piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress Muthuramalingam Karpagavalli, Suganya Sivagurunathan, T. Sayamsmruti Panda, Nagesh Srikakulam, Reety Arora, Lamiya Dohadwala, Basant K. Tiwary, Sudha Rani Sadras, Jayamuruga Pandian Arunachalam, Gopal Pandi, Subbulakshmi Chidambaram Molecular Omics, 2024 piRNAs profiled from human retina/RPE share seed sequence homology with miRNAs and lncRNAs. They play regulatory roles in intracellular transport, circadian rhythm, oxidative stress, and retinal neurodegeneration.
Plant Viruses: An Inquisitive Journey from Old to New World New and Emerging Plant Viruses the Threat to Food Security, 2024
Evidence of microRNAs origination from chloroplast genome and their role in regulating Photosystem II protein N (psbN) mRNA Asha Anand, Shailja Chauhan, Aparna Chodon, Kavitha Velayudha Vimala Kumar, Saravanakumar S., Gopal Pandi Biotechnologia, 2024 The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naVve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus, we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches. The gene sequence for a miRNA, designated as AecpmiRNA1 (A. esculentus chloroplast miRNA), is potentially located in both the genomic DNA, i.e., nuclear and chloroplast genome. In contrast, the gene sequences for the other two miRNAs (AecpmiRNA2 and AecpmiRNA3) are exclusively present in the chloroplast genome. Target prediction revealed many potential mRNAs as targets for AecpmiRNAs. Further analysis using 5′ RACE-PCR determined the AecpmiRNA3 binding and cleavage site at the photosystem II protein N (psbN). These results indicate that AecpmiRNAs are generated from the chloroplast genome, possessing the potential to regulate mRNAs arising from chloroplast gene(s). On the other side, the possibility of nuclear genome-derived mRNA regulation by AecpmiRNAs cannot be ruled out.
Extending Omega 3/6 Fatty Acid Pathway in Arabidopsis thaliana using Microalgal Gene Δ6Des for Stearidonic acid and Dihomo-γ-linolenic acid Production Ram Kumar Muthu, Thiyagarajan Sekar, Parthasarathy Ayothi, Govendan Subhas, Dinesh Babu Kandhalu Sagadevan, Gopal Pandi, Babu Rajendra Prasad Venugopal, Kathiresan Shanmugam South African Journal of Botany, 2022 To enhance the quality and quantity of oils in plant systems, specific candidate genes such as desaturase and elongase that can extend the biosynthetic pathways of very long chain poly unsaturated fatty acids (VLCPUFAs) are essential. In general, plant systems are capable of synthesizing essential fatty acids (EFAs). However, incorporation of a preliminary gene, Δ6Desaturase (Δ6Des), in the fatty acid biosynthetic pathway will elongate the pathway further to produce successive fatty acids. In this study, Δ6Des gene extracted from the marine microalga Isochrysis sp. was used to extend the omega (ω) 3/6 fatty acid biosynthetic pathway in a model plant Arabidopsis thaliana using Agrobacterium-mediated genetic transformation. Hygromycin-resistant plants were (25 mg/L) used for GUS and GFP assays and for molecular confirmation. GUS assay showed an intense blue color in F1 transgenic A. thaliana plant tissues grown in the selection medium, which confirmed the presence of GUS gene in the T-DNA region, whereas non-transformed plant tissues such as leaf or stem did not show any blue color. GFP analysis also showed a green fluorescent color in tissues such as leaf, stem, and floral parts of F1 transgenic A. thaliana plants, which confirmed the presence of T-DNA. PCR and Southern blotting analyses also clearly showed the presence of Δ6Des in the T-DNA region of the F1 transgenic plants. The fatty acid profile of F1 transgenic plants showed the production of new fatty acids such as stearidonic acid (SDA-0.58%) and dihomo-γ-linolenic acid (DGLA-25.34%) that were not observed in non-transformed control plants. All these results showed the synthesis of new fatty acids in the transgenic plant, which proved that PUFA biosynthetic pathway can be extended in oilseed plants if specific genes are introduced through genetic transformation. This is the first study to report the productions of new fatty acids like SDA and DGLA in A. thaliana using Δ6Des gene from marine microalga Isochrysis sp.
High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica Nagesh Srikakulam, Ganapathi Sridevi, Gopal Pandi Frontiers in Genetics, 2022 The Reference Transcriptomic Dataset (RTD) is an accurate and comprehensive collection of transcripts originating from a given organism. It holds the key to precise transcript quantification and downstream analysis of differential expressions and regulations. Currently, transcriptome annotations for most crop plants are far from complete. For example, Oryza sativa indica (O. sativa indica) is reported to have 40,759 transcripts in the Ensembl database without alternative transcript isoforms and alternative splicing (AS) events. To generate a high-quality RTD, we conducted RNA sequencing of rice leaf samples collected at various time points during Rhizoctonia solani infection. The obtained reads were analyzed by adopting the recently developed computational analysis pipeline to assemble the RTD with increased transcript and AS diversity for O. sativa indica (IndicaRTD). After stringent quality filtering, the newly constructed transcriptome annotation was comprised of 122,968 non-redundant transcripts from 53,695 genes. This study identified many novel transcripts compared to Ensembl deposited data that are important for regulating molecular and physiological processes in the plant system. Currently, the assembled IndicaRTD must allow fast quantification of transcript and gene expression with high precision.
An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection Nagesh Srikakulam, Ashirbad Guria, Jeyalakshmi Karanthamalai, Vidya Murugesan, Vignesh Krishnan, Kasthuri Sundaramoorthy, Shakkhar Saha, Rudransh Singh, Thiveyarajan Victorathisayam, Veeraputhiran Rajapriya, Ganapathi Sridevi, Gopal Pandi Frontiers in Genetics, 2022 Sheath blight (ShB) disease, caused by Rhizoctonia solani, is one of the major biotic stress-oriented diseases that adversely affect the rice productivity worldwide. However, the regulatory mechanisms are not understood yet comprehensively. In the current study, we had investigated the potential roles of miRNAs in economically important indica rice variety Pusa Basmati-1 upon R. solani infection by carrying out in-depth, high-throughput small RNA sequencing with a total data size of 435 million paired-end raw reads from rice leaf RNA samples collected at different time points. Detailed data analysis revealed a total of 468 known mature miRNAs and 747 putative novel miRNAs across all the libraries. Target prediction and Gene Ontology functional analysis of these miRNAs were found to be unraveling various cellular, molecular, and biological functions by targeting various plant defense-related genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to validate the miRNAs and their putative target genes. Out of the selected miRNA-specific putative target genes, miR395a binding and its cleavage site on pentatricopeptide were determined by 5’ RACE-PCR. It might be possible that R. solani instigated chloroplast degradation by modulating the pentatricopeptide which led to increased susceptibility to fungal infection.
Cost-Effective Transcriptome-Wide Profiling of Circular RNAs by the Improved-tdMDA-NGS Method Ashirbad Guria, Priyanka Sharma, Nagesh Srikakulam, Akhil Baby, Sankar Natesan, Gopal Pandi Frontiers in Molecular Biosciences, 2022 Covalently closed circular RNAs are neoteric to the eukaryotic family of long non-coding RNAs emerging as a result of 5′–3′ backsplicing from exonic, intronic, or intergenic regions spanning the parental gene. Owing to their unique structure and stability, circular RNAs have a multitude of functional properties such as micro-RNA and protein sponges, direct and indirect modulators of gene expression, protein translation, and many unproven activities apart from being potential biomarkers. However, due to their low abundance, most of the global circular RNA identification is carried out by high-throughput NGS-based approaches requiring millions of sequencing reads. This lag in methodological advancements demands for newer, more refined, and efficient identification techniques. Here, we aim to show an improved version of our previously reported template-dependent multiple displacement amplification (tdMDA)-NGS method by superimposing the ribosomal depletion step and use of H minus reverse transcriptase and RNase H. Implication of tdMDA using highly replicative Phi29 DNA polymerase after minimizing the linear and ribosomal RNA content further intensifies its detection limit toward even the abysmally expressing circular RNA at a low NGS depth, thereby decreasing the cost of identifying a single circular RNA. A >11-fold and >6-fold increase in total circular RNA was identified from the improved-tdMDA-NGS method over the traditional method of circRNA sequencing using DCC and CIRI2 pipelines, respectively, from Oryza sativa subsp. Indica. Furthermore, the reliability of the improved-tdMDA-NGS method was also asserted in HeLa cell lines, showing a significant fold difference in comparison with the existing traditional method of circRNA sequencing. Among the identified circular RNAs, a significant percentage from both rice (∼58%) and HeLa cell lines (∼84%) is found to be matched with the previously reported circular RNAs, suggesting that the improved-tdMDA-NGS method can be adapted to detect and characterize the circular RNAs from different biological systems.
Characterization of the C4 proteins encoded by okra-infecting geminiviruses in India A Chodon, L Medina-Puche, H Wei, G Pandi, R Lozano-Duran bioRxiv, 2026.02. 03.703481 , 2026 2026
Bhendi yellow vein mosaic virus infection alters Extrachromosomal circular DNA profiles and may contribute to the current understanding of begomoviral genome dynamics and … S Malaiyarasan, N Selvakumar, J Karanthamalai, A Guria, A Chodon, ... Physiological and Molecular Plant Pathology 139, 102794 , 2025 2025
Bhendi yellow vein mosaic virus C4 circumvents the RNA silencing pathway by interacting with SAM synthetase and cystathionine beta synthase J Karanthamalai, N Srikakulam, KSD Babu, A Anand, S Mohite, S Kumar, ... Physiological and Molecular Plant Pathology 136, 102549 , 2025 2025 Citations: 6
Plant Viruses: An Inquisitive Journey from Old to New World S Chauhan, A Chodon, P Lekshmipriya, G Pandi, J Tennyson New and Emerging Plant Viruses, 313-348 , 2024 2024
piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress M Karpagavalli, S Sivagurunathan, TS Panda, N Srikakulam, R Arora, ... Molecular Omics 20 (4), 248-264 , 2024 2024 Citations: 7
Functional investigation of the role of BYVMV (begomovirus) proteins in epigenetic modulation. J Karanthamalai, N Srikakulam, G Pandi MDPI , 2024 2024
Evidence of microRNAs origination from chloroplast genome and their role in regulating Photosystem II protein N (psbN) mRNA A Anand, S Chauhan, A Chodon, KVV Kumar, S Saravanakumar, G Pandi Biotechnologia 105 (1), 19 , 2024 2024 Citations: 1
P-GeT Assay: An Innovative Frontier in CircRNA Enrichment P Sharma, A Guria, G Pandi 2024
Extending omega 3/6 fatty acid pathway in Arabidopsis thaliana using microalgal gene Δ6Des for stearidonic acid and dihomo-γ-linolenic acid production RK Muthu, T Sekar, P Ayothi, G Subhas, DBK Sagadevan, G Pandi, ... South African Journal of Botany 151, 178-186 , 2022 2022 Citations: 4
High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica N Srikakulam, G Sridevi, G Pandi Frontiers in Genetics 13, 995072 , 2022 2022 Citations: 2
An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection N Srikakulam, A Guria, J Karanthamalai, V Murugesan, V Krishnan, ... Frontiers in Genetics 13, 869465 , 2022 2022 Citations: 8
Cost-effective transcriptome-wide profiling of circular RNAs by the improved-tdMDA-NGS method A Guria, P Sharma, N Srikakulam, A Baby, S Natesan, G Pandi Frontiers in Molecular Biosciences 9, 886366 , 2022 2022 Citations: 3
The begomovirus–host interplay in viral replication and movement A Chodon, J Karanthamalai, G Pandi, J Tennyson Geminivirus: Detection, diagnosis and management, 397-419 , 2022 2022 Citations: 4
Identification of Circular RNAs by Multiple Displacement Amplification and Their Involvement in Plant Development A Guria, P Sharma, S Natesan, G Pandi Plant Circular RNAs: Methods and Protocols, 69-91 , 2021 2021 Citations: 2
Generation of transgenic rice expressing circRNA and its functional characterization P Sharma, A Guria, S Natesan, G Pandi Plant Circular RNAs: Methods and Protocols, 35-68 , 2021 2021 Citations: 3
Noncoding RNA: an insight into chloroplast and mitochondrial gene expressions A Anand, G Pandi Life 11 (1), 49 , 2021 2021 Citations: 29
DNA N 6 -Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code J Karanthamalai, A Chodon, S Chauhan, G Pandi Plants 9 (2), 247 , 2020 2020 Citations: 30
Circular RNAs—the road less traveled A Guria, P Sharma, S Natesan, G Pandi Frontiers in molecular biosciences 6, 146 , 2020 2020 Citations: 88
Commercial Applications of Transgenic Crops in Virus Management A Guria, G Pandi Advances in Plant Transgenics: Methods and Applications, 213-238 , 2019 2019 Citations: 1
The first complete genomic sequence of cardamom mosaic virus, a member of the genus Macluravirus (family Potyviridae ) S. Elangovan et al. S Elangovan, N Srikakulam, G Pandi, T Jacob, U Ramakrishnan, ... Archives of Virology 164 (6), 1723-1726 , 2019 2019 Citations: 10
MOST CITED SCHOLAR PUBLICATIONS
MIR-451 and Imatinib mesylate inhibit tumor growth of Glioblastoma stem cells H Gal, G Pandi, AA Kanner, Z Ram, G Lithwick-Yanai, N Amariglio, ... Biochemical and biophysical research communications 376 (1), 86-90 , 2008 2008 Citations: 321
MicroRNA miR-324-3p induces promoter-mediated expression of RelA gene A Dharap, C Pokrzywa, S Murali, G Pandi, R Vemuganti PLoS one 8 (11), e79467 , 2013 2013 Citations: 220
Circular RNA expression profiles alter significantly in mouse brain after transient focal ischemia SL Mehta, G Pandi, R Vemuganti Stroke 48 (9), 2541-2548 , 2017 2017 Citations: 171
Differential roles of C4 and βC1 in mediating suppression of post-transcriptional gene silencing: evidence for transactivation by the C2 of Bhendi yellow vein mosaic virus, a … P Gopal, PP Kumar, B Sinilal, J Jose, AK Yadunandam, R Usha Virus research 123 (1), 9-18 , 2007 2007 Citations: 166
MicroRNA miR-29c Down-Regulation Leading to De-Repression of Its Target DNA Methyltransferase 3a Promotes Ischemic Brain Damage G Pandi, VP Nakka, A Dharap, A Roopra, R Vemuganti PLOS ONE 8 (3), e58039 , 2013 2013 Citations: 125
Circular RNAs—the road less traveled A Guria, P Sharma, S Natesan, G Pandi Frontiers in molecular biosciences 6, 146 , 2020 2020 Citations: 88
Abundant and altered expression of PIWI-interacting RNAs during cardiac hypertrophy KS Rajan, G Velmurugan, P Gopal, T Ramprasath, DDV Babu, S Krithika, ... Heart, Lung and Circulation 25 (10), 1013-1020 , 2016 2016 Citations: 79
Inhibition of miR-141-3p ameliorates the negative effects of poststroke social isolation in aged mice R Verma, RM Ritzel, NM Harris, J Lee, TH Kim, G Pandi, R Vemuganti, ... Stroke 49 (7), 1701-1707 , 2018 2018 Citations: 56
miRNA and piRNA mediated Akt pathway in heart: antisense expands to survive KS Rajan, G Velmurugan, G Pandi, S Ramasamy The international journal of biochemistry & cell biology 55, 153-156 , 2014 2014 Citations: 56
First report of an alphasatellite associated with Okra enation leaf curl virus SA Chandran, RM Packialakshmi, K Subhalakshmi, C Prakash, ... Virus Genes 46 (3), 585-587 , 2013 2013 Citations: 45
Egr-1 mediated cardiac miR-99 family expression diverges physiological hypertrophy from pathological hypertrophy S Ramasamy, G Velmurugan, B Rekha, S Anusha, KS Rajan, ... Experimental cell research 365 (1), 46-56 , 2018 2018 Citations: 35
DNA N 6 -Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code J Karanthamalai, A Chodon, S Chauhan, G Pandi Plants 9 (2), 247 , 2020 2020 Citations: 30
Noncoding RNA: an insight into chloroplast and mitochondrial gene expressions A Anand, G Pandi Life 11 (1), 49 , 2021 2021 Citations: 29
Transcriptomic and proteomic analysis of yellow mosaic diseased soybean BK Pavan Kumar, S Kanakala, VG Malathi, P Gopal, R Usha Journal of plant biochemistry and biotechnology 26 (2), 224-234 , 2017 2017 Citations: 25
Circular RNA profiling by illumina sequencing via template‐dependent multiple displacement amplification A Guria, K Velayudha Vimala Kumar, N Srikakulam, A Krishnamma, ... BioMed Research International 2019 (1), 2756516 , 2019 2019 Citations: 19
Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, Abelmoschus esculentus K Velayudha Vimala Kumar, N Srikakulam, P Padmanabhan, G Pandi Non-coding RNA 3 (2), 19 , 2017 2017 Citations: 16
Comprehensive Leaf Transcriptome of a Non-model Plant, Abelmoschus esculentus for the Functional Genomics Studies CJPG Padmanabhan Priyavathi, Srikakulam Nagesh, Velayudha Vimala Kumar Kavitha Journal of Genetics and Genome Research 5, doi.org/10.23937/2378-3648/1410036 , 2018 2018 Citations: 13