Panmictic stock structure of milkfish (Chanos chanos,Forssål 1775) from Indian waters determined using mtDNA marker.

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.

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.

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.

Population connectivity and genetic structure of Asian green mussel, Perna viridis along Indian waters assessed using mitochondrial markers.

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.

Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean.

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.

Population genetic structure of Macrobrachium rosenbergii (Palaemonidae) from Indian waters using mitochondrial ATPase 6/8 gene.

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.

Hints for panmixia in Scomberomorus commerson in Indian waters revealed by mitochondrial ATPase 6 and 8 genes.

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.

Weak genetic differentiation in cobia, Rachycentron canadum from Indian waters as inferred from mitochondrial DNA ATPase 6 and 8 genes.

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.

Molecular phylogenetics of three species of the genus Rastrelliger using mitochondrial DNA markers.

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.

Mitochondrial ATPase 6/8 genes to infer the population genetic structure of silver pomfret fish Pampus argenteus along the Indian waters.

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.

Mitochondrial ATPase 6/8 genes reveal genetic divergence in the Coilia dussumieri (Valenciennes, 1848) populations of north east and northwest coasts of India.

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.

Molecular characterization of eight Indian Snakehead species (Pisces: Perciformes Channidae) using RAPD markers.

Murrels (Perciformes; Channidei; Channidae) are unique group of freshwater air breathing fishes having a confined distribution to African and Asian continents. The phylogenetic relationship among eight Channid species viz. Channa aurantimaculata, Channa bleheri, Channa diplogramma, Channa gachua, Channa marulius, Channa punctatus, Channa stewartii and Channa striatus were investigated using RAPD markers. Eight random oligodecamers viz. OPAC03, OPAC05, OPAC07, OPAC09, OPAC19, OPA10, OPA11 and OPA16 were used to generate the RAPD profile. Estimates of Nei's (Genetics, 89:583-590, 1978) unbiased genetic distance (D) demonstrated sufficient genetic divergence to discriminate the samples of different species and the values ranged from 0.3292 to 0.800 The present RAPD analyses strongly substantiate the view of earlier morphological and osteological studies of Channid species, the closer association among species in "gachua" and "marulius" groups.