Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach.

BACKGROUND: 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. METHODS AND RESULTS: 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. CONCLUSIONS: 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.

Evaluating the influence of environmental variables on the length-weight relationship and prediction modelling in flathead grey mullet, Mugil cephalus Linnaeus, 1758.

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.

Development of novel microsatellite markers for population differentiation and detection of natural selection in wild populations of butter catfish, Ompok bimaculatus (Bloch, 1794).

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 FST values from 0.1267 to 0.26002 (p < 0.001), with an overall FST 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.

Transcriptome Analysis Revealed Osmoregulation Related Regulatory Networks and Hub Genes in the Gills of Hilsa shad, Tenualosa ilisha, during the Migratory Osmotic Stress.

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 slc16 and slc2 families showed a dissimilar pattern of expressions, while two claudin genes (cldn11 & cldn10), transmembrane tm56b, and voltage-gated potassium channel gene kcna10 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.

Quantitative assessment of sediment delivery and retention in four watersheds in the Godavari River Basin, India, using InVEST model - an aquatic ecosystem services perspective.

Sediment export and retention are important ecosystem processes in any landscape causing soil erosion and sediment loading in waterways consequently affecting the health of aquatic habitats downstream. The present study quantifies sediment export and retention in four watersheds, viz., Hivra, Satrapur, Konta, and Jagdalpur in the Godavari River Basin, India, using Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) ecosystem service modelling tool. The  results revealed that the sediment export yields ranged from 0.75 (Hivra) to 2.77 t/ha/year (Jagdalpur). The mean deviation between modelled values and observed sediment export yield was - 11.11%, which indicated good prediction by the model. The sediment retention ranged from 16.04 (Hivra) to 101.52 t/ha/year (Konta). Most sediment export and retention occurred on cropland or shrubland land use land cover types in all four watersheds. For decision making on soil conservation, soil loss tolerance limits have been established for these watersheds. For aquatic habitats, sediment concentration is considered more important than the total annual sediment export, since water turbidity is an important determinant of water quality, and the aquatic lives therein. Therefore, the temporal distribution of rainfall and corresponding sediment export becomes important, since these two factors determine the sediment concentration as well as turbidity in the waterbody. In current study, "Precipitation Concentration Index adjusted Sediment Export Yield Index" was developed to account for the effects of the temporal rainfall distribution and its impact on sediment export. The index for four watersheds was quantified (Hivra > Satrapur > Konta > Jagdalpur), which is concordant to the turbidity values reported by respective gauge stations. Thus, the proposed index can efficiently capture the impact of temporal rainfall distribution on sediment export, and consequently its effect on water turbidity. The study revealed the potential of InVEST model to quantify the sediment export and retention in the watersheds studied. Together with the proposed index, it would help the policy makers in making informed decisions for planning conservation strategies for aquatic biodiversity.

Anthropogenic risk assessment of riverine habitat using geospatial modelling tools for conservation and restoration planning: a case study from a tropical river Pranhita, India.

The riverine ecosystem provides multiple benefits to human community and contributes to the sustainable development of the ecoregion. The growing dependency on these ecosystems has largely contributed to aggravating the ecological risks, habitat degradation, and loss of ecosystem services. The present study evaluates the ecological risk emanating from nine anthropogenic stressors including river use, hydro-morphology, catchment pollution, and biological stressor on river Pranhita in Godavari Basin of Peninsular India using InVEST (Integrated Valuation of Ecosystem Services and Tradeoffs) Habitat Risk Assessment model. The primary field survey, remote sensing, and secondary data-assisted spatial modelling results revealed low ecological risk (R = 0.65 of 3) in river Pranhita due to anthropogenic activities. Sediment loading, the inflow of nitrogen, and habitat fragmentation were the major stressors with relatively higher risk score (> 1); influence on a sizeable portion of riverine habitat (29-75% of the total area under high-risk zone) indicates the mounting threat from catchment activities. The low-risk value observed in protected river reaches as compared to unprotected areas is likely to be influenced by the abundant presence of intact riparian vegetation which mitigate the catchment stressors and minimal anthropogenic activity within protected areas. This study demonstrates the application of InVEST HRA model for ecological risk assessment of riverine ecosystems and fish assemblages along with their input data generation framework. This has the potential for prioritization of sensitive habitats based on computed ecological risk and stressor identification based on their exposure and consequences for developing appropriate mitigation measures. This model is spatially explicit and accommodates user-defined criteria for ecosystem-level assessment at a regional and national scale to facilitate the resource managers and policymakers for conservation and restoration planning and implementation of targeted management measures for sustainable development.

Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India.

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.

Description of a new Pangasius (Valenciennes, 1840) species, from the Cauvery River extends distribution range of the genus up to South Western Ghats in peninsular India.

A new species of the genus Pangasius, is described based on 17 specimens collected from the Cauvery River, India. It can be distinguished from its sister species from South and Southeast Asia, by its widely placed, small and rounded vomerine and palatine tooth plates, longer maxillary and mandibular barbels, greater vertebrae count 50 (vs. 44-48), and smaller caudal peduncle depth (6.5-8.2% SL vs. 9.89-13.09% SL). The tooth plates of the new species closely resembles that of Pangasius macronema but can be clearly distinguished from the latter by having lesser gill rakers (16-19 vs. 36-45); a smaller eye (2.4-4.4% SL vs. 5.2-9.6% SL); and larger adipose-fin base (1.5-2.9% SL vs. 0.1-1.2% SL). The mitochondrial cytochrome c oxidase (COI) gene sequence of the new species shows the genetic divergence of 3.5% and 5.1% from P. pangasius and P. silasi respectively, the two sister species found in South Asia and India. The species delimitation approaches, Poisson Tree Processes (PTP) and assemble species by automatic partitioning (ASAP) clearly resolved that the P. icaria is distinct from its sister species. Phylogenetic position of the species with its sister species was evaluated using maximum likelihood and Bayesian analysis. The discovery of this previously unknown species of genus Pangasius from the Cauvery River of peninsular India indicates important biogeographical insight that this genus migrated till the southern division of Western Ghats.

Applications of Sentinel-2 satellite data for spatio-temporal mapping of deep pools for monitoring the riverine connectivity and assessment of ecological dynamics: a case from Godavari, a tropical river in India (2016-2021).

Rivers are dynamic ecosystems with diverse habitats that require ample connectivity to ensure the flow of ecosystem services, thus empowering the sustainable development of an entire basin. Geo-spatial tools offer powerful prospects for monitoring of aquatic ecosystems. The usefulness of Sentinel-2 datasets to assess river connectivity has been explored for an un-gauged seasonal river system. The present study was undertaken in five ecologically unique river reaches viz. Wainganga, Wardha, Pranhita, Godavari-mid and Manair in Godavari Basin in the Indian Deccan Plateau to map water spread dynamics at various time scales, i.e., fortnightly, monthly, seasonal, annual and demi-decadal during 2016-2021. The maximum value of perennial water spread per square kilometre of total floodplain area (2016-2021), determined using Sentinel-2 imageries, was observed in river Wardha (0.18) followed by Pranhita (0.12) and Wainganga (0.11). The water spread showed a decreasing trend, while the number of patches in the river corridor increased over time from post-monsoon to pre-monsoon season. The copious perennial habitat with relatively larger patches, incessant flow in river Pranhita and obstructed flow, large-sized patches reported in river Wardha during summer months, hold importance in terms of providing refuge to aquatic biota. This study provides evidence for the impact of water projects on spatio-temporal water spread dynamics in Godavari Basin. The demonstrated utility of Sentinel-2 imagery coupled with gauge station measurements for river continuity assessment and deep pool mapping would aid in enhancing our understanding on environmental flow at a spatial scale, which in turn would aid in effective river management to achieve the Sustainable Development Goals. The implications of this study for sustainable environmental management and limitations are also discussed.

Transcriptome analysis revealed hub genes for muscle growth in Indian major carp, Catla catla (Hamilton, 1822).

Catla (Catla catla) is the fastest growing Indian major carp species and forms an important component of the freshwater aquaculture systems in the Indian sub-continent. The molecular mechanisms of growth of the species in response to seasonal water temperature variations hitherto are still unknown. In the current study, high-throughput transcriptome sequencing was used to study the differential gene expression pattern in catla muscle tissues between pre-winter and post-winter fingerling groups and fast-growing table size fish. Transcriptome analysis identified 1677 differentially expressed genes (DEGs) in three different growth stages and 236 common DEGs between fingerling at low temperature and table fish post-winter, including four genes under GH/IGF1 axis and 163 genes under signature for compensatory muscle growth. Molecular pathways for the mapped genes identified 42 KEGG pathways and the critical pathways under Environmental Information Processing identified were PI3K-Akt signaling, AMPK signaling pathway, Calcium signaling pathway and MAPK signaling pathway. In this study, 14 differentially expressed potential regulatory hub genes for growth were identified, for the first time and categorized into three major GO groups: unfolded protein binding, rNA processing and biogenesis and muscle development and differentiation. These regulatory hub genes, except acta1, were found to be upregulated in fast-growing table size and post-winter fingerling groups. The results provided valuable information about the key genes, with potential to be used as biomarkers of growth in breeding programs and contributed to our understanding of the molecular mechanisms and pathways regulating muscle growth, in response to temperature fluctuations and different growth stages in C. catla.

Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics.

Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species.

Genetic stock identification in Perna viridis (Linnaeus1758) from the Indian Peninsula by using microsatellite markers.

BACKGROUND: Perna viridis (Linnaeus, 1758), the Asian green mussel, is native to the Asia-Pacific region. The species is extensively distributed in the Indian subcontinent and is a candidate species for aquaculture in the Southeast Asian region. Availability of genetic information on wild populations is essential for the effective conservation and management of Perna species. The present study assessed the genetic variation and population structure across the distribution range of this species from the Indian peninsula by using microsatellite markers to determine the genetic structuring among the species. METHODS: A total of 15 microsatellite loci with M13 labeling were used for the genetic characterization of P. viridis along Indian waters. Genotyped data were analyzed using analytical software to determine the genetic stocks and understand the genetic variability across the populations. RESULTS: We identified 15 polymorphic markers to understand the genetic stocks and variability across Perna populations. The mean value of the observed heterozygosity (Hobs: 0.741) for all populations was closer to the expected heterozygosity (Hexp: 0.75). The pairwise Fst values between the west and east coasts of India varied significantly, indicating the existence of significant genetic structure between the populations. CONCLUSIONS: Genetic stock identification using software analysis exhibited two distinct stocks, one along the west coast (Arabian Sea) and another along the east coast (Bay of Bengal). Bottleneck analysis indicated the genetic stability of species in the wild. P. viridis is a commercially vital species in Indian peninsular regions. The present study suggests the adoption of stock-specific relaying programs of the species from Indian waters in future studies.

Discovery of alternatively spliced isoforms and long non-coding RNA in full length brain transcriptomes of anadromous Hilsa shad, Tenualosa ilisha (Hamilton, 1822).

BACKGROUND: Full length transcriptomes, achieved through long-read sequencing, along with the isoform analysis can reveal complexities in the gene expression profiles, as well as annotate the transcriptomes of non-model organisms. METHODS AND RESULT: Full length transcripts of brain transcriptome of Tenualosa ilisha, Hilsa shad, were generated through PacBio single molecule real-time sequencing and were characterized. A total of 8.30 Gb clean reads were generated, with PacBio RSII, which resulted in 57,651 high quality consensus transcripts. After removing redundant reads, a total of 19,220 high-quality non-redundant transcripts and 17,341 full length ORF transcripts were classified to 7522 putative ortholog groups. Genes involved in various neural pathways were identified. In addition, isoform clusters and lncRNAs were discovered, along with Hilsa specific transcripts with coding frames and 29,147 SSRs in 944 transcripts (1141 annotated). CONCLUSION: The present study provided, for the first time, a comprehensive view of the alternative isoforms of genes and transcriptome complexity in Hilsa shad brain and forms a rich resource for functional studies in brain of this anadromous fish.

Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India.

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.

Transcriptome analysis reveals immune pathways underlying resistance in the common carp Cyprinus carpio against the oomycete Aphanomyces invadans.

Infection with Aphanomyces invadans is a serious fish disease with major global impacts. Despite affecting over 160 fish species, some of the species like the common carp Cyprinus carpio are resistant to A. invadans infection. In the present study, we investigated the transcriptomes of head kidney of common carp experimentally infected with A. invadans. In time course analysis, 5288 genes were found to be differentially expressed (DEGs), of which 731 were involved in 21 immune pathways. The analysis of immune-related DEGs suggested that efficient processing and presentation of A. invadans antigens, enhanced phagocytosis, recognition of pathogen-associated molecular patterns, and increased recruitment of leukocytes to the sites of infection contribute to resistance of common carp against A. invadans. Herein, we provide a systematic understanding of the disease resistance mechanisms in common carp at molecular level as a valuable resource for developing disease management strategies for this devastating fish-pathogenic oomycete.

Molecular insights into the mechanisms of susceptibility of Labeo rohita against oomycete Aphanomyces invadans.

Aphanomyces invadans, the causative agent of epizootic ulcerative syndrome, is one of the most destructive pathogens of freshwater fishes. To date, the disease has been reported from over 160 fish species in 20 countries and notably, this is the first non-salmonid disease that has resulted in major impacts globally. In particular, Indian major carps (IMCs) are highly susceptible to this disease. To increase our knowledge particularly with regards to host immune response against A. invadans infection in a susceptible host, the gene expression profile in head kidney of A. invadans-infected and control rohu, Labeo rohita was investigated using RNA sequencing. Time course analysis of RNA-Seq data revealed 5608 differentially expressed genes, involved among others in Antigen processing and presentation, Leukocyte transendothelial migration, IL-17 signaling, Chemokine signaling, C-type lectin receptor signaling and Toll-like receptor signaling pathways. In the affected pathways, a number of immune genes were found to be downregulated, suggesting an immune evasion strategy of A. invadans in establishing the infection. The information generated in this study offers first systematic mechanistic understanding of the host-pathogen interaction that might underpin the development of new management strategies for this economically devastating fish-pathogenic oomycete A. invadans.

Microsatellite marker development in Spanish mackerel Scomberomorus commerson using third generation sequencing technology.

Spanish mackerel S. commerson belonging to family Scombridae, represent a group of highly commercial marine fisheries with an ever-growing demand world over. Analysing the genetic diversity of this species is of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first multiplex panel set of species-specific microsatellite loci for S. commerson that can be applied when assessing both intra- and inter population genetic variation. Microsatellite marker panels were developed in S. commerson, using Third Generation Sequencing technology in PacBio RSII, based on Single-Molecule Real-Time (SMRT). Thirty- two microsatellite loci were isolated and characterized for S. commerson, by genotyping 20 individuals each obtained from the Kochi and Veraval in the Arabian sea and Chennai along Bay of Bengal coast (n = 3). The number of alleles per locus in S. commerson varied from 4 to 17, while the mean observed and expected heterozygosities ranged from 0.656 to 0.753. The Polymorphic Information Content (PIC) were highly informative, 85% loci with PIC value 0 > 0.75. This suite of markers provides the first species specific nuclear multiplex microsatellite marker panels (32 loci) for S. commerson and thus allows assessment of different populations structures of the species across its distribution range, with more specificity. These newly developed loci have also been validated for cross transferability in another scomberid fish Scomberomorus guttatus.

Mitochondrial DNA markers reveal genetic connectivity among populations of Osteoglossiform fish Chitala chitala.

Genetic diversity and population structure in Indian featherback fish, Chitala chitala (Hamilton, 1822) was investigated by combined analyses of two full mitochondrial genes, ATPase 6/8 and Cytochrome b. A total of 403 individuals, collected from 14 rivers yielded 61 haplotypes. Hierarchical partitioning analysis identified 19.01% variance 'among' and 80.99% variance 'within groups and populations'. The mean coefficient of genetic differentiation (FST) was observed to be significant 0.26 (p < 0.05). Mantel tests rejected the hypothesis that genetic and geographic distances were correlated. The patterns of genetic differentiation, AMOVA and principal coordinate analyses indicated that natural populations were sub-structured and comprised of four genetic stocks of C. chitala in Indian rivers. The results also supported the higher resolution potential of concatenated gene sequences. The knowledge of genetic variation and divergence, from this study, can be utilized for its scientific conservation and management in the wild.

Non-invasive Method for Collection of Clarias magur Spermatozoa for Breeding.

Induced spawning is more inefficient in Clarias magur than in other fish species such as cyprinids and salmonids. Ovulation can be induced in the female C. magur by using pituitary extract or synthetic hormones. However, milt from the male C. magur cannot be obtained by hand stripping because the volume of seminal fluid in the testes is extremely low. Notably, similar problems are observed in other male catfishes such as C. gariepinus and C. lazera. Because milt from the males cannot be obtained for use in artificial fertilization of eggs, males are invariably sacrificed, and the testicular tissue is excised and macerated to obtain spermatozoa.•We developed an alternative approach that allowed harvesting of C. magur spermatozoa through surgery for artificial fertilization without sacrificing male fish.•The surgically obtained spermatozoa were used to inseminate C. magur eggs; the cross resulted in healthy progeny with a fertilization rate of 80%-98% and hatching of up to 85% of fertilized embryos; similar to those obtained using the conventional sacrificial approach (hatching percentage range of 45%-85%) [1].•This indicated the viability of partial surgical harvest of testicular tissue in seed production in C. magur for aquaculture without sacrificing male fish.

Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.

This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N50 of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various homeostasis processes. Highest number of genes belongs to cellular calcium ion homeostasis, followed by tissue homeostasis. A total of 97 genes were identified, with 16 GO terms related to water homeostasis. Claudins, Aquaporins, Connexins/Gap junctions, Adenylate cyclase, Solute carriers and Voltage gated potassium channel genes were observed to be higher in number in T. ilisha, as compared to that in other teleost species. Seven novel gene variants, in addition to claudin gene (CLDZ), were found in T. ilisha. The present study also identified two putative novel genes, NKAIN3 and L4AM1, for the first time in fish, for which further studies are required for pinpointing their functions in fish. In addition, 1.6 million simple sequence repeats were mined from draft genome assembly. The study provides a valuable genomic resource for the anadromous Hilsa. It will form a basis for future studies, pertaining to its adaptation mechanisms to different salinity levels during migration, which in turn would facilitate in its domestication.