley SD,┬аChattopadhyay D┬аand Zamir D. (SOL genome consortium). (2005) The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL).┬аComparative and Functional Genomics 6(3): 153-158.

Nayak S, Balaji J, Upadhyay HD, Hash CT, KaviKishore PB,┬аChattopadhyay D, Rodrigues LM, Blair MW, Baum M, McNally K, This D, Hosington D and Varshney R (2009) Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species.┬аPlant Science 177:┬а460-467.

Chattopadhyay D, Ghosh MK, Mal A, and Harter ML (2001) Inactivation of p21 by E1A Leads to the Induction of Apoptosis in DNA-Damaged Cells.┬аJ. Virol. 5: 9844-9856.

Basak S, Raha T,┬аChattopadhyay D, Majumder A, Shaila MS and Chattopadhyay DJ (2003) Leader RNA Binding Ability of Chandipura Virus P protein is Regulated by its Phosphorylation Status: A Possible Role in Genome Transcription-Replication Switch.┬аVirology 307: 372-385.

Mal A,┬аChattopadhyay D, Ghosh M, Poon RYC, Hunter T and Harter ML (2000) p21 and Retinoblastoma protein control the absence of DNA replication in terminally differentiated muscle cells.┬аJour. of Cell Biology 149(2): 281-292.

Raha T,┬аChattopadhyay D┬аand Chattopadhyay D (2000) N-terminal region of P protein of Chandipura virus is responsible for phosphorylation-mediated homodimerization.┬аProtein Engineering 13(6): 437-444.

Raha T,┬аChattopadhyay D, Chattopadhyay D and Roy S (1999). A phosphorylation induced major structural change in the N-terminal domain of the P protein of Chandipura virus.┬аBiochemistry 38(7): 2110-2116.

Chattopadhyay D, Raha T, Chattopadhyay D (1997) PCR mutagenesis:Treatment of megaprimer with mung bean nuclease improves yield.┬аBioTechniques 22: 1054-1056.

Chattopadhyay D, Raha T, Chattopadhyay D (1997) Single Serine phosphorylation within acidic domain of Chandipura virus P protein regulates the transcription in vitro.┬аVirology 239: 11-19.

Chattopadhyay D┬аand Chattopadhyay D (1994). Cloning of Chandipura virus phosphoprotein encoding gene and its expression in E.coli.┬аCell. Mol. Biol. Res. 40: 693-698

Biswas S, Gupta MK,┬аChattopadhyay D┬аand Mukhopadhyay CK (2007). Insulin induced activation of Hypoxia inducible factor-1 requires generation of reactive oxygen species by NADPH oxidase.┬аAm. J. Physiol: Heart Circ. Physiol. 292: 758-766

Reviews:

Singh N, Giri MK, Chattopadhyay D (2025) Lighting the path: how light signaling regulates stomatal movement and plant immunity. Jour. Exp. Bot. 76(3):769-786

Yadav S and Chattopadhyay D (2023) Lignin: the building block of defense responses to stress in plants. Jr. Plant Growth Regulation doi:https://doi.org/10.1007/s00344-023-10926-z

Sharma A, Prakash Subasty, Chattopadhyay D (2022) Killing two birds with a single stone-genetic manipulation of cytokinin oxidase/dehydrogenase (CKX) genes for enhancing crop productivity and amelioration of drought stress response. Frontiers in Genetics. 13:941595 doi: 10.3389/fgen.2022.941595

Malakar P, Chattopadhyay D (2021) Adaptation of plants to salt stress: the role of the ion transporters. Journal of Plant Biochemistry and Biotechnology. 30: 668-683 https://doi.org/10.1007/s13562-021-00741-6

Meena MK, Sardar A, Chattopadhyay D (2019) Decoding and relay of calcium signals by CBL-CIPK module in plants. Proc. Natl. Acad. Sci. India 85:143-156.

Book Chapter

Jain D and┬аChattopadhyay D┬а(2013) Role of DREB-like proteins in improving stress tolerance to transgenic crops. N.Tuteja and SS Gill (Eds.) Plant acclimation to environmental stress. Springer science+Business media NY, pp- 147-162

Patent

“Chimeric Construct of Mungbean Yellow Mosaic India Virus (MYMIV) and its uses thereof” (2013)- US patent 8435732

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