Browsing by Author "Lenka, Sangram K."

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    Genome-wide analysis of the pleiotropic drug resistance (PDR) gene family and putative PDR specific miRNAs: deciphering their functions in development processes and varied stresses in Triticum aestivum L.
    (Springer Nature, 2026-01-13) Kesawat, Mahipal Singh; Kherawat, Bhagwat Singh; Reager, Madan Lal; Lenka, Sangram K.; Chung, Sang-Min; Masika, Fred Bwayo
    Background The pleiotropic drug resistance (PDR) transporter stands out as one of the largest subfamilies within ABC transporters. These transporters play crucial roles in a multitude of biological processes, including detoxification, phytohormone transportation, stomatal movement, the translocation of various secondary metabolites, tolerance to heavy metal and adaptation to the diverse stress conditions. However, the structural and functional characterization of PDR gene family members in wheat has yet to be fully elucidated. Results In this investigation, we identified 66 TaPDR genes in the genome of wheat. The subsequent phylogenetic tree revealed that the genes clustered into four subfamilies. Chromosomal mapping unveiled the dispersal of 66 TaPDR genes across 17 wheat chromosomes. The twenty-two pairs of duplicated gene were identified in the PDR family. Ka/Ks ratio revealed that 22 duplicated TaPDR genes went through purifying selection. It was noted that the TaPDR genes displayed significant diversity in their gene structures. In addition, the presence of numerous cis-regulatory elements in the promoter regions of the TaPDR genes were identified. Differential expression patterns were observed among TaPDR family members across various tissues and in response to multiple stress conditions. Moreover, this investigation explored the miRNAs targeting TaPDR genes and their expression profiles in various tissues. Conclusion Thus, the results of this study establish a strong basis for further investigation of the functions of TaPDR genes across different tissues, developmental stages, phytohormone responses, and diverse stress in wheat.
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    Genome-wide identification and expression analysis of the Small Ubiquitin-like Modifier (SUMO) gene family in Triticum aestivum L.
    (Springer Nature, 2025-12-11) Kesawa, Mahipal Singh; Kherawat, Bhagwat Singh; Reager, Madan Lal; Badu, Meenakshi; Kabi, Mandakini; Mohanty, Ankita; Raju, Kalidindi Krishnam; Lenka, Sangram K.; Alamery, Salman Freeh; Al-ateeq, Talak K.; Masika, Fred Bwayo; Hong, Choo Bong
    Background: Post-translational modification of proteins by SUMO is critical for a wide range of cellular and developmental processes. Although SUMO proteins have been extensively studied in animals and, to some extent, in Arabidopsis, their precise functions in other crop plants are still largely unknown. Results: In this research, we identified 31 TaSUMO genes in genome of wheat. Phylogenetic tree unveiled that genes clustered into thirteen subfamilies. Chromosomal mapping unveiled the dispersal of 31 TaSUMO genes across 11 wheat chromosomes. The eleven pairs of duplicated gene were identified in the SUMO family. Ka/Ks ratio revealed that 8 duplicated TaSUMO genes went through purifying purification. Furthermore, it was noted that TaSUMO genes displayed significant conversation in their gene structure. In addition, analysis of promoters uncovered the presence of numerous cis-regulatory elements in the promoter region of the TaSUMO genes. The differential expression patterns were observed among TaSUMO family members across various tissues and in response to multifaceted stress conditions. Moreover, this investigation explored the miRNAs targeted to TaSUMO genes and expression profile in various tissues. Conclusion: Thus, the results of this study establish a strong basis for further investigation of the functions of TaSUMO genes across different tissues, developmental stages, phytohormone responses, and diverse stress in wheat.
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    Genome-wide survey and expression analysis of peptides containing tyrosine sulfation (PSY) gene family in Cicer arietinum L.
    (Springer Nature, 2026-02-21) Kesawat, Mahipal Singh; Kumar, Vinay; Manohar, Swati; Sohail, Aqib; Rani, Manjusha; Chung, Sang-Min; Kumar, Deepak; Lenka, Sangram K.; Masika, Fred Bwayo
    Background Plant growth and developmental processes are tightly regulated by small secreted peptides, however, the functions and mechanisms of Tyrosine Sulfation-containing Peptides (PSY) remain unclear. In chickpea, knowledge of PSY genes family is limited. Results This study employed comprehensive bioinformatics approaches to identify and characterize seven CaPSY genes in the chickpea genome. The analyses encompass chromosomal localization, evolutionary relationships, gene structure, conserved motif identification, promoter architecture, prediction of PSY-targeting miRNAs, and expression profiling. Chromosomal mapping revealed that CaPSY genes are confined to four specific chromosomes rather than being evenly distributed across the genome. Phylogenetic analysis resolved nine distinct groups, each further subdivided into subgroups. Additionally, CaPSY genes were found to contain one to two introns. Amino acid sequence comparisons demonstrated that each CaPSY gene consistently harbors a PSY domain in its C-terminal end. Promoter analysis of CaPSY genes revealed the presence of multiple hormone-responsive elements, including ABRE, SARE, AuxRE, and MeJARE, as well as stress-related elements such as the drought-responsive MBS, suggesting potential regulatory roles in development and stress adaptation. Further, the expression patterns of CaPSY were evaluated in multiple tissues as well as in response to abiotic stresses. The results indicated differential expression of CaPSY genes among tissues and under multiple abiotic stress conditions. We further detected several miRNAs likely to target CaPSY genes and assessed how they are expressed in different tissues. Conclusion Thus, these findings serve as a crucial resource for basic and applied research, enabling advancements in chickpea productivity and stress tolerance via precise genome editing and innovative breeding methods.
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    Genome-wide survey of peptides containing tyrosine sulfation (PSY) gene family and potential PSY specific miRNA revealed their role in plant development and diverse stress conditions in rice (Oryza sativa L.).
    (Springer Nature, 2025-08-26) Kesawat, Mahipal Singh; Manohar, Swati; Anand, Ankit; Alamery, Salman Freeh; Badu, Meenakshi; Kabi, Mandakini; Mohanty, Ankita; Naik, Islavath Suresh; Kumar, Santosh; Kherawat, Bhagwat Singh; Kumar, Vinay; Lenka, Sangram K.; Verma, Shreya; Shrivastava, Harsha; Kumawat, Giriraj; Masika, Fred Bwayo
    Background Soybean is a fundamental oilseed crop, recognized for its notable protein and oil levels. Tyrosine Sulfation (PSY) genes play an essential role in plant growth, development, and responses to stress. However, the precise functions and mechanisms regulated by PSY are still being explored. Currently, there is insufficient information on the PSY gene family in soybean. Therefore, this study conducted a comprehensive genome-wide survey to detect and PSY family members were categorized in soybean. Results The phylogenetic analysis revealed that PSY family was categorized into nine distinct groups. Further, we precisely mapped the locations of the 12 GmPSY genes across seven soybean chromosomes. Examination of gene duplication revealed six pairs of duplicated genes within the PSY gene family in soybean. A consistent gene structure pattern was observed among GmPSY gene family members. The alignment of GmPSY protein amino acid sequences revealed a conserved PSY domain present in all proteins. Furthermore, RNA-seq data from the Soybean Expression Atlas revealed varying expression patterns of GmPSY genes across different tissues. To validate the expression profiles, qRT-PCR analysis was performed on selected GmPSY genes using root tissues from contrasting soybean accessions. In addition, identified eight out of the 12 GmPSY genes as targets for ten specific miRNAs. Moreover, we constructed a protein-protein interaction network to explore the connections between GmPSY and other soybean proteins. Conclusion Thus, these discoveries lay a robust groundwork for future research aimed at elucidating the specific roles of GmPSY members across different tissues and under various stress conditions in soybean.