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Although farmed shrimp contribute to global food security and foreign exchange, the development of genomic resources such as single nucleotide polymorphisms for these shrimp is at slow pace. Public genomic resources like Genbank and Ensembl do not host polymorphism data for shrimp. Therefore, through analysis of the short RNA‐sequence reads generated on pooled‐individual samples, using the latest bioinformatics tools, this study documents data of single nucleotide polymorphisms in two shrimp species, Penaeus vannamei and Penaeus indicus, and presents these data in a searchable user‐friendly webtool, the dbVAST. The webtool also hosts the information about the possible effects that the variations could have on the functioning of the coded protein. This is the first open‐access SNP database of shrimp intended to benefit researchers and academicians by showcasing variations in shrimp transcripts. [ABSTRACT FROM AUTHOR]

The Asian Green Lipped mussel, Perna viridis one of the widely distributed bivalves act as a source of low cost protein providing nutritious meal to the coastal population in the form of well balanced amino acids and micronutrients. The immune system produces antibodies to certain class of proteins present in shellfish meat thereby causing hypersensitive reactions in the body. The next generation integrated transcriptome sequencing approach identifies all the potential allergenic proteins expressed in an animal very effectively. The present study describes the transcriptome of P. viridis based on the sequence data generated using five tissues. Transcriptome level candidate allergens and epitopes were observed and identified that might play a role in hypersensitive reaction to shellfish proteins including certain novel candidate allergens like Ran protein and a filamin A like protein. The existence of epitope hotspots in an important protein, arginine kinase was also observed and the unigenes identified would be a valuable resource for conduct of functional studies. [ABSTRACT FROM AUTHOR]

When no reference genome exists for a species, prior estimation of genome size is essential to understand the genome content and the read depth in NGS (Swathi et al., 2018). Keywords: flow cytometry; genome; genome size; Mugil cephalus EN flow cytometry genome genome size Mugil cephalus 1151 1158 8 01/21/22 20220215 NES 220215 INTRODUCTION The striped grey mullet, I Mugil cephalus i , is the most widespread and economically important high-value species among the family Mugilidae (Order: Mugiliformes), which comprises a total of 26 valid genera and 79 valid species (Eschmeyer et al., 2021). Hence, before assigning a genome size value to this fish species, we have used several tissues and larval stages of fish to minimize the variations and to get an average estimate of the genome size. The approach to estimate genome size from different larval stages and tissues using flow cytometry was to eliminate variations arising due to endogenous or exogenous factors, which might influence the genome size estimate in an organism. [Extracted from the article]

Flow cytometry analysis of haemocytes from control and WSSV-infected shrimps (Group I) revealed that maximum cells were in the G1 phase of the cell cycle as only un-replicated cells are found in this phase (Figure 1a). Many viruses are known to interfere and block the cell cycle (Davy & Doorbar, 2007) or promote cell cycle progression as this would benefit the virus to use the host machinery for its own replication. Other studies also showed a significant increase in ROS during the early infection stages of WSSV with the highest value (2.7 times as compared with the control group) appearing at 3 h after WSSV injection and the high levels were maintained till 48 h post WSSV infection (Ji et al., 2011). Keywords: cell cycle; cytoplasmic free calcium; flow cytometry; Penaeus vannamei; respiratory burst; white spot syndrome virus EN cell cycle cytoplasmic free calcium flow cytometry Penaeus vannamei respiratory burst white spot syndrome virus 320 324 5 12/20/21 20220101 NES 220101 DNA viruses are known to interfere with host cell cycles, which helps in viral replication and adopt different strategies to act on cell cycle regulators for creation of a favourable cell environment (De Beeck & Caillet-Fauquet, 1997). [Extracted from the article]

Shrimp aquaculture over the years has made tremendous progress. The application of modern biotechnological tools, including next-generation sequencing (NGS) techniques, has revolutionized the genomics of commercially important aquaculture species. Genetic improvement programmes targeting desired economic traits are being implemented worldwide with knowledge gained through development of genetic resources. These genetic resources form the basis to understand and develop the strategy for selective breeding of aquaculture species for improved performance. In view of serious disease outbreaks in shrimp aquaculture, and lack of understanding of key biological, reproductive and physiological functions at the molecular level, it has become critical to develop and exploit the available genomic resources to the full potential. This review presents recent progress in development of genetic resources such as transcriptomics, genomics, DNA markers and linkage maps having future potential in selective breeding programmes for commercially important penaeid species. [ABSTRACT FROM AUTHOR]

The health of the pond environment in shrimp farming is important for sustainable and profitable aquaculture, in which sediment–water interface is the most important influencing area. With this objective, the key parameters of water and sediment at the interface was studied in shrimp ponds with varying salinities and compared with the surface water and soil to understand the variations and the underlying causes. Total ammonia nitrogen and total alkalinity were higher in water at the interface as compared to surface water, whereas pH, nitrite, oxide forms of nitrogen (NO3), phosphorus (PO4) and oxidizing bacteria were observed to be lower. There was no significant difference with respect to macrominerals such as sodium, potassium, calcium and magnesium between water at the interface and surface. These changes are profoundly influenced by the uppermost 1.0‐cm thick sediment layer, where the maximum transition of nutrients takes place with the water column. The outcome of the study highlights the effectiveness of water sampling for metabolites at the interface, which reflects at an early stage any potential deterioration of pond environment, which will help the farmer to initiate timely mitigation measures. [ABSTRACT FROM AUTHOR]

Background: Shrimp culture is a fast growing aquaculture sector, but in recent years there has been a shift away from tiger shrimp Penaeus monodon to other species. This is largely due to the susceptibility of P. monodon to white spot syndrome virus disease (Whispovirus sp.) which has impacted production around the world. As female penaeid shrimp grow more rapidly than males, mono-sex production would be advantageous, however little is known about genes controlling or markers associated with sex determination in shrimp. In this study, a mapped set of 3959 transcribed single nucleotide polymorphisms were used to scan the P. monodon genome for loci associated with resistance to white-spot syndrome virus and sex in seven full-sibling tiger shrimp families challenged with white spot syndrome virus. Results: Linkage groups 2, 3, 5, 6, 17, 18, 19, 22, 27 and 43 were found to contain quantitative trait loci significantly associated with hours of survival after white spot syndrome virus infection (P < 0.05 after Bonferroni correction). Nine QTL were significantly associated with hours of survival. Of the SNPs mapping to these and other regions with suggestive associations, many were found to occur in transcripts showing homology to genes with putative immune functions of interest, including genes affecting the action of the ubiquitin-proteasome pathway, lymphocyte-cell function, heat shock proteins, the TOLL pathway, protein kinase signal transduction pathways, mRNA binding proteins, lectins and genes affecting the development and differentiation of the immune system (eg. RUNT protein 1A). Several SNPs significantly associated with sex were mapped to linkage group 30, the strongest associations (P < 0.001 after Bonferroni correction) for 3 SNPs located in a 0.8 cM stretch between positions 43.5 and 44.3 cM where the feminisation gene (FEM-1, affecting sexual differentiation in Caenorhabditis elegans) mapped. Conclusions: The markers for disease resistance and sexual differentiation identified by this study could be useful for marker assisted selection to improve resistance to WSSV and for identifying homogametic female individuals for mono-sex (all female) production. The genes with putative functions affecting immunity and sexual differentiation that were found to closely map to these loci provide leads about the mechanisms affecting these important economic traits in shrimp. [ABSTRACT FROM AUTHOR]

Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i) four landing centres around the east coastline (EC) of India, (ii) survivors of a severe WSSV infection during pond culture (SUR) and (iii) the Andaman Islands (AI) in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. De novo transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp) with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16–129 and 13–130 markers, of length between 139–10.8 and 109.1–10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively) with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits. [ABSTRACT FROM AUTHOR]

Pearlspot ( 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 highyielding 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 ( F ST = 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 ( F CT = 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 demographic 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.