Mitochondrial DNA based diversity studies reveal distinct and sub-structured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters

Not AvailablePearlspot (Etroplus suratensis) is one of the most commercially important brackish water fish species widely found along the coastal regions of peninsular India and Sri Lanka. Pearlspot is known for its tender flesh, delectable taste, culinary tourism and high yielding market value. Information on the genetic makeup of stocks/populations is extremely vital as it forms the basis for future genetic studies. For this, we utilized ATPase6/8 genes of mtDNA of pearlspot populations collected from nine different locations ranging from Ratnagiri in Maharashtra state on the west coast to Chilika in Odisha on the east coast. Sequence analyses of these genes revealed 33 polymorphic sites, which include 17 singleton and 16 parsimony informative sites. Pair-wise genetic differentiation study (FST = 0.75) indicated significant (P <0.001) differences among all the pairs of stocks except those from Chilika and Nagayalanka. The spatial analysis of molecular variance (SAMOVA) significantly delineated the population into four groups (FCT = 0.69, P = 0.0001), namely northwest (Ratnagiri and Goa); southwest (Mangalore and lakes at Vembanad, Ashtamudi and Vellayani in Kerala); southeast (Pulicat in Tamil Nadu) and northeast (Chilika in Odisha and Nagayalanka in Andhra Pradesh). The above delineation is supported by clades of the phylogenetic tree and also the clusters of median joining haplotype network. The high haplotype diversity (0.84), low nucleotide diversity (0.003), and negative values of Tajima’s D (–1.47) and Fu’s Fs statistic (–14.89) are characteristic of populations having recently undergone demo graphic expansion. Mantel test revealed significant isolation by distance. The study identifies highly delineated structured populations with restricted gene flow. If such a stock is overfished, it is highly unlikely that it would recover through migration. For any future breeding programme in this species, it would be desirable to form a base population which incorporates the genetic material from all the locations so that we get a wide gene pool to select from.Not Availabl

Splicing Dysregulation Contributes to the Pathogenicity of Several F9 Exonic Point Variants

Background: Pre‐mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease‐inducing mechanism of synonymous variants, its contribution toward disease phenotype of non‐synonymous variants is underappreciated. Methods: In this study, we analyzed 415 disease‐causing and 120 neutral F9 exonic point variants including both synonymous and non‐synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. Results: The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. Conclusion: Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non‐synonymous variants

Insilico and Invitro anthelmintic properties of phytocompounds in Rostellularia quinquangularis (J. Koenig ex Roxb.) Nees

The present study aimed to evaluate the anthelmintic activity of various extracts of Rostellularia quinquangularis (R. quinquangularis) against adult Indian earthworms (Pheretima posthuma). Petroleum ether extract (PERQ), ethyl acetate extract (RQEA), and ethanol extract (RQEE) of R. quinquangularis were tested at different concentrations (10, 20, 50, and 100 mg/mL), along with the positive control (albendazole) and negative control (normal saline). Anthelmintic activity was assessed based on the duration of paralysis and mortality. The RQEE extract showed significant anthelmintic activity, with the highest activity observed at a concentration of 100 mg/mL, exhibiting paralysis time of 1.62 min and death times of 19.9 min, compared to the standard albendazole. Further, HR LC-MS analysis of the RQEE extract revealed the presence of various phytoconstituents based on m/z signals. Molecular docking analysis using AutoDock Vina indicated that Columbianetin, Dunnione, Cryptochlorogenic acid, Gaylussacin, Luvangetin, and Albendazole showed docking scores of -8.1, -7.9, -7.4, -7.3, -7.2, and -6.8 Kcal/mol, respectively. These results suggest that R. quinquangularis possesses potent anthelmintic activity, supporting its traditional use in medicinal practices.

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus

BackgroundThe genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature.MethodsWe have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes.ResultsWe have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases.ConclusionsPathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes

MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus

Abstract Background The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. Methods We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. Results We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. Conclusions Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes

RNA-Seq based discovery of novel candidate hypersensitive transcripts in Perna viridis

The present study has been envisaged to investigate the transcriptome level candidate hypersensitive transcripts and epitopes that might play a role in shellfish allergy based on the sequence data generated using tissues of P. viridis for understanding the species specific nature of allergy. </p

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Not AvailableShrimp production in India has gradually increased since 2009 with the introduction of Penaeus vannamei. Most coastal states in India have been important contributors to P. vannamei production. However, among the many challenges faced in sustainable shrimp farming, prevention of viral diseases and pond water quality management remain major concerns. In this study, 27 shrimp ponds located in Kalpakkam and Elavur regions of Tamil Nadu were monitored to characterise the pond water parameters including pH, salinity, temperature, alkalinity, ammonia, nitrite, hardness, dissolved oxygen (DO) and Vibrio spp. load. Sudden outbreaks of white spot syndrome virus (WSSV) were observed in some ponds which were found to be associated with variations in abiotic parameters. Parameters such as pH, DO and nitrite were observed to be within the permissible range, while temperature, salinity, Vibrio spp. load and ammonia were relatively higher in certain ponds. The influence of these abiotic factors triggering WSSV outbreak were investigated in this study.Not Availabl

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Not AvailableThe integration of genome information into fisheries and aquaculture management is important to ensure long-term sustainable fishery harvest and aquaculture production. In the present study, a combination of PacBio, Illumina, and Arima Hi-C technologies were applied to construct the genome assembly of M. cephalus, an economically important brackish water aquaculture species.ICAR-CR

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