Biology subjects

Trivedi, P. K.

Publications and source records attributed to Trivedi, P. K..

10 recordsLinked to original sources

bioRxiv2026

A high-quality chromosome-scale reference genome assembly for Asparagus racemosus var. CIM-Shakti (Shatavari), a medicinal plant of Ayurvedic importance

Asparagus racemosus Wild., commonly known as Shatavari, is an important medicinal plant in Ayurveda and is valued for its steroidal saponins, particularly shatavarin compounds, which contribute to its adaptogenic, galactagogue, immunomodulatory, and therapeutic properties. Despite its medicinal and economic importance, genomic resources for this species have remained limited, restricting molecular breeding, pathway discovery, and comparative evolutionary studies within Asparagaceae. Here, we report a high quality chromosome scale reference genome assembly of A. racemosus var. CIM Shakti generated using PacBio HiFi long read sequencing and Omni C chromatin conformation scaffolding. The pseudo haploid assembly spans 817 Mb across 53 scaffolds, with a scaffold N50 of 98.50 Mb, L50 of 5, and a largest scaffold of 113.80 Mb. Ten major chromosome scale pseudomolecules were resolved, corresponding to the haploid chromosome complement of A. racemosus. The assembly showed high gene space completeness, with BUSCO completeness of 99.8% against the Eukaryota dataset and 98.0% against the Embryophyta dataset. BlobToolKit profiling further supported assembly quality, with GC content of approximately 39 to 40% and no major evidence of contamination. EDTA based repeat annotation identified 580.93 Mb of interspersed repetitive elements, accounting for 71.06% of the 817.57 Mb genome assembly. The repeat landscape was dominated by LTR retrotransposons, particularly Gypsy elements, which accounted for 25.01% of the assembly, followed by unclassified LTR elements at 26.58% and Copia elements at 4.84%. Structural and functional annotation identified 29,199 protein coding genes represented by 29,199 transcript models, 138,433 exons, and 125,201 CDS features. The annotation was structurally robust, with an average gene length of 4,605.1 bp, 4.74 exons per transcript, and 97.80% of transcripts containing multiple exons. The CIM Shakti reference genome provides a foundational genomic resource for investigating steroidal saponin biosynthesis, sex chromosome evolution, repeat driven genome expansion, and comparative genomics in Asparagaceae. This assembly will support future studies on medicinal trait improvement, conservation genomics, and genomics assisted breeding of climate resilient Shatavari cultivars.

bioinformatics↗

bioRxiv2026

First haplotype-resolved genome assembly of citral-rich lemongrass Cymbopogon flexuosus var. Krishna

Cymbopogon flexuosus var. Krishna (lemongrass) is an aromatic grass valued for its high citral content, which is widely used in the fragrance, flavor, and pharmaceutical industries. C. flexuosus, a member of the Poaceae family, is a predominantly outcrossing species characterized by a highly heterozygous genome. Despite its economic importance and widespread cultivation, a high-quality reference genome has been lacking. Here, we report the first chromosome-scale genome assembly of lemongrass, generated using PacBio HiFi long-read sequencing combined with Omni-C chromatin conformation capture data. The resulting pseudo-haploid assembly spans approximately 798 Mb, organized into 10 chromosomes, and exhibits a scaffold N50 of 64.35 Mb. The assembly demonstrates high completeness, with 99.8% BUSCO recovery, and comprises [~]37,254 predicted protein-coding genes. In addition, we generated haplotype-resolved assemblies that capture the allelic diversity of this heterozygous genome. The haplotypes have sizes of [~]750 Mb and [~]726 Mb, representing 95-98% of the pseudo-haploid genome, and together they provide phase-resolved information for gene families and biosynthetic pathways. These high-quality assemblies establish a foundational genomic resource for advancing molecular breeding, comparative genomics, and metabolic engineering of lemongrass and related aromatic grasses.

genomics↗

bioRxiv2024

ELONGATED HYPOCOTYL 5 regulates light-mediated squalene biosynthesis and development in Arabidopsis thaliana

Terpenoids are diverse groups of metabolite families that are crucial for plant development and required in cosmetics and pharmacological industries. Various development processes and environmental factors, including light, have been shown to affect terpenoid biosynthesis. However, regulatory factors involved in such regulation have not been explored much. Squalene synthases (SQSs), key enzymes in the terpenoid pathway, are pivotal for sterol and triterpene biosynthesis across various organisms. In this study, we report that AtSQS1 expression and squalene content are higher in the dark, and light through ELONGATED HYPOCOTYL 5 (HY5) negatively regulates the AtSQS1 gene and squalene biosynthesis in Arabidopsis thaliana. Our study shows that the AtSQS1 gene is unaffected in the hy5-215 mutant during light and dark conditions, but it is down-regulated in WT and HY5OX lines. The histochemical GUS assays and GFP expression patterns indicate a negative regulation of squalene biosynthesis by AtHY5. Yeast one-hybrid assays, EMSA, and ChIP experiments have confirmed the physical binding of AtHY5 on light-responsive elements of the AtSQS1 promoter. We have validated our results by developing AtSQS1 promoter: reporter transgenic lines in WT, hy5-215 mutants, and HY5OX backgrounds and conducted expression, metabolite quantification, and histochemical GUS assays. The metabolites quantification of squalene and phytosterols through GC-MS further confirms that AtHY5 negatively regulates the squalene biosynthesis in a light-dependent manner in Arabidopsis.

plant biology↗

bioRxiv2024

MYB transcription factor, NtMYB308, regulates anthocyanin and lignin content, and fungal tolerance in tobacco

Anthocyanins are secondary metabolites synthesized through the phenylpropanoid pathway. They attract pollinators, possess antioxidant properties that scavenge free radicals during environmental stress, and provide protection against various stress conditions. Lignin, another secondary metabolite, plays crucial roles in providing mechanical support, facilitating water and solute transport, and protecting against pathogens. MYB transcription factors, particularly R2R3 MYBs, are key regulators of secondary metabolism, especially within the phenylpropanoid pathway. These factors act as both activators and repressors. The N-terminal region of R2R3-MYB repressors contains a conserved bHLH-binding domain, while the C-terminal domain is divergent and includes an EAR repressor domain. R2R3-MYB proteins notably target sequences such as the MYB-response element and AC elements. In this study, we identified and characterized the Nicotiana MYB transcription factor, NtMYB308, and explored its regulatory function in anthocyanin and lignin biosynthesis in tobacco. Our Virus Induced Gene Silencing (VIGS) and Protein-DNA interaction studies suggest that NtMYB308 is a negative regulator of anthocyanin and lignin biosynthesis by binding to the promoters of genes involved in these pathways. To validate our findings, we developed CRISPR/Cas9-based knockout mutant plants of tobacco, NtMYB308CR, which showed up-regulation of anthocyanin and lignin biosynthesis. Conversely, NtMYB308 overexpression (NtMYB308OX) plants exhibited the opposite effect. Enhanced anthocyanin and lignin levels in NtMYB308CR plants provided tolerance against the fungus Alternaria solani, while NtMYB308OX lines were susceptible. This study advances our understanding of the regulatory mechanisms governing anthocyanin and lignin biosynthesis and their role in biotic stress in tobacco. One Sentence SummaryA R2R3 MYB transcription factor, NtMYB308, negatively regulates anthocyanin and lignin content, and fungal tolerance in tobacco.

plant biology↗

bioRxiv2024

Steroidal glycoalkaloid biosynthesis and fungal tolerance are regulated by ELONGATED HYPOCOTYL 5, SlHY5, in tomato

Tomato (Solanum lycopersicum L.) is one of the highest consumable fruit crops, rich in nutrients, and has been an important target for enhancing the accumulation of various metabolites. Tomato also contains cholesterol-derived molecules, steroidal glycoalkaloids (SGAs), which contribute to pathogen defence but are toxic to humans and considered anti-nutritional compounds. Previous studies suggest the role of various transcription factors in SGA biosynthesis; however, the role of light and associated regulatory factors has not been studied in tomatoes. Here, we demonstrated that SGA biosynthesis is regulated by light through the ELONGATED HYPOCOTYL 5 homolog, SlHY5, by binding to light-responsive G-boxes present in the promoters of the structural and regulatory genes. Our analysis suggests that SlHY5 could complement the Arabidopsis thaliana and Nicotiana tabacum, hy5 mutants at molecular, morphological, and biochemical levels. We report the development of CRISPR/Cas9-based knockout mutant plants of tomato, slhy5CR, and show down-regulation of the SGA and phenylpropanoid pathway genes leading to a significant reduction in SGA (-tomatine and dehydrotomatine) and flavonol contents, whereas SlHY5 overexpression (SlHY5OX) plants show opposite effect. An enhanced SGA and flavonol levels in SlHY5OX lines provided tolerance against Alternaria solani fungus, while SlHY5CR was susceptible to the pathogen. This study advances our understanding of the HY5-dependent light-regulated biosynthesis of SGAs and flavonoids and their role in biotic stress in tomatoes. One Sentence SummaryLight-associated transcription factor, ELONGATED HYPOCOTYL 5, regulates biosynthesis of anti-nutrient molecules, steroidal glycoalkaloids, and fungal tolerance in tomato

molecular biology↗

bioRxiv2024

miR858a-encoded peptide, miPEP858a, interacts with miR858a promoter and requires C-terminus for the associated functions

MicroRNAs (miRNAs) play a crucial role in regulating gene expression as processed products of primary miRNAs (pri-miRNAs). Recent studies suggest that certain pri-miRNAs encode miRNA-encoded Peptides (miPEPs), influencing miRNA function. Despite this emerging insight, molecular mechanisms and the specific domain or essential amino acid residues required for the functionality of these miPEPs have yet to be explored. Here, we report that the pri-miR858a-encoded peptide, miPEP858a, interacts with the promoter region of the MIR858 gene and its C-terminal region consisting of 14 amino acid residues is indispensable for its functionality. DNA-protein interaction through Yeast-one-hybrid and ChIP-qPCR analysis revealed that miPEP858 interacts with specific region in the MIR858 promoter. An exogenous application of a truncated peptide, the C-terminal region, resulted in enhanced expression and related phenotypic effects, similar to complete miPEP858. Furthermore, C-terminal region of miPEP858a complemented mutant plants lacking miPEP858, highlighting their regulatory role in miR858a expression and associated target genes, impacting flavonoid biosynthesis and plant development. These findings suggest that full-length miPEP858a may not be essential for its functionality. Identifying functional domains of other peptides offers promise, potentially reducing synthesis costs for application in crop plants and avoiding laborious biotechnological approaches to enhance agronomic traits.

plant biology↗

bioRxiv2022

miRNA408 and its encoded peptide, miPEP408, regulate arsenic stress response in Arabidopsis

MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various stresses. Based on the recent findings, it has been shown that some of the pri-miRNAs encode small regulatory peptides, microRNA-encoded peptides (miPEP). miPEPs are reported to regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides in different stresses has not been explored yet. Here, we reported that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. Plants overexpressing miR408 showed severe sensitivity under low sulphur (LS), Arsenite As(III) and LS+As(III) stress, while miR408 mutant developed through the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulphur reduction pathway and affect sulphate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 or miPEP408 overexpression led to sensitivity in plants under LS, As(III) and combined LS+As(III) stress compared to control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses. One-sentence summarymiR408 and peptide encoded by miR408, miPEP408, regulate arsenic stress and low sulphur responses in Arabidopsis.

plant biology↗

bioRxiv2022

Tobacco HY5, NtHY5, positively regulates flavonoid biosynthesis and enhances salt stress tolerance

Tobacco remains one of the most commercially important crops due to the parasympathomimetic alkaloid nicotine used in cigarettes. Most genes involved in nicotine biosynthesis are expressed in root tissues; however, their light-dependent regulation has not been studied. We identified the ELONGATED HYPOCOTYL 5 homolog, NtHY5, from Nicotiana tabacum and demonstrated its role in nicotine biosynthesis. We report the development of CRISPR/Cas9-based mutant plants, NtHY5CR, and show down-regulation of the nicotine biosynthetic pathway, whereas NtHY5 overexpression (NtHY5OX) plants show the opposite effect. Grafting experiments using wild type, NtHY5CR, and NtHY5OX indicated that NtHY5 moves from shoot-to-root to regulate nicotine biosynthesis in the root tissue. We conclude that shoot HY5, directly or through enhancing expression of the HY5 in the root, promotes nicotine biosynthesis. The CRISPR/Cas9-based mutants developed, in this study; with low nicotine accumulation in leaves could help people to overcome their nicotine addiction and the risk of death from tobacco use.

plant biology↗

bioRxiv2021

miPEP858/miR858-MYB3-PSK4 module regulates growth and development in Arabidopsis

Small molecules, peptides and miRNAs, are the crucial regulators of plant growth. Here, we show the importance of cross-talk between miPEP858a/miR858a and Phytosulfokine (PSK4) in regulating plant growth and development in Arabidopsis. Genome-wide expression analysis suggested modulated expression of PSK4 in miR858 mutant and overexpression, miR858OX, plants. The silencing of PSK4 in miR858OX plants compromised the growth, whereas over-expression of PSK4 in miR858 mutant rescued the developmental defects. The exogenous application of synthetic PSK4 further complemented the plant development in mutant plants. Exogenous treatment of synthetic miPEP858a in PSK4 mutant led to clathrin-mediated internalization of the peptide however did not enhance growth as in the case of wild-type plants. We also demonstrate that the MYB3 is an important molecular component participating in miPEP858a/miR858a-PSK4 module. Finally, our work highlights the signalling between miR858/miPEP858-MYB3-PSK4 in modulating the expression of key elements involved in auxin responses leading to the regulation of growth. One-sentence summarySignaling network between small molecules, miPEP858a/miR858a and phytosulfokine, regulates plant growth in Arabidopsis.

plant biology↗

bioRxiv2019

miRNA-encoded peptide, miPEP858, regulates plant growth and development in Arabidopsis

MicroRNAs (miRNAs), small non-coding endogenous RNAs, are processed product of primary miRNAs (pri-miRNAs) and regulate target gene expression. pri-miRNAs have also been reported to encode small peptides, miRNA-Encoded Peptides (miPEPs). Though regulatory role of miPEPs has been speculated, no detailed study has been carried out to elucidate their function through developing knock-out mutants. Here, we report that pri-miR858a of Arabidopsis thaliana encodes a small peptide (miPEP858a) which regulates the expression of pri-miR858a leading to modulation in the expression of target genes involved in the plant growth and development as well as phenylpropanoid pathway. CRISPR-based miPEP858a-edited plants developed phenotypes similar to that of mature miR858-edited plants suggesting crucial role of miPEP858a in mediating miR585a function. miPEP858a-edited and miPEP858a overexpressing lines altered plant development and accumulated modulated levels of flavonoids due to changes in expression of associated genes. Exogenous treatment of synthetic-miPEP858a to the miPEP858a-edited plants complemented phenotypes and the gene function suggesting a significant role of miPEP858a in controlling the miR858 function and plant development.\n\nOne sentence summarySmall peptide, miPEP858a, encoded by primary miRNA for miR858a regulates plant growth, development and flavonoid biosynthesis\n\nThe authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors

plant biology↗