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Over the last two decades genetic and phylogeographic studies in cephalopods around the world have identified many species complexes and cryptic species. Indian Ocean, in the tropical region remained least studied one. In the present study Sepiella inermis samples were collected from different landing centres along Indian coasts to investigate the distribution of these species in a phylogeographic context. Phylogenetic analyses were performed using the mitochondrial Cytochrome Oxidase I gene and 16S rRNA gene.The currently described species consists of two genetically distinct clades (pair-wise genetic divergence varied in between 7.7 to 9.1%). One clade composed of individuals collected in Arabian Sea and the other from Bay of Bengal (northern and north-eastern part of Indian Ocean). The study led to the identification of potential cryptic speciation within Sepiella inermis. Mean intraspecific and interspecific nucleotide distances for COI were 0–2% and 2–7%, respectively, while these values for 16S rRNA sequences were 0–1% and 1–4%. Furthermore, this study also provides evidence of previously undocumented sub-population structuring in the Indian waters.

Marine waters of Andaman and Nicobar Islands, India in the tropical Indian Ocean, is a poorly explored high faunal diverse region. The present study documents new records of batoids from the region, identified during the fishery and diversity monitoring surveys conducted during November 2016 to June 2019 at different fish landing centers of Andaman and Nicobar Islands. Fifteen elasmobranch species including 2 wedgefishes, 1 skate and 12 rays were identified and confirmed as new reports for the region. Results of this study indicate that the elasmobranch diversity, especially batoid diversity of Andaman and Nicobar Islands are poorly documented and future systematic surveys including that of deeper reef habitat may help to explore the diversity in the region.

The diverse germplasms pool already available in the vast and varied water resources of India has potential to cater to the need of the fisheries and aquaculture sector, but introduction of fish species for different purposes is still continuing. The exotic fishes introduced into India for different purposes covers nearly 13.6% of total fish diversity. Due to wider tolerance limit and generalist nature, some alien fish species have acclimatised to diverse eco-climatic conditions. Some of these introduced fishes are now established in the open water bodies including rivers, wetlands and reservoirs and some others are in the process of establishment. Degraded open waters and wanton destruction of fishery resources in the rivers have resulted in depletion of the sensitive fish species and appearance of exotic fishes. The potential risk areas for appearance of the alien species are mushrooming fish culture units in different parts of the country, porous boundaries, farming of alien fishes in flood prone areas, rapid expansion of aquaculture and ornamental fish trade. Eradication of an introduced species is usually difficult or impossible once it is established in open water bodies. Therefore, there is an urgent need to regulate the import of alien fish species, based on their merit and likely impacts on open waters.

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.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.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.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.

Taxonomic ambiguity exists in genus Systomus and recently many new species were described under this genus. Systomus sarana subnasutus is considered a valid subspecies of S. sarana sarana although revisions have been done by some researchers. We employed a combination of morpho-meristics and molecular tools (Cytochrome c oxidase I, 16S and Cytochrome b genes of mitochondrial genome) to resolve the two species. Three morpho-meristic characters, head length/maxillary barbel length (HL/MxBL), Lateral Line Scales (LLSs) as well as two truss-based characters, had discernible variation between the two taxa. The sequence analysis (2353 nucleotides) depicted a separate clad of S. sarana subnasutus with high bootstrap support. The findings from combined use of morphology, meristics and mitogenes were concordant. The corroborative results suggest the possibility of two different species. The results suggest to adopt suitable management measures, accordingly.

DNA barcode data of the South Asian bagrid catfish genus Sperata indicate the presence of at least five species in the Indian subcontinent. Those results, which are supported by morphological data, show a marked increase in species diversity from the recent taxonomic and fishery literature, although each of the five species had been previously named. Two species are restricted to rivers of peninsular India south of the Godavari: Sperata aorides from the Cauvery river basin and S. seenghala from the Krishna river basin. Most literature records of S. seenghala from the Ganges-Brahmaputra-Meghna river basins likely refer to S. lamarrii, a species which appears to also be present in the Indus river basin. Some genetic data reported as S. seenghala from the Ganges-Brahmaputra-Meghna river basins refer to S. aorella. S. aor is widespread in the Ganges-Brahmaputra-Surma river basins in India and Bangladesh, extending southwards to the Godavari river.

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.

Burgeoning population growth, increasing affluence, and changing dietary habits of people have caused a phenomenal rise in fish demand over the years in India. Diversification of aquaculture species aimed at increasing yield and providing a wider choice of fish protein to the consumers has led to the introduction of several more affordable species into the culture system. Of these, few fish species are yet to get government nod for culture, but these have increasingly been adopted by the farmers. Red-bellied pacu, Piaractus brachypomus is one of such kinds which has increased its spread in culture system to more than 2500 ha ever since its introduction in 2003–2004. The present attempt envisaged a systematic study to find the status of this species in the culture system, especially in the three States, i.e. Andhra Pradesh, Kerala, and West Bengal where its adoption has increased considerably. A total of 351 pacu farms were surveyed using a structured open-ended questionnaire during the period 2011–2015 in these three States. The survey revealed a gradual increase in culture area and production of pacu during the five years. There was a proportionately higher increase in the sale price of pacu compared to other concurrent major cultured species such as the Indian major carps and striped catfish. The majority of the farmers (87%) practicing pacu farming in the three studied states opined in favour of the culture of pacu due to its overall profitability. The findings of this study will be helpful for making informed decisions by the policymakers for the expansion of its culture in the country.

Parapenaeopsis stylifera (H. Milne Edwards, 1837), popularly known as Kiddi shrimp, constitutes an important fishery resources along the Indian coast with wide geographical distribution. Despite its economic importance, the genetic stock structure of the species is not investigated so far. Knowledge on genetic structure is essential for formulating sustainable management and conservation measures. Present study is carried out to characterize the five geographically isolated stocks of P. stylifera along the Indian coast using microsatellite markers. Eleven polymorphic microsatellites were developed in P. stylifera and used for genetic stock characterization. Including all the stocks, a total of 174 alleles were observed with a mean of 15.81 alleles per locus. Mean observed (Ho) and expected (He) heterozygosity values ranged from 0.641 to 0.692 and 0.710–0.743, respectively. Six loci shown deviation from Hardy-Weinberg equilibrium and no significant linkage disequilibrium between loci pairs were detected. Pair-wise FST, AMOVA and Structure analyses indicated low genetic structure between the stocks of east (Bay of Bengal) and west (Arabian Sea) coasts of India. Based on the present study, P. stylifera stocks of east and west coast of India can be proposed as single management units (MUs), which require single monitoring and management practices.

Cobia, Rachycentron canadum is a candidate species for aquaculture, distributed across the Indo-Pacific waters to the southern Atlantic Ocean. Information on genetic diversity and population structure of cobia is crucial for sustainable utilization and management of the species in natural waters. In the present study, we used 14 polymorphic microsatellite loci and mitochondrial cytochrome b gene (980 bp) to investigate the genetic diversity and population structuring of R. canadum along the Indian coast. Microsatellite analysis suggests a relatively high level of genetic diversity of cobia in the Indian region, with a mean Ho and He of 0.76 and 0.73. The PIC was also highly informative (0.841), with a mean no. of alleles of 11.304. Hierarchical AMOVA and genetic differentiation co-efficient between the populations was found to be low, but significant (FST = 0.035, P

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.

Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence.

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 (FST: 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.

The growth rate of a species in any aquatic environment is an indicator of the water quality of the system. In the current study, the Length-weight relationship (LWR) and the condition factor of Dawkinsia filamentosa from various aquatic ecosystems especially lotic, lentic and brackish lentic systems were compared. It was observed that growth rate of the fish was more in brackish lentic systems. The study showed that already reported growth rate (b) of the species in brackish lentic systems is around 3.273 indicating proximity towards the isometric growth pattern as compared to the growth rate in reservoirs (2.3184) and that in lentic systems (3.116) obtained from present study. Similar studies supplemented with environmental variables can be used to study the health status of the ecosystem. The best system suitable for the adaptive growth of the species can be ascertained only after a holistic approach involving environmental variables.

Aenigmachanna mahabali, a new species of troglophilic snakehead is described on the basis of a single specimen recovered from a well in Kerala, India, over 200km south of the type locality for the only known species in the genus. The new species can be distinguished from its congener in possessing fewer dorsal fin rays (53 vs 56-57), fewer total vertebrae (61 vs 64), fewer scales in lateral series (76 vs 83-85) and in the pectoral-fin rays being extended beyond the margin of the membrane into filaments.

In this study, a new cell line derived from the caudal fin of the freshwater angelfish Pterophyllum scalare was developed and characterized. The cell line was designated angelfish fin (AFF) and subcultured 44 times since its development. These cells grew well in Leibovitz's -15 medium supplemented with 10% foetal bovine saline (FBS) at 28° C and the modal chromosome number (2n) was 48. The AFF cell-line is mainly comprised of epithelial cells as confirmed by immunocytological technique using anti-cytokeratin antibodies, an epithelial cell marker. This cell line was tested for growth in a temperatures range from 20 to 37° C and at various FBS concentrations of 5-20% at 28° C. The cell line was cryopreserved at different passage levels and revived successfully with 80% survival rate. Polymerase chain reaction amplification and sequencing of partial mitochondrial 16s rRNA and coI genes confirmed that the AFF cell-line originated from angelfish. Mycoplasma sp. contamination was not detected in AFF cells and checked by Hoechst 33258 fluorescence staining. At the 42nd passage the cells were transfected with 2 μg of pAcGFP1-N1 expression vector. The AFF cells exhibited cytotoxic effects when exposed to the bacterial extra cellular products from Serratia marcescens and Proteus hauseri. The AFF cells and cells from kidney and brain did not show cytopathic effect when exposed to cyprinid herpes virus2 and viral nervous necrosis virus. The newly developed AFF cell line will be useful for the isolation of viruses affecting angelfishes, such as iridoviruses, in the future.

Silver pomfrets are spread along the Indo-West Pacific: from the Persian Gulf to Indonesia, Japan, West and Southwest of Korea and Eastern parts of China and forms a commercial fishery in all these countries. For formulating fishery management strategy of the silver pomfret, accurate population information is necessary. The genetic stock structure of silver pomfret in the Northern Indian Ocean was explored using 12 polymorphic microsatellite markers. Morphological and molecular studies confirmed that the silver pomfrets along the Northern Indian Ocean is Pampus candidus. Pampus candidus populations along Arabian Sea and Bay of Bengal region (FST =0.049, P

Aeromonas hydrophila was identified the causative agent of a disease outbreak in goldfish, Carassius auratus from four ornamental fish farms in Kerala, India. Seven bacterial isolates viz., Plesiomonas shigelloides (NPPS-1), Aeromonas hydrophila (NPAH-1, 2, 3 and 4), Citrobacter freundii (NPCF-1) and Acinetobacter spp. (NPA-1) were isolated from the affected fish. Further, all four A. hydrophila (NPAH-1, 2, 3 and 4) isolates were identified by amplification of gyrB and rpoD genes. The RAPD profile using 3 primers confirmed that all four A. hydrophila were genetically similar. No cytopathic effect was observed on goldfish fin (GFF) cell line after inoculation of the tissue homogenate from the affected fish and affected tissues were found negative for koi herpesvirus (KHV), cyprinid herpesvirus-2 (CyHV-2) and spring viraemia of carp virus (SVCV). Experimental challenge resulted in mortality of fish injected with A. hydrophila only. A. hydrophila was observed to be cytotoxic on GFF cell line and exhibited haemolytic activity on 5% sheep blood agar. A. hydrophila possessed multiple virulence genes viz., enterotoxins, haemolytic toxins and outer membrane protein as determined by PCR. A. hydrophila was sensitive to Cefixime, Chloramphenicol, Nitrofurantoin, Kanamycin, Ciprofloxacin, Furazolidone and Cefixime/Clavulanic acid. After treatment with the suggested antibiotics, the fish were recovered from the disease.

Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.

Macrobrachium rosenbergii, giant freshwater prawn, is one of the most commercially important crustaceans. In the present study, primers for ATPase 6/8 region of mt-DNA were designed and successfully amplified (827 bp) in the species. The nucleotide variation in ATPase 6/8 gene revealed the population structuring in natural populations of M. rosenbergii in Indian waters. A total of 35 haplotypes were observed in 93 individuals collected from different locations. Low nucleotide diversity and high haplotype diversity were noticed for the ATPase 6/8 gene. Significant pairwise FST and, haplotype network indicated occurrence of distinct populations. Observed mismatch distribution and Tajima’s D test suggested demographical stability of giant freshwater prawn. The genetic stock structure revealed in this study will be helpful for conservation and management of stocks of M. rosenbergii in Indian waters.

Mitochondrial cytochrome C Oxidase I (COI) sequence variation among the clariid fishes of India (Clarias magur, C. dussumieri and C. gariepinus) and their relationship with other representative clariids was studied in this work. Three species were sampled and together with 23 COI sequences from GenBank were used to reconstruct phylogenetic relationships in the family Clariidae. The study revealed two clades: one consisting of the African species with C. dussumieri, and the other of Asian species suggesting the prevalence of intra-continental diversification of catfishes. This study further revealed that the genus Clarias is monophyletic. For the COI gene, the interspecies genetic divergence ranged from 0.056 to 0.182. The mean genetic difference between C. dussumieri and other selected African species in this study is 12.1%. It was also observed that the morphological similarity of C. dussumieri and C. magur was not replicated in the genetic level. Clarias dussumieri was more close to African catfish C. gariepinus thus indicating the utility of COI phylogeny to identify the well-known African-Asian relationships within catfishes. The results also showed that C. magur and C. batrachus are genetically distinct from each other.

Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution.

Pathogenic strain of Serratia marcescens (NPSM-1) with multiple drug resistance was isolated from guppy Poecilia reticulata with clinical signs of fin rot and was confirmed by biochemical tests and 16S rRNA gene sequencing. The extra cellular proteins (ECP) of the bacteria exhibited marked cytotoxic activity in vitro on Cyprinus carpio koi fin (CCKF) cell line. The in vivo challenge studies confirmed that the isolate was highly pathogenic to fish when the fishes were injected with1 x 104 CFU/fish and the same bacterium was re-isolated from infected fish, post-challenge. S. marcescens produced large zones of haemolysis on 10% sheep blood agar. The bacteria was found to carry virulence genes; extracellular metalloprotease gene (Pr596) and AHL synthase gene (SpnI). The bacterial isolate was tested to determine sensitivity against 16 antibiotics and was sensitive to only 5 viz., cefixime, chloramphenicol, ciprofloxacin, gentamycin and erythromycin. The study indicates that S. marcescens can cause disease in ornamental fish and the bacterium being a known human pathogen, may also cause infections in humans having direct contact with infected fishes. This is the first report describing S. marcescens as a pathogen of freshwater ornamental fish in India.

Astronotus ocellatus, commonly called the oscar, is one of the popular cichlids among aquarium hobby. The present study deals with the development and characterization of a new cell line from caudal fin of A. ocellatus. The cell line was cultured in Leibovitz’s L−15 medium supplemented with 10% fetal bovine serum at 28 °C. The optimum temperature and FBS concentration for cell growth were tested with temperature ranges from 20 to 37 °C and FBS concentrations of 5–20% at 28 °C. The Astronotus ocellatus fin cell line has been subcultured 45 times since its development and the modal chromosome number (2n) is 48. The cell line is composed mainly of epithelial cells as confirmed by immunocytological technique using anti-cytokeratin antibodies. The cell line was cryopreserved at different passage levels and the revival efficiency showed 80% survival rate. Partial sequence amplification and sequencing of two genes, mitochondrial 16S ribosomal RNA and cytochrome oxidase I, confirmed the origin of cell line. The cell line did not show Mycoplasma contamination. The cells showed good transfection efficiency when transfected with 2 μg of pAcGFP1-N1 expression vector. The extracellular products of fish bacterial pathogens viz., Aeromonas hydrophila and A. caviae, were cytotoxic to AOF cells but were not susceptible to Cyprinid herpes virus 2. The development of AOF cell line will have significant applications in fish virology and will prove useful to isolate pathogens in the event of sudden viral disease outbreak and for the development of vaccines and diagnostic kits.

Conservation, management and sustainable utilisation of biological resources depend on the accurate identification of exploited taxa, which emphasises the need for systematic taxonomic research. Chondrichthyans (sharks, rays, skates and chimaeras) are considered to be one of the most vulnerable exploited marine resources, however, the basic taxonomic study of these groups in Indian waters needs improvement to achieve better management for their sustainable exploitation. We discuss issues concerning chondrichthyan taxonomic research in India and provide an extended, updated checklist of chondrichthyans listed/reported from Indian waters, together with comments on their occurrence. Keywords: Chondrichthyans, checklist, taxonomy, status, India, diversity, management, conservation. Introduction India has many different climatic, ecological and bio-geographical zones, and diverse faunal and floral groups in its ecosystems. Conservation and management of this diversity is important to maintain the equilibrium of ecosystems and for their potential human usage. Conservation, management

Pampus argenteus (Euphrasen 1788) is one of the commercially important marine food fish in India, having high value and demand in both domestic and export market. Pomfrets in Indian waters showed a steady decline in catch due to capture of undersized, juvenile fishes. Baseline information on the genetic stock structure is important for conservation and sustainable harvest of this species. Fish stock structure and genetic variation can be evaluated/identified through microsatellite molecular markers. An alternative for finding polymorphic microsatellites is cross-species amplification between genetically closely related species.

Scomberomorus commerson is an economically important migratory fish distributed worldwide. The genetic stock structure of S. commerson distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 23 haplotypes with mean low nucleotide diversity and high haplotype diversity. Co-efficient of genetic differentiation (FST) values obtained for pair wise populations were low and non-significant with an overall value of −0.02074. The high haplotype and low nucleotide diversity values together with mismatch distribution analysis suggested a history of genetic bottleneck events or founder effect, with subsequent population expansion in S. commerson. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.

Silver pomfret, Pampus argenteus is an economically important seafood species. The fishery resource of pomfret in Indian waters shows a dwindling catch since the last few years and the pomfrets caught were mostly undersized which calls for immediate attempts for management of resources. An accurate definition of population structure is important for management of this species. The genetic stock structure of P. argenteus distributed along Indian coast was identified using analysis of 842 bp of complete ATPase 6/8 genes of mitochondrial DNA. Altogether, 83 silver pomfret (P. argenteus) collected from 4 locations along Indian coast (Gujarat, Kerala, Tamil Nadu and West Bengal) were sequenced. Twenty four haplotypes were identified among 83 individuals with haplotype diversity (0.87) and nucleotide diversity (0.0025). The significant pair-wise FST and AMOVA values, between samples from West Bengal (east coast) and other locations along the west coast (Gujarat and Kerala) indicated the occurrence of distinct population structure in silver pomfret along the coast.

Narrow barred Spanish mackerel, Scomberomorus commerson (Lacepede 1800) is one of the commercially important fish in Indian waters. For sustainable management of the species, it is necessary to understand the genetic stock structure of the species. Accurate delineation of genetic stock structure can be achieved using nuclear microsatellite markers. A study was carried out to identify and validate polymorphic microsatellite markers in S. commerson using information available from closely related fish species. The study could identify 10 polymorphic microsatellite loci which can be effectively utilised for identifying genetic stock structure of the species. Validation of the identified loci was also done by testing the loci in natural populations of the species. The findings of the present study will be useful in devising stock-specific management measures for conservation and sustainable utilisation of this commercially important fish species in Indian waters.

A disease outbreak was reported in adult koi, Cyprinus carpio koi, from a fish farm in Kerala, India, during June 2015. The clinical signs were observed only in recently introduced adult koi, and an existing population of fish did not show any clinical signs or mortality. Microscopic examination of wet mounts from the gills of affected koi revealed minor infestation of Dactylogyrus sp. in a few koi. In bacteriological studies, only opportunistic bacteria were isolated from the gills of affected fish. The histopathological examination of the affected fish revealed necrotic changes in gills and, importantly, virus particles were demonstrated in cytoplasm of gill epithelial cells in transmission electron microscopy. The tissue samples from affected koi were negative for common viruses reported from koi viz. cyprinid herpesvirus 3, spring viraemia of carp virus, koi ranavirus and red sea bream iridovirus in PCR screening. However, gill tissue from affected koi carp was positive for carp edema virus (CEV) in the first step of nested PCR, and sequencing of PCR amplicons confirmed infection with CEV. No cytopathic effect was observed in six fish cell lines following inoculation of filtered tissue homogenate prepared from gills of affected fish. In bioassay, the symptoms could be reproduced by inoculation of naive koi with filtrate from gill tissue homogenate of CEV-positive fish. Subsequently, screening of koi showing clinical signs similar to koi sleepy disease from different locations revealed that CEV infection was widespread. To our knowledge, this is the first report of infection with CEV in koi from India.

DNA barcoding was successfully used for the accurate identification of chondrichthyans in the Indian commercial marine fishery. About 528 specimens of 111 chondrichthyan species and 34 families, collected from the Indian EEZ, were barcoded for a 655 bp region of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Generally, five specimens per species were barcoded, but numbers ranged from 2 to 13. The average Kimura 2 parameter (K2P) distance separating individuals within species was 0.32%, and the average distance separating species within genera was 6.73%. Ten species were suggested as putative new species requiring formal descriptions. Based on the morphology and molecular support, 11 elasmobranch species were confirmed first records for Indian waters. The present study confirms the ability of DNA barcoding for the accurate identification of sharks, rays, and their products from Indian waters.

Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.

The comparative assessment of genetic diversity using allozymes, random amplified polymorphic DNA (RAPD), and microsatellite markers was conducted in endemic and endangered yellow catfish (Horabagrus brachysoma) sampled from three locations in Western Ghats river systems of India. Among the three markers, microsatellites show more polymorphism, having 100% polymorphic loci, whereas allozymes show the least (56%). In RAPD, 60.5% of fragments were polymorphic. Observed heterozygosity and F(ST) values were very high in microsatellites, compared with the other markers. Microsatellite and RAPD markers reported a higher degree of genetic differentiation than allozymes among the populations depicted by pairwise F(ST)/G(ST), AMOVA, Nei's genetic distance, and UPGMA dendrogram. The three classes of markers demonstrated striking genetic differentiation between pairs of H. brachysoma populations. The data emphasize the need for fishery management, conservation, and rehabilitation of this species.

A fibroblastic-like cell line was established from the ornamental ¢sh, red-line torpedo (Puntius denisonii). The red-line torpedo fin (RTF) cell line is being maintained in Leibovitz’s L-15 mediumsupplementedwith 10% fetal bovine serum (FBS) for over 1year at 28 1C on a continuous basis in normal atmosphere. The growth rate of RTF cells increased as the FBS proportion increased from 5% to 20% at 28 1C with optimum growth at the concentrations of 10% FBS. The morphology of RTF cell was predominantly fibroblastic like. Propagation of these cell lines was serum dependent, with a low plating efficiency (o15%). Karyotyping analysis of RTF cells at the 25th passage indicated that the modal chromosome number was 2n550. The cell line was cryopreserved in liquid nitrogen at �196 1C and could be recovered from storage after 6 months with good cell viability. Polymerase chain reaction amplification of a fragment of two mitochondrial genes, 16S rRNA and CO1, con¢rmed the identity of these cell lines with those reported from this animal species, confirming that the cell lines originated from P. denisonii. The bacterial extracellular products from Vibrio cholerae MTCC3904 and Aeromonas hydrophila were found to be toxic to RTF. The cell lines were not susceptible to viral nervous necrosis virus, a marine ¢sh virus.

Random-amplified polymorphic DNA (RAPD) and microsatellite markers were developed and used for the analysis of genetic variability in the critically endangered yellow catfish Horabagrus nigricollaris, sampled from the Chalakkudy River, Kerala, India. Eight RAPD and five microsatellite markers were detected to genotype the species. In RAPD, the 73 fragments were 20.55% polymorphic, whereas 4 polymorphic loci (80%) were obtained in microsatellites. In microsatellites, the number of alleles across the 5 loci was 1-5, and the range of heterozygosity was 0.25-0.5. The mean observed number of alleles was 2.4, and the effective number was 1.775 per locus. The average heterozygosity across all investigated samples was 0.29, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods report a low degree of gene diversity and lack of genetic heterogeneity in the population of H. nigricollaris, emphasizing the need for fishery management, conservation, and rehabilitation of this species.

The two species of yellow catfish, Horabagrus brachysoma and H. nigricollaris are categorized as 'endangered' and 'critically endangered' respectively in their wild habitat. Proper knowledge of genetic structure and variability of these endangered species are highly essential for the management, conservation and improvement of fish stocks. Therefore, genetic variation and phylogenetic relationships between these species of yellow catfish sampled from Chalakkudy River in the hot spot of biodiversity-Western Ghats region, Kerala, India were analyzed by using Random amplified polymorphic DNA (RAPD) and microsatellite markers. 85 RAPD and five microsatellites loci were detected to analyze the genetic variation and phylogenetic relationships among these species. Out of 85 RAPD loci produced only 52.94% were polymorphic whereas in microsatellite, all 5 loci were polymorphic (100%). Species-specific RAPD bands were found in both species studied. In microsatellite, the number of alleles across the five loci ranged from 1 to 8. The observed heterozygosities in H. brachysoma and H. nigricollaris were 0.463 and 0.443, respectively. Here, both RAPD and microsatellite methods reported a low degree of gene diversity and lack of genetic heterogeneity in both species of Horabagrus which strongly emphasize the need of fishery management, conservation and rehabilitation of these species.

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic and endangered yellow catfish, Horabagrus brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy and Nethravathi River systems. Of the 124 total RAPD fragments amplified, 49 (39.51%) were found to be shared by individuals of all 3 populations. The remaining 75 fragments were found to be polymorphic (60.48%). In microsatellites, six polymorphic microsatellite loci were identified by using primers developed for Pangasius hypophthalmus, Clarias macrocephalus and Clarias gariepinus. The identified loci were confirmed as microsatellite by sequencing after making a clone. The nucleotide sequences of 6 loci were published in NCBI genbank. The number of alleles across the six loci ranged from 4 to 7 and heterozygosities ranged from 0.07 to 0.93. The mean number of alleles and effective number of alleles per locus were 5.00 and 3.314, respectively. The average heterozygosity across all investigated samples was 0.72, indicating a significant deficiency of heterozygotes in this species. RAPD and microsatellite methods reported a high degree of gene diversity and genetic distances depicted by UPGMA dendrograms among the populations of H. brachysoma.

India has a rich natural heritage and nurtures a unique bio-diversity, placing it among the 12 most biodiverse countries. Globally the number of valid fish species recorded so far is more than 31000, with the addition, at an average, of 100–150/year. Among these 2,508 are indigenous to Indian subcontinent (877 freshwater, 113 brackish water and 1,518 marine species). DNA barcoding is a molecular method for species identification and classification of biological organisms based on the analysis of short, standardized gene sequences. In most animals, the fragment of mitochondrial gene cytochrome c oxidase subunit I (COI) has been used as the target sequence. This novel system is designed to provide rapid, accurate, and automatable species identifications by using short, standardized gene regions as internal species tags. Of this rich natural biodiversity, comprising over 1518 native marine species, at present barcodes of about 500 marine fish species are available, which is approximately 33 % of total Indian marine fish diversity. Whereas major portion of registered marine fishes remain untouched. Hence more emphasis should be given to DNA barcoding, with mandate of barcoding all the species to establish global comprehensive reference libraries. The traditional taxonomists will play a vital role in completing such a global database; hence there is a pressing need to make a integration of DNA barcoding with traditional taxonomy. In a nutshell, it can be said that DNA barcoding can be taken up as pragmatic approach for resolving unambiguous identification of the fish fauna which can play a crucial role in biodiversity assessment and conservation of marine ecosystem of country.

In this study, a new cell line derived from the caudal fin of the freshwater angelfish Pterophyllum scalare was developed and characterized. The cell line was designated angelfish fin (AFF) and subcultured 44 times since its development. These cells grew well in Leibovitz's -15 medium supplemented with 10% foetal bovine saline (FBS) at 28° C and the modal chromosome number (2n) was 48. The AFF cell-line is mainly comprised of epithelial cells as confirmed by immunocytological technique using anti-cytokeratin antibodies, an epithelial cell marker. This cell line was tested for growth in a temperatures range from 20 to 37° C and at various FBS concentrations of 5-20% at 28° C. The cell line was cryopreserved at different passage levels and revived successfully with 80% survival rate. Polymerase chain reaction amplification and sequencing of partial mitochondrial 16s rRNA and coI genes confirmed that the AFF cell-line originated from angelfish. Mycoplasma sp. contamination was not detected in AFF cells and checked by Hoechst 33258 fluorescence staining. At the 42nd passage the cells were transfected with 2 μg of pAcGFP1-N1 expression vector. The AFF cells exhibited cytotoxic effects when exposed to the bacterial extra cellular products from Serratia marcescens and Proteus hauseri. The AFF cells and cells from kidney and brain did not show cytopathic effect when exposed to cyprinid herpes virus2 and viral nervous necrosis virus. The newly developed AFF cell line will be useful for the isolation of viruses affecting angelfishes, such as iridoviruses, in the future.

Indian white shrimp, Fenneropenaeus indicus, is an important crustacean species in the commercial fish landings of southwest and southeast coasts of India. It also forms a major fishery in African coast (Mozambique, Tanzania and Kenya), Sri Lanka, Red Sea and Persian Gulf. To reveal the genetic stock structure and gene mapping studies of F. indicus, we developed 81 polymorphic microsatellites through crossamplification after screening 396 primer pairs from other penaeids. This genetic information will be of immense use in management of stocks and selective breeding programmes of F. indicus.

Cobia, Rachycentron canadum, is an economically important migratory fish distributed in tropical waters worldwide and is a candidate fish species for aquaculture practices. The genetic stock structure of R. canadum distributed along the Indian waters was identified using mitochondrial ATPase 6 and 8 genes. A total of 842 bp sequence of ATPase 6/8 genes obtained in this study revealed 15 haplotypes with mean low nucleotide diversity (π = 0.001) and high haplotype diversity (h = 0.785). AMOVA indicated the genetic differentiation of 90.47% for individuals within the population. This is well supported by co-efficient of genetic differentiation (FST) values obtained for pairwise populations that were low and non-significant with an overall value of 0.002. The parsimony network tree revealed star-like phylogeny and all the haplotypes were connected with each other by single mutational event. The findings of the present study indicated the panmixia nature of the species which can be managed as a unit stock in Indian waters.

Moribund koi carp, Cyprinus carpio koi, from a farm with 50% cumulative mortality were sampled with the aim of isolating and detecting the causative agent. Three bacterial species viz., Citrobacter freundii (NSCF-1), Klebsiella pneumoniae (NSKP-1) and Proteus hauseri [genomospecies 3 of Proteus vulgaris Bio group 3] (NSPH-1) were isolated, identified and characterized on the basis of biochemical tests and sequencing of the 16S rDNA gene using universal bacterial primers. Challenge experiments with these isolates using healthy koi carp showed that P. hauseri induced identical clinical and pathological states within 3 d of intramuscular injection. The results suggest P. hauseri (NSPH-1) was the causative agent. In phylogenetic analysis, strain NSPH-1 formed a distinct cluster with other P. hauseri reference strains with ≥99% sequence similarity. P. hauseri isolates were found sensitive to Ampicillin, Cefalexin, Ciprofloxacin and Cefixime and resistant to Gentamycin, Oxytetracycline, Chloramphenicol, and Kanamycin. The affected fish recovered from the infection after ciprofloxacin treatment.

Cyprinus carpio koi fin (CCKF) cell line was established and characterized from the caudal fin tissue of ornamental common carp, C. carpio koi. This cell line has been maintained in L-15 medium supplemented with 15% foetal bovine serum (FBS) and subcultured more than 52 times over a period of 24 mo. The CCKF cell line consisted of epithelial cells and was able to grow at temperatures between 22 and 35°C with an optimum temperature of 28°C. The growth rate of these cells increased as the proportion of FBS increased from 2 to 20% with optimum growth at the concentrations of 15% FBS. Karyotype analysis revealed that the modal chromosome number of CCKF cells was 2n = 100. Partial amplification and sequencing of fragments of two mitochondrial genes 16S rRNA and COI confirmed that CCKF cell line originated from ornamental common carp. The CCKF cells showed strong reaction to the cytokeratin marker, indicating that it was epithelial in nature. The extracellular products of Vibrio cholerae MTCC 3904 and Aeromonas hydrophila were toxic to the CCKF cells and not susceptible to viral nervous necrosis virus (VNNV). These CCKF cells were confirmed for the absence of Mycoplasma sp. by polymerase chain reaction. Furthermore, 90% of viable cells could be effectively revived 4 mo after cryopreservation from CCKF cell population suggesting the possibility of long-term storage of the cells.

Asian seabass or barramundi (Lates calcarifer) is an important food fish with commercial value and a wide geographic distribution. Though some reports based on molecular and/or morphological data exist, a comprehensive effort to establish species identity across its range is lacking. In order to address this issue and especially to ascertain whether the wide-spread distribution has resulted in bifurcation of the species, we collected Asian seabass samples from various locations representing the Western and Eastern Coastline of India, Andaman and Nicobar Islands, Bangladesh and Australia. Samples from Malaysia, Indonesia, Thailand and Singapore were collected as part of a previous study. DNA sequence variations, including cytochrome c oxidase subunit 1 (COI), 16S rDNA and the highly variable D-loop (or control region), were examined to establish species delineation. Data from all the sequences analyzed concordantly point to the existence of at least two distinct species - one representing the Indian subcontinent plus Myanmar, and a second, representing Southeast Asia (Singapore, Malaysia, Thailand and Indonesia) plus Northern Australia. These data are useful for conservation ecology, aquaculture management, for establishing the extent of genetic diversity in the Asian seabass and implementing selective breeding programs for members of this species complex.