The shrimp industry has seen remarkable growth over the last four decades in India and the culture of P. monodon is experiencing a resurgence due to shifts in market demand, ecological considerations and broodstock and farming management. This study employs a transcriptomics approach to investigate the gene expression profiles of Penaeus monodon from two different origins. Large-scale transcriptomes generated 130,684 super-transcripts (GC 39.18%), with 92.94% BUSCO completeness and 39,974 have functional annotations, and 125 GO terms were identified. A total of 41,108 annotated transcripts examined, 19,637 SSR were identified and SNP mining resulted in identification of 69,028 SNPs with 26,785 indels, which included SNP within the genes of known function were found to be 504 nonsynonymous and 176 synonymous. Differentially expressed 79 genes between two locations fell under 12 GO terms, of which 4 GO terms were under biological process with 5 genes under glycolytic process and 4 under gluconeogenesis. Thus, the cSSRs and cSNP associated with coding genes identified could be a part of the marker set, which would be useful as marker loci or candidate genes to be use in construction of smaller SNP arrays for pedigree analysis and/or genomic selections.

Neolissochilus pnar, identified as the world’s largest cave fish, belongs to the family Cyprinidae and is endemic to one of India’s biodiversity hotspots, specifically in the limestones caves of Meghalaya, India. This species is notably different from its closely related counterpart, Neolissochilus hexastichus, primarily in its lack of pigmentation and the absence or reduction of eyes. While juvenile N. pnar may have small or reduced eyes, adults exhibit a absence of external ocular features. Thus, genome sequence resources of this species would be an effective tool for bioprospecting and mining of novel genes responsible for the important traits. In this study, genome sequencing was done through long reads technology (PacBio) and high quality draft genome assembly, of 1.56 Gb in size with 1,423 contigs, N50 of 18.990 Mb was generated, which showed 99% (BUSCO) genome completenes. The genome assembly contains 44.30% repetitive elements, 1,416,376 SSRs, and 37,559 functionally annotated genes. Single-copy orthologs (SOGs) analysis indicated N. pnar to be in the same cluster with other cave dwelling Cyprinids used in the sudy.The extensive genomic information generated in present study would be a useful resource for understanding evolutionaly significance and genes governing the traits including the body colour and eye development in Mahseer species.

Freshwater aquaculture in India mainly relies on three Indian major carps, with rohu (Labeo rohita) being the most important species in polyculture systems. Quality hatchery seed production plays a vital role in enhancing aquaculture production. However, unorganised and poorly managed broodstock in hatcheries affect the seed quality leading to economic losses for farmers. These challenges can be tackled through the establishment ofscientifically managed brooders. Developing an optimal female-to-male ratio for brooders requires maintenance of a large number of individuals for an entire year, as sex can only be determined at the maturity stage only. To address this issue, the current study developed a molecular marker and a Loop Mediated Isothermal Amplification (LAMP) assay for early gender determination, enabling the identification of the gender of rohu, even at the fingerling stage. This marker would enable the hatchery professionals and farmers to maintain an optimal male-to-female ratio from the early stage, leading to better broodstock management, reduced inbreeding and enhanced seed quality and quantity, which would ultimately benefit the aquaculture industry and promote sustainable fish farming practices in India Keywords: Early gender determination, LAMP, Quality hatchery seed, Rohu, Sex-specific marker

Ammonia is a major environmental pollutant in freshwater aquatic systems, significantly impacting the survival and growth of aquatic organisms. In the present study, we investigated the changes in blood physiological parameters and gill structure in Heteropneustes fossilis under hyper-ammonia stress (25 mM NH4Cl) for experimental exposure durations of 1, 3, 6 and 9 h, as well as after a 24 h recovery period in normal water following 9 h of exposure (9h+N). Results indicated a progressive increase in blood ammonia levels up to 6 h, with fluctuations thereafter, however, even after recovery period, it was significantly more than that of control (p<0.05). This was accompanied by a corresponding rise in urea concentration, reaching up to a four-fold increase at 6 h exposure, followed by a decrease at 9 h and to that of control level at 9h+N. Blood glucose exhibited a continuous increase with prolonged exposure till 9 h exposure and then significantly decreased during recovery period. Serum glutamic-oxalacetic transaminase (SCOT) showed significant increase at 6 h, while serum glutamic-pyruvic transaminase (SGPT) at both 3 and 6 h. There was a fluctuating pattern of serum lactate dehydrogenase (LDH). No significant changes were observed for haemoglobin, haematocrit, serum protein and serum creatinine. Histological examination of gill tissues revealed extensive damage, particularly after 9 h of ammonia exposure. At this time point, 78% of the gills exhibited severe structural alterations, including the loss of secondary lamellae tips and 51% showed oedematous changes.

Background: Common carp is the third most widely farmed fish, globally. It is tolerant to cold stress and resistant to EUS pathogenic infections, when it faces lower temperatures. In the present study, common carp was used as the research model to examine the interplay of temperature and immunity. Methods: High-throughput transcriptome sequencing was used to study the differential gene expression profiles of kidney tissues, reared at two different temperatures; 30oC (control) and 20oC (experimental). Result: Out of 588 differential expressed genes (DEGs), genes under GO terms for abiotic stress were categorised under oxidative stress, response to heat, mechanical stimulus and cold. Fifteen DEGs were found under the immune category, which out of which twelve were under the innate immune category, included 5 lectin family members and 1 tumor necrosis factor. The information generated in common carp would form a transcriptome resource for tolerance to abiotic stress. At the lower temperature studied, modulatory immune response, through the cytokine-cytokine interaction pathway, seems to be a major player, besides higher energy production, up-regulated stress responses, cell growth and survival. These results have the potential to be developed into bio-markers for temperature stress tolerance and modulatory immune responses in aquaculture pond production during the lower temperature conditions.

The study of the mitogenome of Neolissochilus pnar, the world’s largest cave fish, uncovered its structural features, gene content and evolutionary dynamics within mahseer. Its mitogenome is of 16,440 base pairs, resembling those of the teleost species and exhibits a high degree of conservation in genes arrangement. It comprises 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs) and a control region. Notably, the distribution of genes on the L- and H-strands is consistent with that of the typical teleost. The study reveals the lengths and variations in PCGs in mahseer species, displaying a range from 164 to 11,404 bp. The tRNA and rRNA genes and the control region also demonstrate conservation among the species. A robust phylogenetic analysis, employing Bayesian and ASAP methods, supports the classification of N. pnar within the Neolissochilus genus and validates the taxonomic status of this species. Selection pressure analyses indicate positive selection in seven genes: COII , COIII, Cytb, ND1, ND2, ND5 and ND6. These findings suggest the dynamic nature of mitochondrial evolution in mahseer species. The purifying selection preserve essential mitochondrial functions, and additionally, the specific sites in ND5 and ND6 genes undergo episodic positive or diversifying selection, likely in response to environmental changes or selective pressures. In conclusion, this research enriches our understanding of N. pnar visa-vis other mahseers’ mitogenomes, pointing to its possible mitogenome evolution to adaptation to cave environment.

Genetic diversity and population structure are essential aspects for understanding the evolutionary history, conservation as well as species diversification in freshwater aquaculture. This study aimed to investigate the genetic variation and population structure of Ompok bimaculatus, commonly known as the butter catfish, using mitochondrial DNA markers, i.e., cytochrome b and ATPase 6/8 genes, as well as their concatenated sequences. The Cytochrome b, ATPase 6/8 and combined genes revealed a large number of haplotypes and low nucleotide diversities. AMOVA results indicated a high level of variance, attributed to differences within populations with significant FST values and the presence of population structure in natural populations. High levels of genetic differentiation within populations of O. bimaculatus were observed. Population-specific haplotype highlighted genetic differentiation among the four studied natural populations, which indicated the presence of distinct genetic characteristics within each population. Molecular variance analysis and pairwise FST values based on cyt b (FST: 0.02227 to 0.58236), ATPase 6/8 (FST: 0.000 to 0.28410) and concatenated (FST: 0.00504 to 0.41511 (Gomti-Kaveri)) further confirmed the genetic differentiation and population structure. The findings of this study provide valuable insights into the species’ genetic characteristics, which can aid in the development of targeted conservation strategies to preserve genetic diversity and ensure the long-term viability of O. bimaculatus populations.

Common carp is a widely farmed and economically important freshwater fish species that thrives in diverse aquatic habitats. In the present study, two temperature conditions were used to maximise and capture the transcript repertoire. High-throughput transcriptome sequencing data were used to identify transcriptome and immune related genes, as well as associated simple sequence repeats (SSRs). A total of 67.44 GB of high-quality paired-end reads were generated, which were then assembled and clustered into 133,419 transcripts with a GC content of 51.63%. SSRs were identified in 6,245 genes, with the highest number of dinucleotide repeats (33.42%), followed by tri-nucleotide repeats (13.24%) and tetra/penta/hexa/septa/nona/deca nucleotide repeats (2.43%). Further classification analysis identified 1,355 immune genes, of which the largest groups under innate immune response were co-stimulatory molecules (234), followed by cytokines (203) and RIG-I-like receptors (186). Adaptive immune genes included Immunoglobulins (104) and Interleukin (106), followed by negative regulators of immune system (60). Among the immune categories, 142 SSRs were identified in innate immune genes, 67 in adaptive immune genes and 6 in negative regulators. The generated data of transcriptome-derived SSRs in this study offer a wealth of marker resources related to immune mechanisms for molecular marker development and characterization of germplasm, which will aid in understanding genetic diversity and their application in molecular marker assisted breeding of C. carpio for improving aquaculture sustainability.

This article presents the development of an online information system for aquatic genetic resources of India named, Aquatic Genetic Resource Information System of India (AqGRISI). The system is designed with integrated data and user management capabilities. The growing importance of online information systems in management of the biological diversity and agrobiodiversity has invited attention of the researchers to make such information publicly accessible through digital platforms. AqGRISI is developed as a concept framework and validated for use and is presently accessible at URL: https://aqgrisi.nbfgr.res.in/#/. It is designed to manage compiled data from authenticated published sources, using a database management system and programming for online information presentation. It ensures accessibility through web technologies within the Windows operating environment. The system will provide comprehensive information of the fish species, from a single page, covering various aspects such as biology, distribution, taxonomy and type specimens. The database is integrated with information from in-house databases such as HRGFish, FMiR, FBIS, FishKaryome, and FishMicrosat along with patent information. Additionally, AqGRISI is linked to other nationally and internationally significant online resources and serves as a repository for fish accessions preserved in the National Fish Museum and Repository. It includes data on cell lines and facilitates the intake of information on the voucher specimens, cryopreserved sperm accessions and tagged fish species maintained at live germplasm resource centers of ICAR-National Bureau of Fish Genetic Resources. AqGRISI is enriched with dynamic digital maps featuring geospatially tagged type specimens with details on species occurrence. These type specimens are also linked to the National Museum of Natural History, Paris, France, allowing users to access images of holotypea, syntypea, paratypes and neotypes along with relevant taxonomic information. Among the available online resources on aquatic animals, AqGRISI envisages to serve as a centralised platform providing researchers, academicians, managers, planners and other stakeholders, with a single-point access to information on fish species. Currently the system is validated for information on finfish species; however, future expansions will enable customisation of this conceptual framework to include other components of aquatic biodiversity, such as shellfish, seaweeds and more. The concept framework also holds the possibility for usage by other countries especially in Asia, which share ancestral aquatic gene pools. Keywords: Aquatic Genetic Resource Information System, Database, Fish, India

Clarias dussumieri, a near threatened freshwater catfish, is endemic to peninsular India and has aquaculture potential. Unlike its sister species, C. magur, the male fish needs not be sacrificed during captive breeding. Thus, the generation of genomic information of this species becomes significant for effective genome mining through the bioprospecting of novel genes for important production traits. In this study, the genome assembly was undertaken to address this gap by generating high quality chromosome level genome assembly using PacBio long reads and Hi-C scaffolding. The total assembled genome was found to be 918.72 Mb in size and showed 95.23% completeness. Its characterization exhibited 41.46% repeats, 1,174,725 SSRs and 25,369 predicted genes with functional annotations. The Single copy orthologs analysis placed C. dussumieri in a distinct position with C. magur. The comprehensive genomic information offers resources for comparative genomics with other Clarias species for improvement of economic traits.

Hemibagrus punctatus (Jerdon, 1849) is a critically endangered bagrid catfish endemic to the Western Ghats of India, whose population is declining due to anthropogenic activities. The current study aims to compare the mitogenome of H. punctatus with that of other Bagrid catfishes and provide insights into their evolutionary relationships. Samples were collected from Hemmige Karnataka, India. In the present study, the mitogenome of H. punctatus was successfully assembled, and its phylogenetic relationships with other Bagridae species were studied. The total genomic DNA of samples was extracted following the phenol–chloroform isoamyl alcohol method. Samples were sequenced, and the Illumina paired-end reads were assembled to a contig length of 16,517 bp. The mitochondrial genome was annotated using MitoFish and MitoAnnotator (Iwasaki et al., 2013). A robust phylogenetic analysis employing NJ (Maximum composite likelihood) and ASAP methods supports the classification of H. punctatus within the Bagridae family, which validates the taxonomic status of this species. In conclusion, this research enriches our understanding of H. punctatus mitogenome, shedding light on its evolutionary dynamics within the Bagridae family and contributing to the broader knowledge of mitochondrial genes in the context of evolutionary biology. The study’s findings contribute to a better understanding of the mitogenome of H. punctatus and provide insights into the evolutionary relationships within other Hemibagrids.

The freshwater aquaculture species, Cirrhinus mrigala, commonly known as mrigal, holds significance in the carp-dominated aquaculture system, globally. Despite constituting 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. However, its genome and associated information is not available. This study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, revealed 39,091 genes with functional annotations. The orthology analysis based on direct orthologs and single copy ortholgs places C. mrigala in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.

The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 x 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.

The Asian seabass, Lates calcarifer, is an important species in the Asia-Pacific region and is cultured widely. The growing demand for its seed has led to an increase in commercial introductions from other nations to India. In the current study, we developed novel microsatellite markers and analysed the natural genetic diversity of L. calcarifer. The whole genome was sequenced on PacBio RSII to generate low-depth data. A total of 519 microsatellites were mined from the assembled genome. Genetic diversity and population structure were analysed in L. calcarifer using the newly developed set of microsatellite loci. Most of the loci exhibited high polymorphic information content (PIC) with an average of 0.637. A total of 213 alleles were detected. The mean observed and expected heterozygosity were 0.548 and 0.679, respectively. The probability of identity (PID/PIDsib) demonstrated the utility of loci for individual identification. Moderate to high levels of genetic diversity was evident, with an overall F-ST of 0.031. The pairwise F-ST and AMOVA results showed significant divergence among the populations and suggested that the samples were not drawn from a single gene pool. The clustering (PCoA and DAPC) suggested the possibility of the presence of distinct genetic populations on Indian coasts. The study developed a validated marker set for deciphering genetic diversity and will be useful for various purposes of conservation and aquaculture, such as identifying selection signatures, parentage assignment, and genetic improvement.

Background Butter catfish ( Ompok bimaculatus ) is a preferred species in South East Asia, with huge aquaculture potential. However, there is limited information about genetic stock composition due to insufficient markers. The goal of this study was to develop de novo microsatellite markers. Methods and results For sequencing, genomic SMRT bell libraries (1.5 Kbp size) were prepared for O. bimaculatus . A total of 114 SSR containing sequences were used for primer designing. Polymorphic loci were validated by genotyping 83 individuals from four distant riverine populations, viz., Brahmaputra, Bichiya, Gomti and Kaveri. A total of 30 microsatellite loci were polymorphic, of which five were found to be associated with functional genes and eight (four positive and four negative) loci were found to be under selection pressure. A total of 115 alleles were detected in all loci and PIC ranged from 0.539 to 0.927 and pair-wise F ST values from 0.1267 to 0.26002 (p < 0.001), with an overall F ST value of 0.17047, indicating the presence of population sub-structure. Cross-species transferability of 29 loci (96.67%) was successful in congener species, Ompok pabda . Conclusion The novel SSR markers developed in this study would facilitate stock characterization of natural populations, to be used in future selection breeding programs and planning conservation strategies in these species. Identified non-neutral markers will give insights into the effect of local adaptation on genetic differentiation in the natural population of this species.

Tenualosa ilisha (Hilsa shad), an anadromous fish, usually inhabits coastal and estuarine waters, and migrates to freshwater for spawning. In this study, large-scale gill transcriptome analyses from three salinity regions, i.e. , fresh, brackish and marine water, revealed 3277 differentially expressed genes (DEGs), out of which 232 were found to be common between marine vs freshwater and brackish vs freshwater. These genes were mapped into 54 KEGG Pathways, and the most significant of these were focal adhesion, adherens junction, tight junction, and PI3K-Akt signaling pathways. A total of 24 osmoregulatory genes were found to be differentially expressed in different habitats. The gene members of slc 16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes ( cldn11 & cldn10 ), transmembrane tm56b , and voltage-gated potassium channel gene kcna 10 were downregulated in freshwater samples, as compared to that of brackish and marine environment. Protein–protein interaction (PPI) network analysis of 232 DEGs showed 101 genes to be involved in PPI, while fn1 gene was found to be interacting with the highest number of genes (36). Twenty-five hub genes belonged to 12 functional groups, with muscle structure development with seven genes, forming the major group. These results provided valuable information about the genes, potentially involved in the molecular mechanisms regulating water homeostasis in gills, during migration for spawning and low-salinity adaptation in Hilsa shad. These genes may form the basis for the bio-marker development for adaptation to the stress levied by major environmental changes, due to hatchery/culture conditions.

Fish stocks that are grown under diverse environmental conditions have different biometric relationships and growth patterns. The biometric length-weight relationship (LWR) is an essential fishery assessment tool, as fish growth is continuous and depends on genetic and environmental factors. The present study attempts to understand the LWR of the flathead grey mullet, Mugil cephalus Linnaeus, 1758, from different locations. The study area encompassed its distribution in the wild across freshwater location (one), coastal habitats (eight locations), and estuaries (six locations) in India to determine the relationship between various environmental parameters. Specimens (n = 476) of M. cephalus were collected from commercial catches and the length and weight of individual specimens were recorded. Monthly data from the study locations were extracted for nine environmental variables from the datasets downloaded from the Physical Oceanography Distributed Active Archive Center (PO.DAAC) and the Copernicus Marine Environment Monitoring Service (CMEMS) over 16 years (2002 to 2017) on the Geographical Information System platform. The parameters of the LWR, intercept ‘a’ and slope or regression coefficient ‘b’, varied from 0.005321 to 0.22182 and 2.235 to 3.173, respectively. The condition factor ranged from 0.92 to 1.41. The partial least squares (PLS) score scatter plot matrix indicated differences in the environmental variables between the locations. PLS analysis of the regression coefficient and environment parameters revealed that certain environment variables viz., sea surface temperature, salinity, dissolved oxygen, nitrate, and phosphate, played a positive role. However, chlorophyll, pH, silicate, and iron played a negative role in influencing weight growth across various locations. The results revealed that the M. cephalus specimens from three locations, Mandapam, Karwar, and Ratnagiri, possessed significantly higher fitness to their environment than those from the other six locations. The PLS model can be used to predict weight growth under the various environmental conditions of different ecosystems. The three identified locations are useful sites for the mariculture of this species considering their growth performance, the environmental variables, and their interactions. The results of this study will improve the management and conservation of exploited stocks in regions affected by climate change. Our results will also aid in making environment clearance decisions for coastal development projects and will improve the efficiency of mariculture systems.

The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.