A new deep-water conger eel of the genus Rhynchoconger (Anguilliformes: Congridae) from the south-west coast of India, Arabian Sea.

A new species of deep-water conger eel, Rhynchoconger bicoloratus sp. nov., is described herein based on three specimens collected from the deep-sea trawlers landing at Kalamukku fishing harbour, off Kochi, Arabian Sea, from a depth beyond 200 m. The new species is distinguished from its congeners by having the following combination of characters: head larger than trunk, rictus at posterior margin of pupil, dorsal fin origin slightly before the pectoral fin insertion, eye diameter 1.7-1.9 times in snout length, ethmovomerine teeth patch broader than long with 41-44 recurved pointed teeth in six or seven rows, vomerine teeth patch pentagonal shaped with single tooth on posterior end, 35 pre-anal vertebrae, body bicoloured, peritoneum and stomach black. Genetically, the new species differs from its congeners with a divergence of 12.9%-20.1% in the mitochondrial COI gene.

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.

A new species of the congrid eel genus Ariosoma (Anguilliformes: Congridae) from the south-west coast of India.

A new congrid eel species, Ariosoma maurostigma sp. nov., is described on the basis of 24 specimens collected from the deep-sea trawl by-catch, Kalamukku Fishing Harbour, off Kerala, Arabian Sea. The new species differs from all other congeners in having the following combination of characters: dark mark or spot on the posterodorsal margin of the eyes; dorsal surface of head with two faint darkish bands across the anterior and posterior margin of the eye; origin of the dorsal fin before the pectoral-fin base; short vomerine teeth patch, ST pores 3, 1 median pore and 1 lateral pore on each side just behind the median pore; preanal vertebrae 47-51; precaudal vertebrae 54-57; total vertebrae 136-142; total pores 129-134. The phylogenetic analysis reveals that the new species is closely related to Ariosoma melanospilos and Ariosoma anale, with divergences of 13.8% and 14.9%, respectively.

Ariosoma indicum sp. nov., a new species of congrid eel (Anguilliformes: Congridae: Bathymyrinae) from the Indian waters.

Ariosoma indicum sp. nov. is described herein based on 12 specimens [(335-433 mm total length (TL)] collected off the Arabian Sea of southwest coast of India and 7 specimens from Digha Mohana, off the Bay of Bengal of northeast coast of India. The new species is distinguished from congeners in having the following combination of the characters: anus positioned anterior to middle of total length, pre-anal length 40.0%-43.1% of TL; short wedge-shaped pointed vomerine teeth patch, three or four rows in anterior portion, tapering posteriorly with four uniserial teeth; supraorbital canal with four or five pores; pre-dorsal vertebrae 9-10; pre-anal vertebrae 49-53; total vertebrae 141-146; body greenish-brown in colour; extremities of the lower jaw with minute dark pigmentation patches before the rictus, bicoloured pectoral fin. A. indicum shares few characters with the Indian water species, Ariosoma gnanadossi, but readily differs from the latter in having more pre-anal vertebrae (49-53 vs. 47 in A. gnanadossi); fewer lateral-line pores (130-137 vs. 145); shorter tail (54.9%-57.9% TL vs. 60.1% TL); smaller eye (15.1%-17.7% HL vs. 19.2% HL); smaller interorbital width (11.8%-15.7% HL vs. 18.2% HL); longer upper jaw (26.9%-30.2% HL vs. 19.2% HL). In addition, molecular analysis using partial mitochondrial COI gene suggests that A. indicum is genetically closer to Ariosoma maurostigma and Ariosoma melanospilos with a divergence of 15.0% and 15.8%, respectively, and forms a well-supported monophyletic clade.

Co-infection of Lactococcus garvieae and Tilapia lake virus (TiLV) in Nile tilapia Oreochromis niloticus cultured in India.

Tilapia lake virus (TiLV) and Lactococcus garvieae are 2 major pathogens of cultured Nile tilapia Oreochromis niloticus. In June-July 2018, a disease outbreak was reported in Nile tilapia cultured in brackish water floating cages in Kerala, India. Affected fish died gradually, and cumulative mortality reached ~75% within 1 mo. In the present study, TiLV and L. garvieae were isolated from the infected fish and confirmed. Nucleotide analysis of the partial sequence of segment 3 revealed that the present TiLV isolate showed 100% similarity with TiLV MF574205 and 97.65% similarity with TiLV KU552135 isolated in Israel. The partial 16S rDNA nucleotide sequence of L. garvieae shared 99% similarity with the 16S rDNA nucleotide sequence of L. garvieae isolated from Nile tilapia in Brazil. Eight virulence genes (hly1, hly2, hly3, NADH oxidase, adhPav, LPxTG-1, LPxTG-4, adhC1) were amplified in the present isolate. In the experimental challenge study, the onset of mortality started earlier in fish co-infected with TiLV and L. garvieae (3 d post-infection [dpi]) compared to other groups. Cumulative mortality (90% at 12 dpi) was significantly higher in the co-infected group than in fish infected with TiLV (60% at 12 dpi) and L. garvieae (40% at 12 dpi) alone. This study reveals that synergistic co-infection with TiLV and other bacteria may increase mortality in disease outbreaks. To the best of our knowledge, this is the first reported co-infection of L. garvieae with TiLV associated with mass mortality in Nile tilapia in India.

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.

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.

Depletion of endogenous germ cells in striped catfish Pangasianodon hypophthalmus (Sauvage, 1878) by heat-chemical treatments.

Germ cell (GC) transplantation (GCT) is a proven powerful reproductive technique to enhance the production efficiency of domesticated animals and aid to the recovery of endangered germ lines. In mammals, several methods have been adopted for the eradication of GCs such as treatment with cytotoxic drugs, irradiation, cold ischaemia and hyperthermic treatment. Some of these methods have also been tried in fishes, and conditions for sterilization of gonads have been established. Here, we report the production of GC-depleted male striped catfish Pangasianodon hypophthalmus in 12 weeks by the combination of heat and chemical treatments. The cytotoxic drug busulphan (40 mg/kg) was intraperitoneally injected into the animals at 2-week intervals (six doses in total) and maintained in water at 38°C between weeks 1 and 12. The effectiveness of the treatment was assessed using gonadal index and histology. At the end of 12 weeks, very severe gonadal degeneration was observed in fish treated with the heat-chemical combination, and 100% of sampled fish (n = 5) were found devoid of endogenous GCs. On contrary, high temperature alone caused minor gonadal degeneration. Results obtained in this study suggest that endogenous GCs of large-bodied fish such as P. hypophthalmus can also be sterilized by heat and chemical treatments within a considerably short period.

Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes).

In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.

Hypoxic stress -responsive genes in air breathing catfish, Clarias magur (Hamilton 1822) and their possible physiological adaptive function.

The Indian catfish, Clarias magur (previous name C. batrachus) is an air breathing fish, inhabitant of aquatic bodies characterized by low dissolved oxygen levels. It is exposed to hypoxic conditions in its natural habitat. Thus, it can be useful model to study the mechanism of hypoxia stress tolerance. In C. magur, molecular processes facilitating its adaptation to hypoxia stress remain largely unexplored, in part due to unavailability of genomic resources. The suppression subtractive hybridization technique (SSH) was employed to compare the differential expression of transcripts under experimental hypoxic conditions, to that of normoxic conditions. Twelve subtracted cDNA libraries (six each forward and reverse) were constructed from brain, heart, liver, muscle, spleen and head kidney tissues. A total of 2020 clones were screened and sequenced, resulting into 1805 high quality expressed sequence tags (ESTs). Annotation of these differentially expressed ESTs resulted into the identification of genes involved in vast majority of pathways/processes affecting metabolism, cellular processes, signal transduction and/or immune functions. Additionally, 18 potential novel genes expressed in hypoxia stress exposed fish were also identified. The study had catalogued the differentially expressed genes from hypoxia stress induced C. magur, where most of them are reported for the first time in a hypoxia-tolerant fish species. The results not only provided insights for the hypoxia stress altered cellular functions in C. magur, but also generated a valuable functional genomics resource to assist targeted studies on functional genomics and future genome projects.

Fish cell line: depositories, web resources and future applications.

Cell lines are important bioresources to study the key biological processes in the areas like virology, pathology, immunology, toxicology, biotechnology, endocrinology and developmental biology. Cell lines developed from fish organs are utilized as a model in vitro system in disease surveillance programs, pharmacology, drug screening and resolving cases of metabolic abnormalities. During last decade, there were consistent efforts made globally to develop new fish cell lines from different organs like brain, eye muscles, fin, gill, heart, kidney, liver, skin, spleen, swim bladder, testes, vertebra etc. This increased use and development of cell lines necessitated the establishment of cell line depositories to store/preserve them and assure their availability to the researchers. These depositories are a source of authenticated and characterized cell lines with set protocols for material transfer agreements, maintenance and shipping as well as logistics enabling cellular research. Hence, it is important to cryopreserve and maintain cell lines in depositories and make them available to the research community. The present article reviews the current status of the fish cell lines available in different depositories across the world, along with the prominent role of cell lines in conservation of life on land or below water. Supplementary Information: The online version contains supplementary material available at 10.1007/s10616-023-00601-2.

A new species of the congrid eel genus Conger (Anguilliformes: Congridae) from the southwest coast of India.

A new species of Conger eel is described from a single specimen (569 mm total length) collected off Kanyakumari, Southwest coast of India, Arabian Sea. The following characters distinguish the new species from other congeners: dorsal-fin origin behind the pectoral-fin tip; head larger, 18.5% TL; longer predorsal length 24.0% TL; relatively shorter trunk, uniserial teeth at the posterior end of vomerine patch; body blackish to dark brown; pectoral fin completely darker; cephalic pores rim whitish; SO pores 3; IO pores 6; pectoral rays 19; total vertebrae 141+. Genetic analysis of the mitochondrial COI gene revealed that the new species is closely related to Conger verreauxi Kaup, 1856 and Conger macrocephalus Kanazawa, 1958, with a genetic divergence of 5.7% and 5.9% respectively.

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.

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.

Mitochondrial DNA variation in natural populations of endangered Indian feather-back fish, Chitala chitala.

Genetic variation at mitochondrial cytochrome b (cyt b) and D-loop region reveals the evidence of population sub-structuring in Indian populations of highly endangered primitive feather-back fish Chitala chitala. Samples collected through commercial catches from eight riverine populations from different geographical locations of India were analyzed for cyt b region (307 bp) and D-loop region (636-716 bp). The sequences of the both the mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The patterns of genetic diversity, haplotypes networks clearly indicated two distinct mitochondrial lineages and mismatch distribution strongly suggest a historical influence on the genetic structure of C. chitala populations. The baseline information on genetic variation and the evidence of population sub-structuring generated from this study would be useful for planning effective strategies for conservation and rehabilitation of this highly endangered species.

New record of Urocaridella antonbruunii (Bruce, 1967) from Southern India with taxonomic Keys of Urocaridella Borradaile, 1915 (Decapoda; Palaemonidae).

The cleaning rock pool shrimp commonly inhabit the shallow waters of reef and crevices regions at 0.5-3.0 m depth. Recent exploration conducted off the Gulf of Mannar and Agatti Island yielded the species, Urocaridella antonbruunii (Bruce, 1967) from the bottom curve of the coral boulder at a depth of 0.5-1.0 m. This is the new record for the Gulf of Mannar and Lakshadweep waters. Major distinguishing morphological characters of the congener's were described and illustrated. The molecular analysis confirmed the species occurrence in Indian waters followed the intraspecific and interspecific genetic divergences (16S gene) were estimated between 0.3-2.1% for within species and 6.4-11.2% for between species respectively. Additionally, we updated and provided the illustrative key characters for all members of the genus Urocaridella.

A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives.

Disease outbreaks caused by bacterial and viral pathogens is a major impediment to the sustainable growth of aquaculture. Rapid and accurate diagnosis of pathogens is crucial for the successful maintenance of fish health and productivity in aquaculture. This review manuscript provides a brief description of conventional disease diagnosis techniques and a detailed description of immunological techniques such as ELISA, immunofluorescence, immunohistochemistry and lateral flow immunoassay. Specific emphasis has been given to detail the molecular techniques, such as PCR and its variants, including the novel isothermal amplification techniques like LAMP and RPA, that can cater to the need of rapid and sensitive point-of-care diagnostics. Hybridization-based methods and molecular typing methods have also been discussed as they find specific applications in diagnostics. The potential of novel techniques such as MALDI-TOF-MS, flow cytometry, and nanotechnology-based methods have also been outlined as they are likely to revolutionise disease diagnosis in the future. This manuscript provides an update on the principle, strengths, weaknesses, applications and variations of each technique, so as to eliminate the qualms for the adoption of these techniques in aquaculture diagnostics.

Study on amyloodiniosis outbreak in captive-bred percula clownfish (Amphiprion percula) and improved control regimens.

The amyloodiniosis outbreak was documented with high mortality of percula clownfish (Amphiprion percula) and subsequently, various therapeutics were evaluated to control the infection. The affected fish exhibited symptoms such as discoloration of the skin and jerky movement with severe respiratory stress. Microscopic examination of the gill and body surface of the infested moribund fish showed the presence of brown coloured spherical shaped trophonts with the size range of 150-300 µM. Copper sulphate (10 ppm) and hydroxychloroquine phosphate (10 ppm) treatment with 14 days of continuous bath showed 76 ± 5.3 and 66 ± 4.3% survival rates. However, formalin (10 ppm) and malachite green (10 ppm) treated groups showed a survival of 41 ± 1.7 and 32.7 ± 1.2% respectively. The present results suggest that, use of copper sulphate to treat amyloodiniosis in clownfish will relatively more effective than other treatment options. The findings will be helpful to mitigate amyloodiniosis in marine finfish aquaculture, particularly marine ornamentals.

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.

Evaluation of genetic variation in the clown Knifefish, Chitala chitala, using allozymes, RAPD, and microsatellites.

Twenty-seven enzyme systems, six random amplified polymorphic DNA (RAPD) primers, and two microsatellite loci were tested to determine intraspecific divergence in the natural population of the endangered Indian featherback fish, Chitala chitala, for the first time. The 262 samples of C. chitala were collected from six riverine locations in India: the Satluj, Ganga (Ghagra, Bhagirathi, and Brahmaputra), Mahanadi, and Narmada river systems. The analysis revealed population subdivisions, with an F(ST) value from 0.1235 (95% confidence 0.0868-0.1621) for RAPD and a combined F(ST) of 0.0344 (95% confidence 0.0340-0.0350) for microsatellite loci. An analysis of 38 allozyme loci did not reveal any polymorphism in the samples from any of the riverine localities; a possible explanation for this could be that the ancestors of Chitala could have faced a population reduction in prehistoric periods, as low allozyme variation is also reported for other species of Chitala from south Asia.