Browsing by Author "Kumar, Shailesh"

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Absence of correlation between chimeric RNA and aging
(MDPI AG, 2017) Huang, Reyna; Kumar, Shailesh; Li, Hui
Chimeric RNAs have been recognized as a phenomenon not unique to cancer cells. They also exist in normal physiology. Aging is often characterized by deregulation of molecular and cellular mechanisms, including loss of heterochromatin, increased transcriptional noise, less tight control on alternative splicing, and more stress-induced changes. It is thus assumed that chimeric RNAs are more abundant in older people. In this study, we conducted a preliminary investigation to identify any chimeric RNAs with age-based trends in their expression levels in blood samples. A chimeric RNA candidate list generated by bioinformatic analysis indicated the possibility of both negative and positive trends in the expression of chimeric RNAs. Out of this candidate list, five novel chimeric RNAs were successfully amplified in multiple blood samples and then sequenced. Although primary smaller sample sizes displayed some weak trends with respect to age, analysis of quantitative PCR data from larger sample sizes showed essentially no relationship between expression levels and age. Altogether, these results indicate that, contradictory to the common assumption, chimeric RNAs as a group are not all higher in older individuals and that placing chimeric RNAs in the context of aging will be a much more complex task than initially anticipated.
AlnC: An extensive database of long non-coding RNAs in angiosperms
(PLOS, 2021) Singh, Ajeet; Vivek, A. T.; Kumar, Shailesh
Long non-coding RNAs (lncRNAs) are defined as transcripts of greater than 200 nucleotides that play a crucial role in various cellular processes such as the development, differentiation and gene regulation across all eukaryotes, including plant cells. Since the last decade, there has been a significant rise in our understanding of lncRNA molecular functions in plants, resulting in an exponential increase in lncRNA transcripts, while these went unannounced from the major Angiosperm plant species despite the availability of large-scale high throughput sequencing data in public repositories. We, therefore, developed a user-friendly, openaccess web interface, AlnC (Angiosperm lncRNA Catalogue) for the exploration of lncRNAs in diverse Angiosperm plant species using recent 1000 plant (1KP) trancriptomes data. The current version of AlnC offers 10,855,598 annotated lncRNA transcripts across 682 Angiosperm plant species encompassing 809 tissues. To improve the user interface, we added features for browsing, searching, and downloading lncRNA data, interactive graphs, and an online BLAST service. Additionally, each lncRNA record is annotated with possible small open reading frames (sORFs) to facilitate the study of peptides encoded within lncRNAs. With this user-friendly interface, we anticipate that AlnC will provide a rich source of lncRNAs for small-and large-scale studies in a variety of flowering plants, as well as aid in the improvement of key characteristics in relevance to their economic importance. Database URL: http://www.nipgr.ac.in/AlnC
ANNInter: A platform to explore ncRNA-ncRNA interactome of Arabidopsis thaliana
(Elsevier B.V., 2025) Vivek, AT; Sahu, Namrata; Kalakoti, Garima; Kumar, Shailesh
Eukaryotic transcriptomes are remarkably complex, encompassing not only protein-coding RNAs but also an expanding repertoire of noncoding RNAs (ncRNAs). In plants, ncRNA-ncRNA interactions (NNIs) have emerged as pivotal regulators of gene expression, orchestrating development and adaptive responses to stress. Despite their critical roles, the functional significance of NNIs remains poorly understood, largely due to a lack of comprehensive resources. Here, we present ANNInter, a comprehensive platform that integrates computational predictions with experimental datasets to systematically identify and analyze NNIs. The current version catalogs over 90,000 interactions spanning eight categories of sRNA-to-longer ncRNAs, each extensively annotated with interaction types, identification methods, and functional descriptions. The integrated schema and advanced visualization framework in ANNInter enable users to explore intricate interaction networks, providing system-wide insights into ncRNA-mediated regulation. These interaction data provide unparalleled opportunities to uncover the regulatory roles of NNIs in key biological processes such as growth regulation, stress adaptation, and cellular signaling. By providing an extensive, curated repository of computational and degradome-based interaction data, ANNInter will provide a platform to the study of ncRNA biology, elucidating the complex mechanisms of NNIs and supporting the concept of competing endogenous RNAs (ceRNAs) in gene regulation. The platform is freely accessible at https://www.nipgr.ac.in/ANNInter/.
AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes
(Elsevier B.V., 2026) Shukla, Jagriti; Mukherjee, Kanka; Sahu, Namrata; Kumar, Shailesh
The rapid expansion of publicly available genome assemblies has made genome annotation an increasingly challenging task, particularly for large-scale analyses across prokaryotic and eukaryotic organisms. While several tools exist for assembly evaluation and annotation, their use often involves fragmented workflows that require extensive manual coordination. To overcome this limitation, we introduce AquaaG, an automated and reproducible genome annotation pipeline. AquaaG integrates genome assembly retrieval from NCBI, assembly quality assessment using QUAST, organism-specific annotation using Prokka for prokaryotes and BRAKER3 for eukaryotes, gene-space completeness evaluation using BUSCO, and functional annotation using EggNOG-mapper. The pipeline is configured through simple YAML files and supports species-level, kingdom-level, and custom assembly-based analyses with optional submitter-based filtering. AquaaG therefore provides a practical and reproducible framework for high-throughput genome annotation and assessment.
AraNSdb: a dedicated database of stress-responsive non-coding RNAs in Arabidopsis thaliana
(Springer Nature Publishing AG, 2026) Vivek, A.T.; Bhatia, Manika; Sahu, Namrata; Kalakoti, Garima; Kaushik, Love; Mukherjee, Kanka; Kumar, Shailesh
Plants, as sessile organisms, are constantly exposed to biotic and abiotic stresses, making their ability to respond crucial for survival. Non-coding RNAs (ncRNAs) have emerged as key regulators in these stress responses, with several studies identifying numerous stress-responsive ncRNAs (SRNs). However, a comprehensive collection of SRNs derived from sequencing data in Arabidopsis thaliana has been lacking. To address this, we utilized high-throughput experimental data and mined published studies to construct AraNSdb (Arabidopsis ncRNA Stress Database), a systematic resource for storing and querying SRNs. AraNSdb documents over 1,000 expression profiles from diverse stress datasets, encompassing 6,616 SRNs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The database features an intuitive web interface for exploring SRNs associated with specific stress types and provides detailed ncRNA annotations to support functional and regulatory studies. AraNSdb offers a valuable platform for advancing our understanding of ncRNA-mediated stress responses and is freely accessible at http://www.nipgr.ac.in/AraNSdb.
AtFusionDB: A comprehensive database of fusion transcripts in model plant Arabidopsis thaliana
(Springer Nature Publishing AG, 2026) Shree, Tanu; Kumar, Shailesh
Fusion transcripts are chimeric RNAs, produced by the joining of two different RNAs at the RNA level or as a product of gene fusion at the DNA level. In this era of high-throughput sequencing technologies, it is easy to identify novel molecules like fusion transcripts in different systems. That's because, initially, supposed to be the well-known cancer biomarkers, fusion transcripts are also validated in normal human physiology. In Planta, discrete reports are available, indicating the presence of fusion transcripts but no dedicated web resource is available for the plant-specific fusion transcripts. This chapter describes the first plant-specific database of fusion transcripts, i.e., AtFusionDB ( http://www.nipgr.res.in/AtFusionDB ), which contains the information on fusion transcripts identified in the model plant Arabidopsis thaliana. This database can be exploited to get significant information about gene/transcript fusion in plants.
AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana
(Oxford University Press, 2019) Singh, Ajeet; Zahra, Shafaque; Das, Durdam; Kumar, Shailesh
Fusion transcripts are chimeric RNAs generated as a result of fusion either at DNA or RNA level. These novel transcripts have been extensively studied in the case of human cancers but still remain underexamined in plants. In this study, we introduce the first plant-specific database of fusion transcripts named AtFusionDB (http://www. nipgr.res.in/AtFusionDB). This is a comprehensive database that contains the detailed information about fusion transcripts identified in model plant Arabidopsis thaliana. A total of 82 969 fusion transcript entries generated from 17 181 different genes of A. thaliana are available in this database. Apart from the basic information consisting of the Ensembl gene names, official gene name, tissue type, EricScore, fusion type, AtFusionDB ID and sample ID (e.g. Sequence Read Archive ID), additional information like UniProt, gene coordinates (together with the function of parental genes), junction sequence, expression level of both parent genes and fusion transcript may be of high utility to the user. Two different types of search modules viz. ‘Simple Search’ and ‘Advanced Search’ in addition to the ‘Browse’ option with data download facility are provided in this database. Three different modules for mapping and alignment of the query sequences viz. BLASTN, SW Align and Mapping are incorporated in AtFusionDB. This database is a head start for exploring the complex and unexplored domain of gene/transcript fusion in plants. Database URL: http://www.nipgr.res.in/AtFusionDB
athisomiRDB: A comprehensive database of Arabidopsis isomiRs
(Oxford University Press, 2024) Vivek, A.T.; Arya, Ajay; Swain, Supriya P.; Kumar, Shailesh
Several pieces of evidence challenge the traditional view of miRNAs as static molecules, revealing dynamic isomiRs originating from each miRNA precursor arm. In plants, isomiRs, which result from imprecise cleavage during pre-miRNA processing and post-transcriptional alterations, serve as crucial regulators of target microRNAs (miRNAs). Despite numerous studies on Arabidopsis miRNAs, the systematic identification and annotation of isomiRs across various tissues and conditions remain limited. Due to the lack of systematically collected isomiR information, we introduce the athisomiRDB database, which houses 20 764 isomiRs from Arabidopsis small RNA-sequencing (sRNA-seq) libraries. It comprises >2700 diverse samples and allows exploration at the sample, miRNA, or isomiR levels, offering insights into the presence or absence of isomiRs. The athisomiRDB includes exclusive and ambiguous isomiRs, each with features such as transcriptional origin, variant-containing isomiRs, and identifiers for frequent single-nucleotide polymorphisms from the 1001 Genomes Project. It also provides 3ʹ nontemplated post-transcriptional additions, isomiR–target interactions, and trait associations for each isomiR. We anticipate that athisomiRDB will play a pivotal role in unraveling the regulatory nature of the Arabidopsis miRNAome and enhancing sRNA research by leveraging isomiR profiles from extensive sRNA-seq datasets. Database URL: https://www.nipgr.ac.in/athisomiRDB
Bioinformatics tools for epitope prediction
(Springer Nature Publishing AG, 2020) Jaiswal, Mohini; Zahra, Shafaque; Kumar, Shailesh
Immunological protection is conferred by immune cells, i.e., B and T cells, which can efficiently develop pathogen-specific memory and thus involved in adaptive immunity. More specifically, these immune cells can recognize a specific portion of their respective antigens termed as epitopes which possess their own significant values. There is a noble reason to identify the antigenic region of an antigen as it is having a great empirical cause, which includes exploration of disease etiology, the advancement of diagnosis assays, immune monitoring, and to design epitope-based vaccines. It requires detection and prediction of epitopes which is a considerable concern in the preparation of a peptide-based vaccine that is the centralized issue of immunoinformatics. Experimental screening is involved for large arrays of probable epitope candidates; thereby it is pricey and tedious. There is a requirement of more-advanced immunoinformatics tools as a prodigious amount of information has accumulated because of the onset of next-generation sequencing approaches for collection, analysis, and interpretation of data. Further, development of in silico epitope prediction methods has substantially reduced the difficulties related to epitope mapping by shortening potential epitope candidates list for experimental testing. These software tools have diverse applications in diagnosis of infectious diseases and allergies, understanding immune system function, vaccine designing, and prognosis of cancer. This chapter presents an outlook on how these tools are capable to predict epitopes of various antigens.
Breaking and making genes: the genesis of novel traits in plants
(John Wiley & Sons, 2026) Hamid, Fiza; Arora, Simran; Kumar, Shailesh
Understanding the mechanisms by which plants adapt, evolve, and acquire new traits is crucial for enhancing agricultural resilience and productivity in the face of global challenges. Among the various mechanisms that drive new gene evolution, gene fusion has emerged as a significant yet relatively understudied contributor. It can arise through chromosomal rearrangements or RNA processing mechanisms, merging segments from different genes to produce novel fusion transcripts. In plants, these fusion events have been associated with key biological functions, including the regulation of specialized metabolism, stress responses, and developmental changes. While fusion genes have been extensively studied in humans, mainly due to their oncogenic potential, their prevalence and functional relevance in plants remain relatively underexplored. This review offers a detailed overview of the molecular mechanisms underlying gene fusion formation, highlighting their participation in gene evolution, functional diversification, and plant adaptation. In addition, we discuss current methodologies for detecting and validating fusion events, including high-throughput sequencing technologies and emerging single-cell sequencing platforms, and outline promising directions for future research aimed at elucidating their biological significance. Collectively, these insights emphasize the expanding importance of gene fusions in plant biology and underscore the need for further investigation into their regulatory and evolutionary roles.
BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development
(Springer Nature Publishing AG, 2022) Chitkara, Pragya; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
BURP domain-containing proteins are a plant-specific protein family which play an important role in plant metabolism and development. These proteins have also been involved in various abiotic and biotic stress responses. In this study, genome-wide identification and characterization of BURP domain protein encoding gene family is performed in four important legumes, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Vigna radiata. BURP genes were distributed randomly across chromosomes in all four legume plants. The phylogenetic analysis classified all BURP proteins into five major subfamilies, namely, USP-like, RD22-like, BNM2-like, PG1β-like, and BURPV. Our findings revealed that BURP gene family descended from common ancestors with segmental gene duplication events playing a critical role in their evolution and expansion in legumes. The intron–exon and conserved protein motifs analysis revealed that BURP genes are structurally conserved in legumes. The promoter analysis revealed the presence of hormone, and stress-responsive cis-regulatory elements in BURP promoters, implying that BURP functions in both hormone and abiotic stress signaling. Global expression analysis revealed that several BURP genes in all four legumes express differentially during plant development, and under biotic and abiotic stresses. This indicates crucial role of BURP proteins in regulating the development of legumes and adaptation to different abiotic/biotic stresses. This study will provide the starter for cloning and detail functional investigation of BURP proteins in legume crops.
A comprehensive investigation of lipid-transfer proteins from Cicer arietinum disentangles their role in plant defense against Helicoverpa armigera-infestation
(Frontiers Media S.A., 2023) Saxena, Harshita; Negi, Harshita; Keshan, Radhika; Chitkara, Pragya; Kumar, Shailesh; Chakraborty, Amrita; Roy, Amit; Singh, Indrakant K.; Singh, Archana
Lipid Transfer Proteins (LTPs) play a crucial role in synthesizing lipid barrier polymers and are involved in defense signaling during pest and pathogen attacks. Although LTPs are conserved with multifaceted roles in plants, these are not yet identified and characterized in Cicer arietinum. In this study, a genome-wide analysis of LTPs was executed and their physiochemical properties, biochemical function, gene structure analysis, chromosomal localization, promoter analysis, gene duplication, and evolutionary analysis were performed using in silico tools. Furthermore, tissue-specific expression analysis and gene expression analysis during pest attack was also conducted for the LTPs. A total of 48 LTPs were identified and named as CaLTPs. They were predicted to be small unstable proteins with "Glycolipid transfer protein" and "Alpha-Amylase Inhibitors, Lipid Transfer and Seed Storage" domains, that are translocated to the extracellular region. CaLTPs were predicted to possess 3-4 introns and were located on all the eight chromosomes of chickpea with half of the CaLTPs being localized on chromosomes 4, 5, and 6, and found to be closely related to LTPs of Arabidopsis thaliana and Medicago trancatula. Gene duplication and synteny analysis revealed that most of the CaLTPs have evolved due to tandem or segmental gene duplication and were subjected to purifying selection during evolution. The promoters of CaLTPs had development-related, phytohormone-responsive, and abiotic and biotic stress-related cis-acting elements. A few CaLTP transcripts exhibited differential expression in diverse tissue types, while others showed no/very low expression. Out of 20 jasmonate-regulated CaLTPs, 14 exhibited differential expression patterns during Helicoverpa armigera-infestation, indicating their role in plant defense response. This study identified and characterized CaLTPs from an important legume, C. arietinum, and indicated their involvement in plant defense against H. armigera-infestation, which can be further utilized to explore lipid signaling during plant-pest interaction and pest management.
Comprehensive profiling of rRNA-derived small RNAs in Arabidopsis thaliana using rsRNAfinder pipeline
(Elsevier B.V., 2024) Kalakoti, Garima; Vivek, AT; Kamboj, Anshul; Singh, Ajeet; Chakraborty, Srija; Kumar, Shailesh
Ribosomal RNA (rRNA) gives rise to non-random small RNA fragments known as ribosomal-derived small RNAs (rsRNAs), which despite their biological importance, have been relatively understudied in comparison to other short non-coding RNAs. There exists a compelling necessity to develop a methodology for the identification, categorization, and quantification of rsRNAs from small RNA sequencing (sRNA-seq) data sets, considering the unique characteristics of ribosomal RNA (rRNA). To bridge this gap, we introduce 'rsRNAfinder' a specialized pipeline designed within the Snakemake framework. This analytical approach enables robust identification of rsRNAs using sRNA-seq datasets from Arabidopsis thaliana. Our methodology constitutes an integrated bioinformatic pipeline designed for different kinds of analysis.1.sRNA-seq data analysis: It performs in-depth analysis of reference-aligned sRNA-seq data, facilitating rsRNA annotation and quantification.2.Parametric reporting: Our pipeline provides comprehensive reports encompassing key parameters such as rsRNA size distributions, strandedness, genomic origin, and source rRNA origin.3.Illustrative validation: We have demonstrated the utility of our approach by conducting comprehensive rsRNA annotation in Arabidopsis thaliana. This validation reveals unique rsRNAs originating from all rRNA types, each of them distinguished by distinct identity, abundance, and length.
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq
(Oxford University Press, 2021) Vivek, A.T.; Kumar, Shailesh
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
A CRISPR-Cas9 library to target putative redundant gene sets facilitates their functional exploration in grain development in rice
(Springer Nature Publishing AG, 2025) Yadav, Banita; Sardar, Shaswati; Yadav, Anil; Kumari, Annapurna; Gautam, Mohini; Mandlik, Rushil; Arora, Simran; Kumar, Shailesh; Jewaria, Pawan Kumar; Sonah, Humira; Deshmukh, Rupesh; Chinnusamy, Viswanathan; Ram, Hasthi
Advent of CRISPR-Cas9 library approach has revolutionized the field of high throughput targeted mutagenesis in plants. By identifying an sgRNA spacer that can target multiple paralogous genes in a genome, higher-order knockout plants can be developed. Using this concept, we developed ten CRISPR-Cas9 pool libraries and generated higher-order knockout plants in rice. Towards this, firstly we identified genome-wide sets of genes which are co-expressed and have high sequence similarity and can be targeted by a single sgRNA. Based on the expression pattern, these genes were divided into ten groups, and subsequently ten CRISPR-Cas9 plasmid libraries were developed. One such library designed against seed-expressed genes was transformed into rice and higher-order knockout plants were developed. Genotyping revealed that around 90% T0 plants had editing, and among the edited plants majority of them were higher-order knockouts. Phenotypic analysis in the next generation discovered functions of several seed specific genes in grain length, width, number and 100-grain weight. By analyzing single and double mutants for two Agenet domain-containing proteins, we have discovered an epistatic interaction between them for grain development. Further application of our approach will help to uncover hidden functions of the targeted genes and accelerate functional genomics research in rice. The CRISPR-Cas9 library is a useful approach to generate higher-order knockout mutants and identify functions of the targeted genes in rice.
From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants
(Elsevier B.V., 2020) Vivek, A.T.; Zahra, Shafaque; Kumar, Shailesh
Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.
Fusion transcripts in plants: hidden layer of transcriptome complexity
(Elsevier B.V., 2025) Arora, Simran; Hamid, Fiza; Kumar, Shailesh
In the realm of genetic information, fusion transcripts contribute to the intricate complexity of the transcriptome across various organisms. Recently, Cong et al. investigated these RNAs in rice, maize, soybean, and arabidopsis (Arabidopsis thaliana), revealing conserved characteristics. These findings enhance our understanding of the functional roles and evolutionary significance of these fusion transcripts.
Genome-wide characterization and comparative analysis of the OSCA gene family and identification of its potential stress-responsive members in legumes
(Nature Publishing Group, 2023) Chakraborty, Srija; Gangwar, Rashmi; Zahra, Shafaque; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
Cicer arietinum, Cajanus cajan, Vigna radiata, and Phaseolus vulgaris are economically important legume crops with high nutritional value. They are negatively impacted globally by different biotic and abiotic stresses. Hyperosmolality-gated calcium-permeable channels (OSCA) have been characterized as osmosensors in Arabidopsis thaliana but have not previously reported in legumes. This study provides a genome-wide identification, characterization, and comparative analysis of OSCA genes in legumes. Our study identified and characterized 13 OSCA genes in C. cajan, V. radiata, P. vulgaris, and 12 in C. arietinum, classified into four distinct clades. We found evidence to suggest that the OSCAs might be involved in the interaction between hormone signalling pathways and stress signalling pathways. Furthermore, they play a major role in plant growth and development. The expression levels of the OSCAs vary under different stress conditions in a tissue-specific manner. Our study can be used to develop a detailed understanding of stress regulatory mechanisms of the OSCA gene family in legumes.
Genome-wide identification, characterization, and expression profiling of 14-3-3 genes in legumes
(Springer Nature Publishing AG, 2022) Chakraborty, Srija; Soundararajan, Prabhakaran; Kumar, Shailesh
In plants, a large multigene family encodes 14-3-3 proteins, which are commonly found in eukaryotes. They are involved in plant development and environmental stress regulation. The current study aims to identify and characterize the 14-3-3 gene family in four important legumes, viz. Cicer arietinum, Cajanus cajan, Vigna radiata and Arachis hypogaea. The 14-3-3 proteins were clustered into ε and non-ε groups based on phylogenetic analysis, which was further confrmed by gene structure analysis, and motif composition analysis. Our study suggests that segmental duplication events played a pivotal role in the evolution and expansion of this gene family. Evidence of both stress-responsive, and hormone-responsive cis-regulatory elements in the promoter region of the 14-3-3 genes points to the possibility that they might be involved in the interplay between hormone and stress signalling pathways. The expression profling using RNA-seq data sets showed a variation in expression level in most 14-3-3 genes under multiple stress conditions, and in diferent developmental stages. Hence, this study afrms the participation of the 14-3-3 genes in multiple stress regulation, and in growth and development of the legumes. The results obtained from this study provide crucial information for improved understanding, and stress response analysis of the 14-3-3 gene family in C. arietinum, C. cajan, V. radiata and A. hypogaea.
Identification of NRPS and type II PKS biosynthetic gene cluster (s) encoding decaplanin and kigamicin from Amycolatopsis regifaucium DSM 45072T
(Oxford University Press, 2025) Bisht, Niyati; Mayilraj, Shanmugam; Kumar, Shailesh; Kaur, Navjot
Amycolatopsis regifaucium, a Gram-positive actinomycete, is a prolific source of biologically active compounds, including polyphenol antibiotics like kigamicins. This study presents the draft genome of Amycolatopsis regifaucium DSM 45072T (= GY080T), which spans 8.28 Mbp and is assembled into 62 contigs, with annotation revealing 312 subsystems, 7,966 coding genes, and 52 RNAs, with a GC content of 68.5 mol%. We found a significant genomic diversity within the genus, revealing variations in core and accessory genomic elements across species. Multiple biosynthetic gene clusters (BGCs) have been identified, including a previously unidentified glycopeptide antibiotic (GPA) gene cluster and a type II polyketide synthase (PKS) gene cluster, highlighting the organism's metabolic versatility and potential for the biosynthesis of novel natural products. Our analysis confirmed the production of decaplanin, an antibiotic previously attributed to Amycolatopsis decaplanina DSM 44594T. Correspondingly, the gene cluster responsible for decaplanin biosynthesis is identified in A. regifaucium DSM 45072T and A. decaplanina DSM 44594T. Additionally, a putative type II PKS gene cluster is predicted within the glycopeptide antibiotic-producing clade (Cluster A) of the genus Amycolatopsis. Genomics insights from Amycolatopsis regifaucium DSM 45072T represent it as a promising genetic resource with significant implications for biotechnological and pharmaceutical innovation, particularly in discovering and developing novel antimicrobial agents.