Photoperiod manipulation improves growth performance, haematological indices and economic returns of Indian butter catfish, Ompok bimaculatus (Bloch, 1794).

Photoperiod manipulation is emerging as an effective approach for regulating physiological functions in fish. This study aimed to assess the impact of photoperiod on the growth performance, haematological responses, and economic returns of the endangered and highly valued Indian butter catfish, Ompok bimaculatus. Fish with an average body weight of 28.60 ± 4.78 g were randomly placed in six FRP tanks, each measuring 120 × 45 × 60 cm3. Each tank contained 20 fish exposed to a light intensity of 1500 lx under different photoperiods [24:0 light: dark (L: D), 15 L: 9D, 12 L: 12D, 9 L: 15D, 0 L: 24D and a natural photoperiod (control)], and fed at a daily rate of 2% of their body weight twice daily for 60 days. The fish in the 15 L: 9D photoperiod exhibited the highest final weight (g), percentage weight gain, specific growth rate (SGR) and survival rate, while the lowest was displayed in 24 L: 0D photoperiod group. The feed conversion ratio (FCR) was at its lowest in the catfish subjected to the 15 L: 9D photoperiod. Regarding haematological parameters, the 15 L: 9D photoperiod group showed higher total erythrocyte count, total leukocyte count, haemoglobin levels, and haematocrit values compared to the other groups. Conversely, the 0 L: 24D group, which experienced prolonged darkness, exhibited the lowest values in these parameters. Moreover, the 24 L: 0D, 9 L: 15D, and 0 L: 24D groups displayed a lower mean corpuscular volume (MCV) but higher mean corpuscular haemoglobin (MCH) and mean corpuscular haemoglobin concentration (MCHC) when compared to the control group. The economic analysis revealed that O. bimaculatus reared in a moderate photoperiod (15 L: 9D) displayed better growth, feed utilization, and overall health. This finding suggests that adopting a 15 L: 9D photoperiod can lead to enhanced production and improved economic returns for farmers culturing this high-value catfish in the future.

Understanding feeding competition under laboratory conditions: Rohu (Labeo rohita) versus Amazon sailfin catfish (Pterygoplichthys spp.).

Competitive interactions between species is widely prevalent within the animal world. In this manuscript, we attempted to understand feeding competitions between the Amazon sailfin catfish, an invasive species introduced globally, and rohu, a keystone species native to several countries within southeast Asia. We used two different size classes of each species, large-size having total length (TL, from snout tip to caudal fin) of 15-20cm and fingerling having TL<6cm, and feeding duration was used as a proxy to understand competition. Our results demonstrated that feeding durations of large-size rohu were either similar or significantly (P<0.05) higher in presence of catfish when compared to trials in presence of conspecifics, indicating that large-size rohu is not a weak competitor. However, feeding durations of fingerling rohu was significantly (P<0.05) reduced in presence of both large-size and fingerling catfish, when compared to trials in presence of conspecifics. Moreover, fingerling rohu also displayed freeze (alarm) behavior in presence of the catfish. Interestingly, presence of rohu had no significant (P>0.05) impact on feeding durations of catfish. Overall, the study demonstrated that invasive catfish may behaviorally outcompete fingerling rohu, thus, threatening the sustenance of a species that is native to several freshwaters around the globe.

High Genetic Differentiation and Genetic Diversity in Endangered Mahseer Tor khudree (Sykes, 1839) as Revealed from Concatenated ATPase 6/8 and Cyt b Mitochondrial Genes.

The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species.

Effect of photoperiod on serum biochemistry, electrolytic balance, acute phase response and histopathology of butter catfish, Ompok bimaculatus (Bloch, 1794).

The present study was executed to evaluate the effect of photoperiod on serum biochemical parameters (glucose, cortisol, ALT, AST and LDH), electrolytic balance (Sodium and potassium), acute phase response (CRP) and histopathology (liver, kidney and skin) of an endangered high valued catfish, Ompok bimaculatus. Catfish (21.00 ± 1.53 cm and 30.00 ± 2.31 g) from the acclimatized stock were randomly distributed to six 120 × 45 × 60 cm3 FRP tanks (n = 20 fish per tank) and exposed to 1500 lx light intensity under different photoperiods [24:0 light: dark (L: D), 15L: 9D, 12L: 12D, 9L: 15D, 0L: 24D and a natural photoperiod (control)], and fed at a daily rate of 2% of bodyweight, twice a day for 60 days. Serum glucose, cortisol and enzymes including aspartate transaminase (AST), lactate dehydrogenase (LDH), alanine transaminase (ALT), and acute phase reactant, such as C-reactive protein (CRP) increased significantly (P < 0.05) in continuous light (24L: 0D), continuous dark (0L: 24D) and short day (9L: 15D) photoperiods, whereas in 15L: 9D and 12L:12D photoperiods, those were in decreasing trend. Serum electrolytes, i.e. potassium level was elevated and sodium level was declined in 24L: 0D, 0L: 24D and 9L: 15D photoperiod groups. Moreover, significant histological alterations in the liver, kidney and skin tissue were also evidenced in the experimented catfish. Typical polygonal hepatocytes with normal blood vessels in liver and normal organization of kidney were seen in catfish of 15L: 9D group. Histological analysis of other groups displayed nuclear degeneration, karyorrhexis, karyolysis, melanomacrophages, nuclear hypertrophy, sinusoid dilation and vacuolar degeneration in liver and hyaline droplets accumulation, granular degeneration, fragmentation of glomerulus and focal necrosis of epithelial cells in kidney. Additionally, general structure of the skin was observed in control group as well as in 15L: 9D group. Contrarily, in 24L: 0D group increased number of mucous cells and vacuoles was observed in the skin of butter catfish. In 9L: 15D and 0L: 24D photoperiods, O. bimaculatus exhibited ruptured epithelial cells, enlarged alarm cells, fat cells, necrotic cells and vacuoles in the skin tissue. The present study depicted that 15L: 9D photoperiod can induce better health of catfish, O. bimaculatus, which, in turn, can help farmers to increase the production of this high valued catfish in future.

DNA Methylation Profiling of Ovarian Tissue of Climbing Perch (Anabas testudienus) in Response to Monocrotophos Exposure.

Epigenetic modifications like DNA methylation can alter an organism's phenotype without changing its DNA sequence. Exposure to environmental toxicants has the potential to change the resilience of aquatic species. However, little information is available on the dynamics of DNA methylation in fish gonadal tissues in response to organophosphates. In the present work, reduced-representation bisulfite sequencing was performed to identify DNA methylation patterns in the ovarian tissues of Anabas testudienus exposed to organophosphates, specifically monocrotophos (MCP). Through sequencing, an average of 41,087 methylated cytosine sites were identified and distributed in different parts of genes, i.e., in transcription start sites (TSS), promoters, exons, etc. A total of 1058 and 1329 differentially methylated regions (DMRs) were detected as hyper-methylated and hypo-methylated in ovarian tissues, respectively. Utilizing whole-genome data of the climbing perch, the DMRs, and their associated overlapping genes revealed a total of 22 genes within exons, 45 genes at transcription start sites (TSS), and 218 genes in intergenic regions. Through gene ontology analysis, a total of 16 GO terms particularly involved in ovarian follicular development, response to oxidative stress, oocyte maturation, and multicellular organismal response to stress associated with reproductive biology were identified. After functional enrichment analysis, relevant DMGs such as steroid hormone biosynthesis (Cyp19a, 11-beta-HSD, 17-beta-HSD), hormone receptors (ar, esrrga), steroid metabolism (StAR), progesterone-mediated oocyte maturation (igf1ar, pgr), associated with ovarian development in climbing perch showed significant differential methylation patterns. The differentially methylated genes (DMGs) were subjected to analysis using real-time PCR, which demonstrated altered gene expression levels. This study revealed a molecular-level alteration in genes associated with ovarian development in response to chemical exposure. This work provides evidence for understanding the relationship between DNA methylation and gene regulation in response to chemicals that affect the reproductive fitness of aquatic animals.

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.

Biochemical and histopathological alterations in freshwater fish, Labeo rohita (Hamilton, 1822) upon chronic exposure to a commonly used hopper insecticide, triflumezopyrim.

The present study has been carried out to see the long-term effects of triflumezopyrim in an Indian major carp, Labeo rohita. Fishes were exposed to sub-lethal concentrations triflumezopyrim insecticide, 1.41 ppm (Treatment 1), 3.27 ppm (Treatment 2) and 4.97 ppm (Treatment 3), respectively for 21 days. The liver, kidney, gills, muscle, and brain tissues of the fish were examined for physiological parameters and biochemical parameters such as catalase (CAT), superoxide dismutase (SOD), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), alanine aminotransaminase (ALT), aspartate aminotransaminase (AST), acetylcholinessterase (AChE), and hexokinase. After 21 days of exposure, the activity CAT, SOD, LDH, MDH and ALT got increased and a drop in the activity of total protein was found in all treatment groups in comparison to the control group. Long-term triflumezopyrim exposure increased ROS production, ultimately leading to oxidative cell damage and inhibiting the antioxidant capabilities of the fish tissues. Histopathological analysis showed alteration in different tissues structures of pesticide treated fishes. Fishes exposed to highest sublethal concentration of the pesticide showed higher damage rate. The present study demonstrated that chronic exposure of fish to different sublethal concentration of triflumezopyrim exerts detrimental effect on the organism.

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.

Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture.

Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.

Dietary brewer's spent yeast enhances growth, hematological parameters, and innate immune responses at reducing fishmeal concentration in the diet of climbing perch, Anabas testudineus fingerlings.

A 60-day feeding trial was conducted to optimally reduce the fishmeal level in climbing perch (Anabas testudineus) fingerling diet using a dietary brewer's spent yeast biomass (BSY) based diet. In this study, five isonitrogenous (35% CP) and isocaloric (19.15 MJ/Kg) feeds were prepared by replacing 0 (BSY0), 25% (BSY25), 50% (BSY50), 75% (BSY75) and 100% (BSY100) of fishmeal protein using BSY protein. A total of 225 numbers of uniform-sized climbing perch fingerlings (3.29 ± 0.09 g) were randomly stocked in the 15 rectangular FRP (Fiber-reinforced plastic) tanks (150 L capacity). The experimental fish were fed twice daily at 4% BW for the first fortnight and later reduced to 3% BW based on satiation. At the end of the feeding trial, the weight gain (WG) of fish increased with the increasing BSY incorporation rates corresponding to fishmeal content and peaked at 77.88%, and beyond that, WG decreased. Food conversion ratios decreased as dietary BSY levels increased and peaked at 76.28%. All other growth and feed utilization parameters followed a similar trend of weight gain. Hepatosomatic index (HSI) and viscerosomatic index (VSI), A:G ratio, serum catalase activity, and monocytes were unaffected and the total serum protein, albumin, globulin, alanine aminotransferase (ALT), aspartate aminotransferase (AST), respiratory burst activity, lysozyme levels, myeloperoxidase activity, hemoglobulin, red blood cells, white blood cells, neutrophils, eosinophils, lymphocytes, and gut protease activities were increased significantly (P < 0.05) with the increasing replacement levels and peaked between 25 and 75%. The serum SOD activity and total platelets were decreased, whereas the serum uric acid and gut amylase activities were increased significantly to the increasing levels of FM replacement in the diets (P < 0.05). Among treatments, the BSY100 resulted in an overall poor growth response combined with relatively reduced values in nearly all biochemical parameters. The whole-body composition was nearly unaffected. The integrated biomarker response of various biochemical indicators from the different treatments has shown that the 50% fishmeal protein can be optimally replaced by BSY, which would cause an 18% reduction in the Economic conversion ratio (ECR) and -270.28 gCO2e- reduction in carbon footprint value per kg of climbing perch fingerlings production.

Tenets in Microbial Endocrinology: A New Vista in Teleost Reproduction.

Climate vulnerability and induced changes in physico-chemical properties of aquatic environment can bring impairment in metabolism, physiology and reproduction in teleost. Variation in environmental stimuli mainly acts on reproduction by interfering with steroidogenesis, gametogenesis and embryogenesis. The control on reproductive function in captivity is essential for the sustainability of aquaculture production. There are more than 3,000 teleost species across the globe having commercial importance; however, adequate quality and quantity of seed production have been the biggest bottleneck. Probiotics are widely used in aquaculture as a growth promoter, stress tolerance, pathogen inhibition, nutrient digestibility and metabolism, reproductive performance and gamete quality. As the gut microbiota exerts various effects on the intestinal milieu which influences distant organs and pathways, therefore it is considered to be a full-fledged endocrine organ. Researches on Gut-Brain-Gonad axis (GBG axis) and its importance on physiology and reproduction have already been highlighted for higher mammals; however, the study on fish physiology and reproduction is limited. While looking into the paucity of information, we have attempted to review the present status of microbiome and its interaction between the brain and gut. This review will address a process of the microbiome physiological mechanism involved in fish reproduction. The gut microbiota influences the BPG axis through a wide variety of compounds, including neuropeptides, neurotransmitter homologs and transmitters. Currently, research is being conducted to determine the precise process by which gut microbial composition influences brain function in fish. The gut-brain bidirectional interaction can influence brain biochemistry such as GABA, serotonin and tryptophan metabolites which play significant roles in CNS regulation. This review summarizes the fact, how microbes from gut, skin and other parts of the body influence fish reproduction through the Gut-Brain-Gonad axis.

Aquaculture omics: An update on the current status of research and data analysis.

Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.

Structural, genomic information and computational analysis of emerging coronavirus (SARS-CoV-2).

Background: The emerging viral pandemic worldwide is associated with a novel coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). This virus is said to emerge from its epidemic center in Wuhan, China, in 2019. Coronaviruses (CoVs) are single-stranded, giant, enveloped RNA viruses that come under the family of coronaviridae and order Nidovirales which are the crucial pathogens for humans and other vertebrates. Main body: Coronaviruses are divided into several subfamilies and genera based on the genomic structure and phylogenetic relationship. The name corona is raised due to the presence of spike protein on the envelope of the virus. The structural and genomic study revealed that the total genome size of SARS-CoV-2 is from 29.8 kb to 29.9 kb. The spike protein (S) is a glycoprotein that attaches to the receptor of host cells for entry into the host cell, followed by the attachment of virus RNA to the host ribosome for translation. The phylogenetic analysis of SARS-CoV-2 revealed the similarity (75-88%) with bat SARS-like coronavirus. Conclusion: The sign and symptoms of novel severe acute respiratory syndrome coronavirus 2 are also discussed in this paper. The worldwide outbreak and prevention from severe acute respiratory syndrome coronavirus 2 are overviewed in the present article. The latest variant of coronavirus and the status of vaccines are also overviewed in the present article.

Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing.

BACKGROUND: Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. RESULT: A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. CONCLUSION: This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

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.

Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing.

Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved 'Jayanti rohu' Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPARγ. The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose efficiency in carp species, for sustainable and cost-effective aquaculture production.

The draft genome of Labeo catla.

OBJECTIVE: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time. DATA DESCRIPTION: A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes.

Revealing liver specific microRNAs linked with carbohydrate metabolism of farmed carp, Labeo rohita (Hamilton, 1822).

The role of microRNA in gene regulation during developmental biology has been well depicted in several organisms. The present study was performed to investigate miRNAs role in the liver tissues during carbohydrate metabolism and their targets in the farmed carp rohu, Labeo rohita, which is economically important species in aquaculture. Using Illumina-HiSeq technology, a total of 22,612,316; 44,316,046 and 13,338,434 clean reads were obtained from three small-RNA libraries. We have identified 138 conserved and 161 novel miRNAs and studies revealed that miR-22, miR-122, miR-365, miR-200, and miR-146 are involved in carbohydrate metabolism. Further analysis depicted mature miRNA and their predicted target sites in genes that were involved in developmental biology, cellular activities, transportation, etc. This is the first report of the presence of miRNAs in liver tissue of rohu and their comparative profile linked with metabolism serves as a vital resource as a biomarker.

Liver-Specific microRNA Identification in Farmed Carp, Labeo bata (Hamilton, 1822), Fed with Starch Diet Using High-Throughput Sequencing.

The liver is an important central organ, which controls carbohydrate metabolism through maintaining glucose homeostasis by a tightly regulated system of genes or enzymes. The microRNAs are small non-coding RNAs playing an important role in the regulation of genes associated with developmental biology, physiology, metabolism, etc. Thus, in this study, we have intended to detect liver-specific microRNAs in farmed carp, Labeo bata, upon being fed a diet with different levels of carbohydrates. Here, we have conducted the experiment for 45 days using fingerlings of farmed carp fed with 20% (control), 40%, and 60% gelatinized starch levels. The liver tissues were collected from each treatment and processed for RNA isolation, small RNA library preparation, and high-throughput sequencing using Illumina NexSeq500. Through sequencing, 15,779,417 reads in 20% CHO, 13,959,039 in 40% CHO, and 13,661,950 in 60% CHO reads were generated for control and treated fishes using three small RNA libraries. We have investigated 445 novel and 231 conserved microRNAs in 20%, 40%, and 60% carbohydrate (CHO), respectively, through computational analysis. The differential expression analysis of miRNAs was carried out between different treatments compared with control and this study depicted 117 known and 114 novel miRNA genes involved in carbohydrate metabolic pathways. Further, target prediction and gene ontology analysis revealed that miRNAs were involved in several pathways such as signaling pathway, G protein pathway, complement receptor-mediated pathway, dopamine receptor signaling pathway, epidermal growth factor pathway, and notch signaling pathway. The predicted miRNA sites in targeted genes were associated with cellular activities, developmental biology, DNA binding, Golgi apparatus, extracellular region, catalytic activity, MAPK cascade, etc. Overall, we have generated a vital resource of liver-specific miRNAs involved in metabolic gene regulation. These studies further will help develop miRNA inhibitors to study their role during carbohydrate metabolism in farmed carp.

Dynamics of expression of antibacterial and antioxidant defence genes in Indian major carp, Labeo rohita in response to Aeromonas hydrophila infection.

Cells produce large number of antioxidant molecules to prevent reactive oxygen species-induced self-damage during microbial assault while generating simultaneously number of antimicrobial molecules to target the pathogen. The present study was aimed at looking into molecules involved in antibacterial and self-protection mechanism of a host Labeo rohita when challenged with a pathogenic bacterium Aeromonas hydrophila. Expression profiles of few of the important host antibacterial genes viz., inducible nitric oxide synthase (iNOS), lysozyme G (LysoG), apolipoprotein A-I (ApoA-I) and hepcidin, and self-defence anti-oxidant genes viz., manganese superoxide dismutase (MnSOD), catalase and glutathione peroxidases (GPx3) were examined in skin and muscle tissues of bacteria challenged fish. Transcription levels of iNOS, LysoG, ApoA-I, hepcidin, catalase, GPx3 and MnSOD were significantly upregulated (P < 0.05) in both tissues at different time points post-bacterial challenge. Increased expression of antibacterial genes in the muscle and skin clearly explains strong defensive mechanism activated in fish tissues in terms of both oxygen-dependent (iNOS) and independent (lysozyme) ways of microbe reduction, and bacterial lysis via production of antimicrobial molecules (ApoA-I and hepcidin) in the host. Simultaneous upregulation of MnSOD, GPx3 and catalase genes explains their involvement in patrolling the cells with regulated production of reactive oxygen species and keeping at a safe level to protect the host's own cells from oxidative damage.