Partha Sarathi Tripathy

Background: The vulnerable goonch catfish Bagarius bagarius is an ecologically important riverine species whose evolutionary history and mitochondrial regulation remain poorly understood. In this study, we generated and analyzed the complete mitogenome of B. bagarius using Oxford Nanopore long-read sequencing with adaptive sampling, followed by de novo assembly, annotation, and comprehensive comparative analyses. Results: The circular mitogenome (16,524 bp) contains the typical vertebrate complement of 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region, and exhibits pronounced AT richness and strand-specific compositional asymmetry. Phylogenetic reconstruction based on complete mitogenomes robustly resolves B. bagarius as sister to Bagarius yarrelli , confirming the monophyly of the genus and supporting its placement as an early-diverging lineage within Sisorinae. Homoplasy analyses reveal limited recurrent mutation at shallow phylogenetic scales but substantial homoplasy across deeper sisorid divergences, highlighting both the strengths and limits of mitochondrial inference. Nanopore-based modified-base calling identified candidate adenine- and cytosine-associated signals across the mitogenome, with variation in their strand-wise and regional distributions. Because these signals were derived from a single individual and were not independently validated, they are interpreted as preliminary candidate modification patterns rather than definitive evidence of mitochondrial DNA methylation or functional regulation. Conclusion: Overall, this study provides a complete mitogenomic resource for B. bagarius together with an exploratory dataset of nanopore-derived candidate modified-base signals, supporting future phylogenetic, conservation-genetic, and independently validated investigations of mitochondrial DNA modification in fishes.

Mangrove systems are major blue-carbon reservoirs, storing 4.4 to 11.7 petagrams of organic carbon globally and supporting diverse microalgal communities that drive primary productivity and coastal carbon cycling. The Sundarban, one of the world’s largest (3,629.57 km²) mangrove-dominated coastal systems, holds a substantial carbon stock (26.62 Tg). Rising salinity and anthropogenic pressure are altering the diversity of microalgal communities, highlighting the importance of identifying resilient taxa capable of sustaining carbon fixation. To address this need, we conducted whole-genome metagenomic profiling of degraded mangrove soils. The data revealed six dominant microalgal taxa adapted to prevailing salinity and nutrient stress. These six taxa were subsequently isolated from the same habitats, and a 16-day ambient CO₂ (420 ppm) screening was undertaken to evaluate the specific growth rate and biomass gain of the algae. Among them, three physiologically resilient strains Chlorella sp., Limnospira platensis, and Leptolyngbya boryana were selected for controlled CO₂-enrichment concentrations (0.04%, 0.05%, 0.20%, 10%) to mimic future climate change scenarios. Among those microalgae, the Leptolyngbya boryana showed the highest biomass yield (1.31 g L⁻¹), carbon content (0.52 g C g⁻¹ dry weight), and CO₂-fixation rate (up to 149 mg CO₂ L⁻¹ d⁻¹). Metagenomic analysis further identified that L. boryana possessed the strongest representation of carbon-fixation pathways like Calvin-Benson-Bassham (CBB) cycle and the reductive TCA (rTCA) cycle, regulated by enriched key genes such as cbbL, cbbS, gap2, zwf, and accC. Therefore, this result positions L. boryana as a promising microalgal candidate for carbon sequestration in future CO₂-rich environments under saline coastal ecology.

Bacillus amyloliquefaciens COFCAU_P1, an autochthonous probiotic from Labeo rohita , was genome sequenced (Illumina NovaSeq; GenBank JBHEQH000000000 ). Its 4.09 Mb genome encodes 4,351 genes linked to stress tolerance, nutrient utilization, antimicrobial defense, enzymes, and immunomodulation. Phylogenomics and functional evidence confirm its safety and probiotic potential for aquaculture applications in aquaculture systems.

The study reports a fish pathogenic and multidrug-resistant Proteus mirabilis COFI-RLBCAU-II ( CP181371 ) isolated from diseased Labeo catla . The bacterium belonged to the Enterobacteriaceae family, and its genome length was 3.93 Mb with 3,656 genes.

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent.

Fusarium stalk rot (FSR) caused by the Fusarium species complex is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium spp. obtained from five major maize-growing regions of India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. Geographical separation among four local populations contributed to 7.87% variance, whereas 92.12% of the variance was within popula-tions, suggesting a predominant influence of local adaptation or stochastic events like genetic drift within populations, with geographical separation playing a lesser but significant role in shaping genetic diversity. Genetic differentiation statistics between Fusarium species showed lower gene flow from haplotypes except in the population of F. acutatum and F. andiyazi having high GST values. In contrast, a high Kxy was reported, indicating elevated genetic differentiation between populations. The haplotype network analysis revealed the presence of eight distinct haplotypes which reflected pathogenic evolution and adaptive potential of Fusarium spp. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium spp. causing FSR of maize in the Indian subcontinent.