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Ompok bimaculatus is a commercially important food fish of Northeast India. For higher production of this species, the molecular mechanisms underlying its reproductive physiology is an important aspect to study. Vegetable oils are rich in ω3 and ω6 fatty acids and fat-soluble vitamins, that enhance reproductive performances. In the present study, O. bimaculatus were first fed with vegetable oil at 3, 5, 7 and 9% in the diet. The best treatment was determined by the analysis of relative fecundity, fertilisation rate, Gonadosomatic Index (GSI) and Hepatosomatic Index (HIS). Comparative transcriptomics analysis of gonadal tissues between control and best treatment was done using Illumina NextSeq500. The bioinformatics analysis by Trinity v2.11.0 and edgeR v3.32.1 identified 36 DEGs related to reproduction, those were later validated by qPCR analysis. The Differentially Expressed Genes (DEGs) revealed, regulation of Hypothalamic—pituitary—gonadal axis (HPG) axis through retinoid signalling pathway, IGF pathway and folliculogenesis pathway, including inhibitory effects of dietary vegetable oil on fish gonadal maturation. [ABSTRACT FROM AUTHOR]

Fish pigmentation study can reveal understandings in dermatological research based on functional genomics. Cultured ornamental fish becomes dull coloured and antityrosinase activity through sesame seed may enhance skin colour, which has not been studied. Botia dario is an indigenous fish, having ornamental and aesthetic value and can be studied as a model for fish pigmentation genetics. In this study, fish specimens were fed with 15% marigold petal meal along with 5, 10 and 15% w/w sesame seed in diet. Pigmentation genes, that is, tyr, tyrp1a, asip1, gnaq, kitlga, mc1r, mitf, pax7a, rab38, slc7a11, sox9a, sox10, csf1r, bcdo2 and gsta2 in skin and immunogens, that is, il20, nramp, tlr9 and trail in kidney were studied. Gene expression in tissues revealed enhanced pigmentation and immunity as well as the role of tyr, tyrp1a and asip1 in pigmentation. Immunogenes and blood parameters confirmed the best pigmentation diet. Colorimetric analysis also showed the enhancement of pigmentation. Insights from sesame seed and marigold‐induced antityrosinase effects will be applied in aquaculture to develop natural, dietary formulations that will enhance pigmentation in ornamental fish, leading to improved skin colour and market value. [ABSTRACT FROM AUTHOR]

The Queen loach (Botia dario), an ornamental fish species having export potential, belongs to family Cobitidae of order Cypriniformes. The dull colouration in captive condition as compared to nature is a drawback in ornamental fisheries. We report the first comparative transcriptomic analysis of Cultured (CBD) and Natural (NBD) B. dario using bioinformatics tools. Total 26 and 7 key genes for melanin and carotenoid colouration were found, respectively. KEGG pathway annotations of the genes were carried out, to annotate and describe their relevance for pigmentation. The qPCR validation of genes confirmed their expression pattern in the skin and muscle. Differential expression of, slc7a11 , asip1 , mc1r , dct, tyrp1a, tyr, bcdo2, csf1r, plin2, gsta2, star3 and stard5 in the skin and muscle tissues revealed the reasons for wild versus cultured colour variation. The molecular data was further supported by low yellowness and redness values of CBD skin and muscle in a colorimeter. • Comparative Transcriptomics of wild and cultured Botia dario has been done using next-generation sequencing methods. • Key genes responsible for melanin and carotenoid colouration has been identified in B. dario. • Insights into differentially expressed genes and difference in pigmentation of wild and cultured B. dario has been analyzed. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI , COII , COIII , 16S rRNA , 12S rRNA , Cyt b , ATPase 6 , D-loop , ND1 , ND2 , ND3 , ND4 , ND5 , and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b , 12S rRNA , ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction. Unlabelled Image • We report the first complete mitogenome of Queen loach, Botia dario using next-generation sequencing methods. • Phylogenetics analysis of complete mitogenome of B. dario and some related fish species from the order Cypriniformes. • A study on Cypriniformes based on complete mitogenome and individual mitogenes to find a suitable gene for phylogenetic tree construction. [ABSTRACT FROM AUTHOR]

The genetic basis and expression patterns of key genes are important aspects of study to understand the colouration. This trait differs between wild and domesticated fish which is a matter of research. Botia dario is an indigenous fish, having ornamental and aesthetic value, which shows faded appearance in terms of colour in domesticated condition than wild. In the present study the carotenoid-fed B. dario were examined through incorporation of marigold petal meal in the diets at the rate of 5, 10 and 15% w/w along with wild fish. The carotenoid content of tissues that is skin, muscle and intestine along with intensity of colouration increased in a dose dependant manner of carotenoid in the diet. Important carotenoid-based colouration genes that is csf1r, BCDO2, SR-B1, MLN64, STAR5, GSTA2 and PLIN2 were characterized in the fish, to find out their role in fish pigmentation. The significant difference (p < 0.05) in the expression of these genes in different tissues, when compared among carotenoid-fed domesticated and wild fish, revealed the mechanism responsible for faded colouration and also revealed the means to enhance colour in the fish. [ABSTRACT FROM AUTHOR]

The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8–3.7 ppm), COD (23–29.2 ppm) and organic carbon (0.18–0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem. [Display omitted] • Metagenomic study of microbial communities in sediments of river Ganga stretches. • Highest concentrations of Mn, Fe, and Cr were observed in the polluted sites. • Bacteroidota and Chloroflexota were predominant in all sediment samples. • First report reveals the presence of 13 plastic & 18 xenobiotic degradation enzymes. [ABSTRACT FROM AUTHOR]

Pangas fish (Pangasianodon hypophthalmus) was fermented naturally with salt at room temperature for 180 days and representative culturable bacteria from the entire maturation period at 15 days interval were isolated by plating in media containing 5% and 15% salt and identified using 16SrRNA gene sequence analysis. Total 80 no of bacterial isolates belonging to genera such as Bacillus, Staphylococcus, Oceanobacillus, Halomonas, Chromohalobacter, Virgibacillus etc. were identified from late maturation phase. Staphylococcus, Bacillus and Halomonas spp. were dominant from early maturation phase whereas Chromohalobacter spp. and Virgibacillus spp. appeared from 90th day onward and persisted till the final maturation. Bacillus licheniformis and Chromohalobacter canadensis were dominant bacterial species on 5% and 15% salt containing plates respectively from 90th day until final maturation. The dominant isolates showed good proteolytic and moderate lipolytic activities along with good growth during salt fermentation indicating that they are potential starter cultures for acceleration of the fermentation process. [ABSTRACT FROM AUTHOR]

• Successful DNA barcoding of fishes from Ranganadi River, Arunachal Pradesh, India. • 114 COI barcodes have been generated and submitted to NCBI database and FishBOL. • Haplotype diversity and phylogenetics revealed interesting facts about the studied species. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98–100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification. [ABSTRACT FROM AUTHOR]