The growing challenges of antibiotic resistance and cancer highlight the need for new bioactive compounds from unexplored ecological niches. This study investigates the gut microbiome of the earthworm Eisenia fetida as a source of fungal metabolites with potential therapeutic value. Four fungal species were isolated from the earthworm gut, and their extracts were screened for antimicrobial and anticancer activities. A key bioactive molecule, comenic acid (HE-1), was isolated from Mycothermus thermophilus extract (HF-3) and demonstrated moderate cytotoxicity against prostate cancer cells (IC50 9.92 mu g/mL). In addition, a triglyceride-based compound (DC-2) was isolated from the same fungal extract; however, its functional roles and bioactivities remain to be explored. These findings support E. fetida as a promising source of bioactive fungal metabolites and emphasize the potential of earthworm-associated microbiomes in natural product discovery. Further investigations are required to characterize additional metabolites and evaluate their biological and ecological relevance.

Abstract Cytochrome P450 monooxygenases (CYP450s) are key oxidative enzymes that diversify plant specialized metabolites and play a central role in the biosynthesis of bioactive withanolides in Withania somnifera (L.) Dunal. Despite their importance, genome-wide information on CYP450s in W. somnifera has remained elusive. Herein, the first high-quality genome assembly (2.2 Gb, scaffold N50: 47.4 kb) of an Indian W. somnifera cultivar was generated using a hybrid Oxford Nanopore-Illumina sequencing strategy. Comparative analysis with the NCBI reference genome revealed moderate SNP and indel variations, reflecting intraspecific genetic diversity. A comprehensive CYP450 catalog was established and analyzed phylogenomically across nine plant genomes, encompassing both withanolide-producing and non-producing Solanaceae and non-Solanaceae species. Unique CYP families (CYP450A, CYP1194, and CYP705A) were detected exclusively in W. somnifera, suggesting lineage-specific metabolic innovations, while Solanaceae-restricted (CYP82E/M) and absent (CYP81B, CYP6) lineages highlight taxonomic divergence. Across all analyzed genomes, 36 conserved CYP450 subfamilies, including triterpenoid-associated members, were identified, suggesting a shared oxidative framework adaptable to specialized metabolism. Moreover, potential candidate genes in the triterpenoid pathway, including CYP72A692_1, CYP72A560_4, CYP716A48, CYP724B2, and CYP51G1, were identified through phylogenetic integration with functionally validated triterpenoid-modifying enzymes from other plant species. Gene family evolution analysis further revealed contraction of monoterpenoid-related subfamilies (CYP76A), implying a metabolic shift toward triterpenoid specialization. The comprehensive genome assembly and CYPome of W. somnifera offer a valuable resource for functional characterization, evolutionary analysis, and the identification of genes underlying its specialized metabolism. Furthermore, the study advances our understanding of CYP450 diversity and evolution, revealing lineage-specific innovations, conserved subfamilies, and key candidate genes involved in triterpenoid biosynthesis. Together, these findings lay a foundation for future functional studies and pathway engineering aimed at optimizing the metabolic potential of this important medicinal plant.

Freshwater unionid mussels are ecologically important yet genomically underrepresented relative to marine bivalves. Field surveys conducted across two freshwater streams indicated that Lamellidens corrianus was consistently abundant and widely distributed, motivating its selection for genome-level characterization. We present a draft genome assembly of the freshwater mussel Lamellidens corrianus and characterize its sequence-level genomic features. The 1.41 Gb draft genome assembly, while fragmented (N50 = 1816 bp), captures an overall AT content of 64.82%, while predicted coding sequences showed approximately 57% AT content. Functional annotation of high-confidence gene models revealed representation of conserved pathways related to translation, metabolism, cytoskeletal organization, stress response, and DNA repair, confirming representation of core molecular systems. Codon usage bias (CUB) was evaluated using ENC, CAI, CBI, correspondence analysis, neutrality plots, PR2, ENC-GC3 analysis, and correlation tests. A mean ENC value of 48.9 suggests relatively weak synonymous codon usage bias accompanied by preference for A/U ending codons. Neutrality and ENC-GC3 analyses (slope = 0.1023) indicate that codon usage patterns reflect a mutation-selection balance in which nucleotide composition exerts primary influence with secondary mutational contributions. Comparative RSCU analysis across marine and freshwater bivalves revealed broadly conserved synonymous patterns, with lineage-associated differences in selected codons. Amino acid frequencies were highly conserved, characterized by enrichment of six-fold degenerate residues and consistent prevalence of leucine and scarcity of tryptophan. Orthogroup analysis of predicted proteins identified 959 clusters, with interpretation constrained by assembly fragmentation. These results demonstrate that draft genome assemblies can provide informative insights into compositional bias, codon architecture, and comparative gene content, establishing L. corrianus as a compositional and translational baseline for freshwater unionid research.

Marine nematodes, the most abundant meiofauna in benthic ecosystems, drive critical nutrient cycling and carbon sequestration, yet accurate biomass estimation remains challenging due to morphological variability and reliance on simplistic geometric models like Andr & aacute;ssy's formula, which introduced systematic biases across taxa. This study developed RAH NemaCalc, an open-source Python-based tool with Tkinter GUI and OpenCV integration that semi-automates morphometric analysis by segmenting nematodes into 5-20 conical frustums based on length-diameter ratios, calculating lateral surface area with morphology-specific correction factors (k(total) and frustum geometry factor f), and converting to biomass using an empirically determined density of 1.08 g/cm(3) derived from sucrose gradient centrifugation of 50 genera. The tool processed high-resolution images of 187 specimens from diverse habitats- 50 from Lakshadweep Islands, 87 from Clarion Clipperton Zone abyssal sediments, and 50 from the Nemys database yielding processing times of 1.8-2.1 s/image with manual contour verification. Key results showed the frustum method produced significantly different biomass estimates from Andr & aacute;ssy (Wilcoxon p < 0.0001 across datasets), with median volume reductions of 20-28% in coastal/abyssal samples but up to 260% higher biomass in large tapered genera like Linhomoeus and Halichoanolaimus; Bland-Altman analysis confirmed morphology- and size-dependent bias, while 10-20 segments optimized accuracy for tapered forms. RAH NemaCalc thus established a precise, high-throughput standard for nematode biomass quantification, enabling reliable monitoring of anthropogenic impacts like deep-sea mining on ecosystem functions and informing conservation baselines.

Gut-associated fungal endofauna confronted with stressful conditions have the potential to secrete diverse bioactive metabolites. In this context, the present study aims to uncover the hidden metabolite profiling of less explored fungal gut parasites associated with rhizosphere nematodes of Withania somnifera. The nematode Xiphinema nuragicum, predominantly found in W. somnifera rhizosphere, was explored for its gut endofauna. This study represents the first report on the isolation of X. nuragicum from the rhizosphere of W. somnifera and the exploration of endofauna inhabiting the gut of X. nuragicum. Among different fungal isolates inhabiting the gut of X. nuragicum, Fusarium fujikuroi (R3) was found to be the most potent isolate and was therefore selected for the isolation and identification of its active metabolites. Three compounds were characterized from F. fujikuroi, namely di (2-ethylhexyl) phthalate (DEHP), 2,5-bis(1,1-dimethylethyl) phenol, and 1,4-di-tert-butyl-2-chlorobenzene. The compounds exhibited strong cytotoxic and anti-inflammatory activities with potential therapeutic applications. The present study also revealed the bioremediation potential of X. nuragicum, hosting F. fujikuroi already known for its ability to eliminate environmental pollutants such as DEHP and polycyclic aromatic hydrocarbons (PAHs). Despite these promising findings, in-depth mechanistic studies would be the future perspective of the current study.

This study investigates the complex host-parasite interactions between Unionicola mites and freshwater mussels, focusing on infestation patterns across four mussel species from two river streams. Furthermore, this study explores the metabolic adaptations of a parasitic mite infesting Himalayan freshwater mussels, focusing on producing the macromolecule 13-cis-docosenamide.Lamellidens corrianus emerged as the primary host, with environmental and morphometric factors influencing infestation dynamics. Using combined morphological and molecular taxonomy, the mites were identified as Unionicola (Myanmaratax) savadiensis, and their biochemical adaptations were explored. Metabolomics profiling highlighted the presence of 13-cis-docosenamide in gill-associated mites, indicating a potential host-specific adaptation. This compound is novel to mites and suggests a unique interaction with the host's chemical environment. GC-MS profiling of mussels stated the presence of the precursor docosenoic acid but not the final compound, supporting the hypothesis that mites synthesize 13-cis-docosenamide from host-derived precursors. The absence of this compound in mites from accidental hosts further highlights the specificity of this metabolic adaptation. Additionally, other isolated compounds were identified as polymer additives, which are known for their toxic and endocrine-disrupting properties, exacerbating ecological threats to mussel populations. This study highlights the dual ecological pressures of parasitism and the dynamics of these organisms, advancing our understanding of freshwater ecosystems and their threats.

This study delves into codon usage bias (CUB) across Cannabis sativa and its associated pathogens (Meloidogyne incognita, Alternaria alternata, Aspergillus flavus, Aspergillus niger, and Fusarium oxysporum). It finds an AT-bias in C. sativa and M. incognita, favouring AT ending codons, while fungal pathogens lean towards GC-ending codons. Analysis suggests weak codon bias overall, with host and nematode showing similar preferences, and fungal pathogens preferring GC-ending codons. In ENC/GC3 plot, parity plot analyses both natural selection and mutational pressure influence CUB, slightly favouring T-ending codons.Neutrality plot analysis demonstrated varying degrees of mutational pressure and selection across the organisms. Correspondence analysis revealed indistinguishable CUB effective in all pathogens, despite differences in evolutionary forces. Correlation analysis illustrated the impact of nucleotide composition, mutational pressure, and natural selection on CUB. Additionally, amino acid composition analysis indicated differential usage of amino acids across organisms. Codon context analysis unveiled common trends in codon pairing, emphasizing the prevalence of preferred codons in C. sativa and M. incognita. This comprehensive analysis provides insights into the factors shaping CUB and the evolutionary forces influencing the genomes of the host plant and its associated pathogens, contributing to a deeper understanding of molecular interactions in host-pathogen systems. This data informs conservation for Cannabis sativa by identifying pathogen-resistant genetic traits, guiding breeding and management for biodiversity preservation.

This study examines the ecological ramifications of heavy metal contamination on benthic invertebrate communities, with a focus on Limnodrilus cervix, in a perennial pond situated in the Raipur region of Jammu, India. The study identified 11,587 individuals of Limnodrilus cervix, showing seasonal variations in abundance. Through a multidisciplinary approach encompassing taxonomic analysis, heavy metal quantification, acute toxicity testing, and bioaccumulation assessments, the research explores the intricate dynamics between pollution and aquatic ecosystems. Findings reveal pronounced seasonal fluctuations in L. cervix populations, with copper emerging as the predominant metal. Acute toxicity tests underscore dose-dependent lead (Pb) toxicity with an LC50 value of 0.03mg/L, while bioaccumulation experiments elucidate Pb absorption in worm tissue with a bioconcentration factor (BCF) of 0.4 at 0.005mg/L and 0.7 at 0.01mg/L. The study underscores the urgent need for informed management strategies to mitigate the ecological risks posed by heavy metal pollution and safeguard freshwater habitats and their inhabitants.

Genus Plantago of Plantaginaceae family is bestowed with a repertoire of structurally diverse secondary metabolites that have not only been used as therapeutics but also effect the plant physiology by conferring adaptive advantages under stress. Assuming that domestication process in plants has influenced their secondary metabolites, we performed a comparative transcriptome of wild and cultivated species of Plantago to analyze the variation in the expression of genes related to secondary metabolite pathways. GO and KEGG analysis of DEGs in wild species showed their enrichment in abiotic stresses, oxidation–reduction and secondary metabolite related pathways. Overall, we found upregulation of genes of carotenoid, flavonoid and phenylpropanoid, isoprenoid, terpenoid and alkaloid pathways in wild species of Plantago in particular, P. lanceolata while mucilage pathway-related genes showed higher expression in P. ovata. Moreover, transcriptome data presented putative transcription factors associated with terpenoids, carotenoid and phenylpropanoid biosynthetic pathways which were also identified using co-expression analysis of cluster 9 (secondary metabolite enriched gene cluster). Taken together, the genomic resource obtained from the present study form a valuable repository of genetic information for elucidating and exploring the secondary metabolic circuitry of Plantagos. Further, information on the regulatory aspects of genes related to secondary metabolites, shall aid in the enhanced production of valuable metabolites in these plants.

This study explores the prevalence, distribution, and codon usage bias of nematode species, primarily Heterodera glycines and Heterodera avenae, within saffron corms. Nematode analysis identified H. glycines and H. avenae as the predominant species. Geographical locations exhibited distinct cyst infestation levels, with H. avenae showing higher prevalence. The study reveals the preference of these nematodes for saffron corms, raising concerns for saffron production and suggesting the implementation of monitoring and management strategies. Additionally, the study analyzes the codon usage bias (CUB) of saffron and its associated nematode pathogens. Codon usage bias analysis revealed an AT bias in Crocus sativus and its pathogens. Codon Adaptation Index (CAI) values suggested pathogen adaptation to the host. Correlation analysis highlighted the interplay of nucleotide composition, mutational pressure, and natural selection in codon usage patterns. Amino acid frequency and codon context analyses provided insights into evolution and physiological functions. Furthermore, the study observed a mutual codon preference between the host and pathogens for certain amino acids, highlighting specific interactions at the molecular level. This study provides valuable information for understanding the molecular biology of plant-nematode interactions, and its findings can be useful for developing effective management strategies against these pests in saffron production and other crops such as crop rotation, use of resistant cultivars, and application of nematode-suppressive amendments.

A review of the ciliate (Ciliophora) species associated to rotifers as epibionts and endoparasites is presented, based on published records. Thirty rotifer species from 12 genera are known as hosts of ciliates. Among ciliates, one species of class Suctorea and 14 species of class Oligohymenophorea (12 from subclass Peritrichia, one from Hymenostomatia, and one from Astomatia) have been noted as associated to rotifers. The possible factors responsible for host prevalence of ciliates are discussed.

Freshwater mites of the family Unionicolidae are associated with freshwater mussels and snails in lakes and streams on all continents except Antarctica. The majority of the currently known 265 Unionicolidae species are associated with molluscs during at least one stage of their life cycle. A new host record is presented here from India: Unionicola (Myanamaratax) savadiensis from the host Lamellidens corrianus. In addition to L. corrianus, U. savadiensis was also found associated with two other mussel species, i.e., Lamellidens marginalis and Corbicula cashmiriensis, but DNA evidence confirms parasite-host association between U. (M.) savadiensis and L. corrianus, indicating that its findings in the two other mussel species should be considered as 'vagrant' associations. This report is thus significant for two reasons: (i) the record of the new host and geographic associations of the mite and mussels extends our knowledge on the known mite-mussels associations, and (ii) the study emphasized the importance of including experts from acarology, malacology, and molecular biology, to ascertain the nature of mite-mussel associations.

The present study investigates the phenomenon of codon usage bias (CUB) in Meloidogyne incognita, a parasitic nematode that infests plants. It explores the patterns of CUB, the factors that influence it, and its correlation with gene expression. Understanding codon usage bias in M. incognita is important for developing effective strategies for controlling nematode infections in plants. The results indicated a weak CUB in M. incognita, with an overall AT bias in the genome. The analysis of relative synonymous codon usage (RSCU) revealed that preferred and high-frequency codons mostly ended with G/C, indicating the influence of compositional constraints on codon usage. Further analysis using ENC plot, PR2 plot, Neutrality plot, and correspondence analysis suggested that natural selection and mutation pressure both played a role in observed CUB, with mutation pressure being the decisive factor. Amino acid composition analysis showed that glycine was the most frequently used amino acid, while histidine was the least utilized. Interestingly, the study found a negative correlation between codon usage and gene expression in M. incognita. Overall, this study provides a comprehensive understanding of codon usage bias in M. incognita and highlights its potential implications for gene expression and pathogenesis in plants by understanding preferred, avoided, and unique codons, which could further aid in the development of effective strategies for controlling nematode infections.

Every individual gene or genome follows the phenomenon of codon bias, where the usage among synonymous codons is not equal. The present study was conducted to understand the CUB in E. fetida and its impact on gene expression. The genes of E. fetida were G/Cbiased, where mean of C% was highest followed by G%, T%, and A% at the third codon position. ENC plot, Neutrality plot and Parity plot analysis revealed the codon usage pattern in E. fetida was largely influenced by natural selection. Further, it was observed that CUB had a substantial negative relationship with the gene expression levels (FPKM) at p < 0.05. Altogether, these findings indicate that translational efficiency and accuracy might have modulated the choice of codon selection in the studied earthworm genome.

Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explains the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with effective number of codons (ENC) < 50 had low Fragments Per Kilobase Million (FPKM) value while low codon bias group ENC >50 possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus. The non-significant MILC-based expression level predictor (MELP) and ENC correlation analysis suggested that expression of genes might not be associated with codon usage bias. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping Codon usage patterns. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all the selected species. In addition, the role of Codon usage bias regarding the predilection of fungal pathogens Aspergillus fumigatus, Fusarium oxysporum, Aspergillus niger and Aspergillus flavus towards host plant C. sativus has also been expounded. We found a similar trend of codon usage operative in plant and fungal pathogens as all the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus. Overall, different indices reflected a weak codon bias in the C. sativus, and its associated pathogens.

With the increasing accumulation of genomic sequence information of echinoderms, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern among three echinoderm species Heliocidaris erythrogramma (Sea urchin), Apostichopus japonicus (Sea cucumber) and Asterias rubens (Star fish) belonging to similar habitats. We performed detailed comparative analysis of echinodermal genomes with respect to codon bias. Our analysis reflects that the genome of H. erythrogramma and A. rubens was found to be GC rich, whereas the genome of A. japonicus was found to be AT rich. The RSCU (Relative usage of synonymous codons) analysis revealed dominance of A- and/or C-ending codons in H. erythrogramma and A. rubens while A- and/or U-ending codons were preferred in A. japonicus. Overall, a weak codon bias was prevailed in all the three genomes of selected echinoderm species. The main influencing elements in developing codon usage bias (CUB) appeared to be mutational pressure and natural selection. Despite sharing the same ecological habitat and functional features, CUB analysis revealed a close relationship between H. erythrogramma and A. rubens among the three Echinoderm species chosen for this study. The present study will be helpful in understanding the genetic features prevalent in Echinoderms and would lay a foundation for future research on other Echinoderm species.

Abstract Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explicates the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with ENC < 50 had low FPKM value while low codon bias group (ENC > 50) possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus. The non-significant MELP and ENC correlation analysis suggested that expression of genes might not be associated with CUB. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping CUB. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all three species. In addition, the role of CUB regarding the predilection of fungal pathogens Aspergillus fumigatus and Fusarium oxysporum towards host plant C. sativus has also been expounded. We found a similar trend of codon usage pattern operative in plant and fungal pathogens as both the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus. Overall, different CUB indices reflected a weak codon bias in the C. sativus, F. oxysporum and A. fumigatus genome.

The most tedious and hectic job is to identify the tiny benthic animals by spending thousands of hour under the microscope, since all the fauna need to be counted, sorted, picked and permanently mounted on glass slides for taxonomic identification. All faunal identifications need a lot of preprocessing and it consumes a lot of time to identify a single specimen. Therefore, to reduce the complexity of many such procedures, combined with the desire to identify larger datasets, we came up with new software based on artificial intelligence which can automatically identify the benthic fauna through the microscopic images. In this paper, we propose a machine learning method for automatic visual identification through the images of the benthic fauna. To this end, we propose a neural network model, where we demonstrate that the proposed approach differentiates the fauna based on images. However, it works well with vast amounts of image data and significant computational resources.

Abstract Bioinformatic approaches were utilized to investigate the pattern of codon usage in 109 epilepsy-related genes. The genes were found to be rich in G and C nucleotides, with GC usage 7% higher than AT. Preferred codon analysis confirmed the dominance of G and C at the wobble position of codons. CAG is the most frequently used codon. The ENc analysis, on the other hand, did not reveal any exceptional codon usage bias. Correlation of GC content at the first and second codon positions with the third codon position (neutrality plot) suggested the impact of selection pressure in shaping the GC enriched compositional pattern observed in epilepsy-related genes. It was further confirmed by correspondence analysis. Altogether, our findings imply that the pattern of evolutionary processes (especially selection pressure) operating on epilepsy-related genes. This might aid in identifying disease genes compositional signatures and deciphering the genetic mechanisms underlying epilepsy. Further this information would be useful in facilitating the existing epilepsy related therapies like gene therapy, cell therapy etc.

Circular RNAs (circRNAs) are endogenous RNA formed by the back splicing process. They are ubiquitous, stable, evolutionally conserved, and are tissue-specific. The biochemical and molecular features of circRNAs hold the potential to be used as biomarkers in various diseases to achieve pharmacological goals. CircRNAs have numerous latent modes of action, from acting as sponges for microRNAs and RNA binding proteins to serve as transcriptional regulators, epigenetic alterations, etc. Dysregulated functioning of several circular RNAs lead to the progression of a plethora of diseases. Due to their extremely stable nature and amazing tissue specificity, circRNAs have paved the way for advanced clinical studies as a novel method of early disease detection and treatment efficacy. Therefore, they have been recognized as a latent diagnostic biomarker for neurodegenerative diseases, diabetes, osteoarthritis, and cardiovascular diseases.