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Milkfish ( Chanos chanos ) belongs to the family Chanidae and it is a potential candidate species for aquaculture with the best biological characteristics. This study investigates the genetic diversity and population structure of C. chanos along the Indian coast using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). A total of 90 samples collected from five different locations across the Indian coast were sequenced for analysis using cyt b. The sequencing of a 1100-bp cyt b mtDNA fragment revealed the presence of 38 haplotypes with a haplotype diversity value of 0.835 and a nucleotide diversity value of 0.00400. The variation within and among populations accounted for about 97.33% and 2.67%, respectively. The fixation index analysis indicated that there is no significant genetic divergence among the populations from different geographical areas. Neighbour-joining tree analysis of the haplotype data showed no distinct patterns of phylogeographic structure. Results from this study indicated that there is a lack of genetic divergence between the populations of C. chanos along the Indian coast. The haplotype network showed star-like geneology which indicated the demographic expansion of the C. chanos population in these locations. The recent demographic expansion of the C. chanos population was also supported by the results of Tajima’s  D  statistics. Results from this study can be used for planning effective strategies for the conservation and management of the C. chanos population in the wild.

Thirty polymorphic microsatellites were developed and characterised for the aquaculture important species, Green chromide, Etroplus suratensis through Illumina Sequencing with a mean read quality (Phred score) of 35.8 and the microsatellite primers were designed from the sequenced information, considering various attributes such as the number of repeats, Tm, GC content, Product size, etc. using the software PRIMER 3.0 web tool. The allele numbers ranged from 6 to 18. The mean observed heterozygosity was 0.745 and the mean expected heterozygosity was 0.762. The average PIC value for 30 microsatellite primers was 0.80 and all the loci had PIC values > 0.75. The identified polymorphic loci would help in revealing the genetic stock identification among the Pearlspot population.

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 .

Charybdis (Goniohellenus) omanensis septentrionalis Türkay & Spiridonov, 2006 was collected from off the Kerala coast, Arabian Sea, India. This is the first record of the subspecies from India and the taxonomic characters are similar to the findings of Türkay & Spiridonov (2006) who described the subspecies for the first time. The present work also records molecular sequences from the mitochondrial cytochrome oxidase I gene (COI), used to determine the genetic identity of the species.

In the present study three species of mackerel, Rastrelliger present in Indian waters were taken for genetic identification using cytochrome c oxidase subunit I and 16s rRNA sequences. Accurate identification of these species is important for fishery management as its morphological characters are very similar. In this study, the sequences of COI and 16S rRNA were determined from 19 individuals of three Rastrelliger species, Rastrelliger kanagurta, Rastrelliger brachysoma and Rastrelliger faughni from Andamans and Indian mainland to study the phylogenetic relationship. The intraspecies and interspecies genetic distance ranged from 0.000 to 0.002 and 0.007 to 0.015 respectively based on 16S rRNA sequences. Using COI data analysis, the intraspecies genetic distance ranged from 0.000 to 0.012, while it varied from 0.039 to 0.086 for interspecies. The present study clearly demarcates three species of mackerel based on the mitochondrial genetic sequences and also showed a non-descriptive genetic distance of R. kanagurta from mainland and Andaman Islands.

Milkfish (Chanos chanos Forsskål, 1775) is an economically important species with best biological characteristics for farming. It is valued as a food fish, especially in Southeast Asia. Milkfish aquaculture is an important source of income in many countries such as Taiwan, Indonesia, and the Philippines. Much technical and scientific research has been documented for the development of feeds, farming systems, disease resistance of milkfish etc. This review discusses current scientific studies on milkfish in the relevant areas of aquaculture such as nutrition and feeding, farming systems, diseases, molecular genetics, and economics. It provides a global perspective that will be a benchmark for our current knowledge and facilitate a more oriented focus on the future research needs of this economically valuable fish. This review is helpful for the scientific community by providing an overview of the present state of knowledge, recent research, and developments in milkfish aquaculture.

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.

The golden anchovy, Coilia dussumieri, though possessing discontinuous distribution along northeast and northwest coasts of India, it is being managed as unit stock for fishery assessment purposes. By considering the need for stock specific management of the species, mitochondrial ATP synthase 6 and 8 (ATPase 6/8) genes were analyzed for delineating genetic stock structure of the species. Sequence analysis revealed a total of 34 haplotypes across four populations from both the east and west coasts of India. Haplotype diversity (h) was found in the range of 0.7421–0.9368. Similarly, nucleotide diversity (π) varied from 0.0012 to 0.0025. AMOVA results indicated a high total variance of 72.66 % between east and west coast populations and less (1.34 %) among populations within the respective coast. Phylogenetic tree constructed using pair wise FST also indicated the genetic divergence of populations of east and west coasts of India. The findings of the present study will be helpful in developing stock specific management measures for conservation and sustainable utilization of the species.

Population genetic structure of the pelagic narrow-barred Spanish mackerel ( Scomberomorus commerson ) was examined in 10 populations from the Indo-West Pacific region, based on mitochondrial control region DNA. We examined genetic composition of 56 individuals of S. commerson from the Arabian Sea, Bay of Bengal, and compared them with 40 individuals from previously published data sampled from the ROPME Seas area and South West Pacific Ocean. The overall nucleotide and haplotype diversities were estimated to be 0.072 and 0.995, respectively. Demographic parameters such as Tajima’s D and Fu’s F s statistics were negative, but non-significant across all the populations, except for New Caledonia in the South West Pacific, indicating a stable population of S. commerson in this region. To assess intra-specific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated time of most recent population expansion. AMOVA and F ST values among Indian and Arabian regions revealed non-significant variation among the populations, while separation was noted among the samples of the northern and eastern Indian oceans, as well as with South West Pacific. A parsimony network analysis provided evidence for four separate population segment/stocks in the Indian Ocean and Pacific Ocean, raising a conservation concern. Our results support a need for regional cooperation to ensure the sustainable exploitation of S. commerson in the Indo-West Pacific region.

Perna viridis (Linnaeus, 1758), the Asian green mussel, belonging to the family Mytilidae is widely distributed along the Indian coast. The species is majorly found in southeastern countries and is considered an ideal candidate for aquaculture due to its high nutritional value and growth rate. Obtaining their genetic information is essential for their sustainable capture-based production. In the present study, genetic variation, population structure, and demographic processes of the populations across the distribution of this species were assessed using the mitochondrial DNA ATPase6 and cytb gene. In total, we selected 170 samples from five localities across the Indian subcontinent including Andaman Sea. Sequence analysis of partial cytb (885 bp) and ATPase6 (714 bp) genes revealed 45 and 58 haplotypes, respectively. The significant coefficient of genetic differentiation ( F ST : 0.255 for cytb and 0.252 for ATPase6) and analyses of molecular variance indicated three varieties of stocks, namely Arabian Sea, Bay of Bengal, and Andaman Sea. All the populations showed low nucleotide diversity, suggesting severe historical bottleneck events and high haplotype diversity, indicating population expansion. The genetic variation and demographic process reported in this study will form the baseline information for framing policies, which can be adopted while planning stock specific ranching and relaying programmes in the Indian subcontinent with view to enhance and manage the fishery.