Genetic diversity and latency status of betanodavirus in wild seeds of Asian seabass Lates calcarifer (Bloch) sampled along Indian coasts

288-293Piscine nodavirus is the causative agent of viral encephalopathy and retinopathy in marine and freshwater fish worldwide. The present investigation was carried out to know the persistence and diversity of betanodavirus in wild healthy seabass seeds around east and west coasts of India from three major landing sites. The seeds obtained from two coasts were detected positive by nested PCR using RNA2 coat protein gene-specific primers. Phylogenetic analysis revealed all the three Indian coast sample sequences as close to Indian strain of betanodavirus reported earlier and those belong to red-spotted grouper nervous necrosis virus (RGNNV). These results indicate a strong latency or persistency of betanodavirus among wild healthy seeds of Asian seabass available along Indian coasts that remain as a source of viral inoculum for spreading disease in farm reared fish

Strategies to control invasion of Sailfin Armoured Catfish, Pterygoplichthys spp. in wastewater-fed aquaculture bheries of East Kolkata Wetland, India with suggestion of a modified barrier based on the biological and behavioural characteristics

Sailfin armoured catfish (Pterygoplichthys spp.), an alien invasive species of family Loricariidae has invaded extensively in wastewater-fed large aquaculture ponds (locally called ‘bheries’) of East Kolkata Wetlands (EKW), West Bengal, India. As there is no viable controlling method at present, commonly these fishes are removed by different physical methods and discarded. In the present study, we investigated the effectiveness and suitability of different in-practice Pterygoplichthys spp. control methods, based on on-field sampling, biological and behavioural study of the fish and also response analysis of the stakeholder’s of EKW. The results indicate that in-practice eradication efforts, like ‘repeated seine netting’ with or without removal of Eichhornia sheath of the pond periphery and ‘dewatering of pond’ aiming to reduce or eradicate Pterygoplichthys spp., are not fully effective, because of the capture avoidance ability and burrowing habit of these fishes. We found deep and branching burrows of Pterygoplichthys spp. in aquaculture ponds of EKW, with maximum burrow depth of 58 cm, and water in that burrows even after 12 days of dewatering. Hence, it is suggested stakeholders to keep dewatered pond exposed to sunlight for at least four weeks or above to ensure complete water-out from the burrows in which Pterygoplichthys spp. take shelter or lay their eggs. ‘Multilayer bamboo fencing’ or ‘combination of bamboo fencing and net barrier’ use by the stakeholders of EKW to prevent intrusion or re-intrusion of Pterygoplichthys spp. were found only partially effective, because of the capability of these fishes to damage net-blocking through their hard dorsal and pectoral spines or entry through the holes dug across the barrier in beneath or banks of the sewage intake channel. Based on learning on the biological and behavioural characteristics of Pterygoplichthys spp., we then suggested a modified version of barrier to the stakeholder’s of EKW, incorporating a sewage feeder pipeline, a concrete collection chamber with size separation arrangement made of hard materials like wire mesh and a dam of specific dimensions across the channel, for effective prevention of intrusion of these fishes in their aquaculture bheries

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Not AvailableMicroRNAs (miRNAs) are small non-coding RNAs that control the expression ofgenes by targeting specific mRNAs. Data related to miRNAs are limited for fishspecies, with only 16 out of the 30 000 fish species enlisted in miRBase. In the pre-sent review, we have summarized the recent findings on the implication of miR-NAs in the teleost reproduction with an emphasis on commercially importantcandidates. The information related to various miRNAs and their roles duringdifferent developmental stages of gonads in nine important species has been com-piled. We have focused on the trend of sexual dimorphism in the gonadal miRNArepertoire of teleost species. Species-specific variability is observed in the expres-sion pattern of gonadal miRNAs in both male and female fish. It is noteworthythat our summarization of teleost miRNAs in reproduction has highlighted thegaps in functional information on the identified miRNAs (both conserved andnovel). It is only after functional validation of the miRNA targets, one can usethese findings to enhance reproductive health and production of the commercialteleost species to boost overall aquaculture sector.Not Availabl

Poly- and Perfluoroalkyl Substances (PFAS): Do They Matter to Aquatic Ecosystems?

Poly- and perfluoroalkyl substances (PFASs) are a group of anthropogenic chemicals with an aliphatic fluorinated carbon chain. Due to their durability, bioaccumulation potential, and negative impacts on living organisms, these compounds have drawn lots of attention across the world. The negative impacts of PFASs on aquatic ecosystems are becoming a major concern due to their widespread use in increasing concentrations and constant leakage into the aquatic environment. Furthermore, by acting as agonists or antagonists, PFASs may alter the bioaccumulation and toxicity of certain substances. In many species, particularly aquatic organisms, PFASs can stay in the body and induce a variety of negative consequences, such as reproductive toxicity, oxidative stress, metabolic disruption, immunological toxicity, developmental toxicity, cellular damage and necrosis. PFAS bioaccumulation plays a significant role and has an impact on the composition of the intestinal microbiota, which is influenced by the kind of diet and is directly related to the host’s well-being. PFASs also act as endocrine disruptor chemicals (EDCs) which can change the endocrine system and result in dysbiosis of gut microbes and other health repercussions. In silico investigation and analysis also shows that PFASs are incorporated into the maturing oocytes during vitellogenesis and are bound to vitellogenin and other yolk proteins. The present review reveals that aquatic species, especially fishes, are negatively affected by exposure to emerging PFASs. Additionally, the effects of PFAS pollution on aquatic ecosystems were investigated by evaluating a number of characteristics, including extracellular polymeric substances (EPSs) and chlorophyll content as well as the diversity of the microorganisms in the biofilms. Therefore, this review will provide crucial information on the possible adverse effects of PFASs on fish growth, reproduction, gut microbial dysbiosis, and its potential endocrine disruption. This information aims to help the researchers and academicians work and come up with possible remedial measures to protect aquatic ecosystems as future works need to be focus on techno-economic assessment, life cycle assessment, and multi criteria decision analysis systems that screen PFAS-containing samples. New innovative methods requires further development to reach detection at the permissible regulatory limits

Identification of molecular markers in Labeo rohita towards better carbohydrate utilization

The contribution of aquaculture products in providing nutritional and food security to human is increasing expeditiously with the increase in animal protein demand. Feed cost contributes more than 60% of the cost of aquaculture production. Henceforth, formulation of cheap fish feed is one of the greatest challenges in aquaculture industry. Carbohydrates are the cheap source of dietary energy. So their level of utilization in fish is an exciting area in research for decreasing the fish feed cost.  Molecular markers such as microsatellite and single nucleotide polymorphism (SNP) are used for genetic mapping, quantitative trait loci identification and genome-wide association studies in several aquaculture species. In this experiment, SNPs and microsatellite markers linked to carbohydrate utilization in Labeo rohita were identified. Liver tissue samples of Labeo rohita and Labeo bata were collected from individuals fed with a customized diet with 40% carbohydrate for a period of 21 days. RNA was extracted and cDNA library was prepared and sequenced on Illumina NextSeq 500 platform. 7.5 GB of data was generated from each species. Assembly of rohu data resulted in 70, 225 contigs, out of which 6284 microsatellite markers were identified. Among which, 3838, 1817, 488, 132 and 9 were di-, tri-, tetra-, penta- and hexa-repeats, respectively. Primer modelling was successful for 4190 sequences. Similarly, 2, 14, 071 SNPs were identified using CLC bio v7.0.4 and utilizing Illumina reads obtained from Labeo bata. This study can be helpful in efficient use of carbohydrate in Labeo species for decreasing feed cost globally

Growth Performance, Feeding Ecology and Prey Preference of Bagrid Catfish, Mystus tengara (Hamilton, 1822) in Low Saline Polyculture Ponds of Indian Sundarbans

Growth performances, feeding ecology and prey preferences of Mystus tengara (Hamilton, 1822) reared in low saline homestead traditional polyculture ponds in Sundarbans were studied for 12 months. Mixed carp early fingerlings (4.98±0.61 cm, 1.09±0.26 g) @ 14000 nos ha-1 and wild collected mixed bagrid catfish juveniles (5.09±0.48 cm, 1.38±0.11 g) including M. tengara were stocked @ 5000 juveniles ha-1. Farm yard manure @ 200 kg ha-1 was applied monthly and household dining wastes (11.37±2.08 kg ha-1 day-1) were thrown in the ponds almost daily following traditional practice. Fishes attained 31.56±2.08 g (13.92±0.88 cm) with specific growth rate of 0.95±0.15 % day-1 and exponent value of Length-Weight Relationship (b=2.99) indicated isometric growth. Numeric order of dominance of prey groups in water were Chlorophyceae, Myxophyceae, Bacillariophyceae, Insect parts and larvae, Copepods, Rotifers and Cladoceran, Fish parts and larvae, unidentified materials and Crustacean parts. Whereas, order of dominance of prey groups in stomach were Insect parts and larvae, Copepods, Myxophyceae, Rotifers and Cladoceran, Fish parts and larvae, Bacillariophyceae, Chlorophyceae, Crustacean parts and unidentified materials. Prey electivity analysis indicated significant active selection of Insect parts and larvae (E= +0.36±0.06) and Copepods (E= +0.30±0.12). Crustacean parts, Rotifers and Cladocera and Fish parts and larvae were also positively selected but were not significant. This study reveals that M. tengara is a carnivorous fish mostly preferring Insect larvae and Copepods. M. tengara can be added in low saline polyculture ponds to improve profitability and can be considered as a biological tool for Insect control.</p

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Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics

The complete mitochondrial genome of Labeo catla (Hamilton, 1822) using long read sequencing

Labeo catla is a widely cultured species in monoculture and polyculture systems of the Indian subcontinent. In this study, the complete mitochondrial genome sequence of catla was reconstructed from Oxford Nanopore sequence data. The mitochondrial genome is 16,600 bp in length (accession no. is MN830943) which is larger than the previously reported catla mitogenomes. Like other vertebrate mitochondrial genomes, it has 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. Most of the mitogenes are encoded on H-strand. Phylogenetic analysis showed that Labeo catla is more closely related to Labeo rohita than other labeo species. The catla mtgenome reported here will facilitate population genetics, phylogenetics and molecular taxonomy of Indian major carps