Browsing by Author "Mishra, Neelam"

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Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance
(Springer Nature Publishing AG, 2026) Fernandes, Nithya; Unnati, G. Meher; Bhattacharjee, Surjit; Pandey, Ashutosh; Mishra, Neelam
U-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.
Genome-wide identification, functional characterization of protein phosphatase 2A (PP2A) gene family in Cicer arietinum reveals the potential role of CaPP2A-A1 under abiotic stress
(Springer Nature Publishing AG, 2025) Fernandes, Nithya; Bhattacharjee, Surjit; Anusha, D. M.; Pandey, Ashutosh; Mishra, Neelam
Drought and salt stress are among the primary abiotic factors that negatively impact crop productivity. To cope with these adverse conditions, plants have evolved various adaptive mechanisms, often mediated by specific genes that confer tolerance to different stresses. In this study, we performed a genome-wide identification of PP2A genes in Cicer arietinum using Arabidopsis thaliana genome as a reference. This study identified 21 CaPP2A members distributed across seven chromosomes. Phylogenetic analysis grouped these genes into six distinct subfamilies, each characterized by unique intron-exon structures and conserved motifs. Promoter analysis revealed the presence of cis-acting elements associated with hormone regulation and abiotic stress responsiveness. RNA sequencing analysis demonstrated that nine PP2A genes were significantly responsive to drought and salt stress which was corroborated by quantitative PCR. Notably, the CaPP2A-A1 gene was identified as a key stress responsive since it exhibited significant upregulation in a stress tolerant cultivar, whereas it was downregulated in a susceptible cultivar under both drought and salt stress conditions, suggesting its pivotal role in stress adaptation. Overall, these findings enhance our understanding of the PP2A gene family in chickpea providing a foundation for future functional studies to unravel the PP2A-mediated regulatory networks governing stress tolerance in C. arietinum and facilitate the development of improved breeding strategies for stress-resilient cultivars.
Integrated assessment of in vitro regeneration, ISSR-Based genetic fidelity, and antifungal properties in Holmskioldia sanguinea
(Springer Nature Publishing AG, 2026) Gouda, Triveni; Pandey, Ashutosh; Mishra, Neelam
Holmskioldia sanguinea is valued for its ornamental appeal and traditional medicinal uses for treating rheumatism, dysentery, headaches, hypertension, ulcers, and gynecological disorders, but propagation challenges limit wider cultivation and conservation efforts. To overcome the limitations associated with conventional propagation methods, an effective in vitro regeneration protocol was established using nodal explants. Following surface sterilization, explants were cultured on half strength Murashige and Skoog (MS) medium supplemented with varying concentrations of plant growth regulators for shoot bud initiation and multiplication. The best response was observed with 1.0 mg L−1 BA (Benzyladenine) particularly when combined 0.5 mg L−1 2,4-D (2,4- Dichlorophenoxyacetic acid) Shoot formation was evident within 2 to 3 wk, and rooting was successfully achieved in two wk after transferring the explant with initiated shoots on half strength MS medium supplemented with 1.0 mg L−1 IBA (Indolebutyric acid). Acclimatization involved a two-phase hardening process, beginning with a gradual reduction in external nutrients and followed by transfer to sterile peat moss + sand (2:1, v/v) potting mix, resulting in an impressive 98% survival rate of regenerated plantlets within 8 to 10 wk. The genetic fidelity of regenerants was evaluated using ISSR amplification with ten primers, out of which 6 primers yielded consistent and reproducible monomorphic profiles across wild-type and in vitro derived samples, demonstrating the absence of somaclonal variation and confirming genetic fidelity. In addition to micropropagation and ISSR-based genetic fidelity assessment, the antifungal potential of H. sanguinea was also evaluated. The methanolic leaf extract demonstrated the highest antifungal activity, inhibiting mycelial growth of tested fungi by 98%, indicating its strong potential as a natural antifungal agent. This study established a robust and scalable tissue culture regeneration protocol for H. sanguinea, supporting its conservation and offering opportunities for pharmaceutical applications as a source of natural antifungal compounds.
MAPK cascade gene family in Camellia sinensis: In-silico identification, expression profiles and regulatory network analysis
(BioMed Central Ltd, 2020) Chatterjee, Archita; Paul, Abhirup; Unnati, G. Meher; Rajput, Ruchika; Biswas, Trisha; Kar, Tamalika; Basak, Srijita; Mishra, Neelam; Pandey, Ashutosh; Srivastava, Anurag Prakash
Background: Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in tea. Result: In this study, 5 genes of Mitogen Activated Protein Kinase Kinase (MKK) and 16 genes of Mitogen Activated Protein Kinase (MPK) in Camellia sinensis were found through a genome-wide search taking Arabidopsis thaliana as the reference genome. Also, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the results. The plant species taken for comparative study clearly displayed segmental duplication, which was a significant candidate for MAPK cascade expansion. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of MAPK and MAPKK genes from Tea in response to various abiotic factors. In addition, the expression of these genes was analysed in various tissues. Conclusion: This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the MAPK cascade regulatory network in C. sinensis.