Genome assembly at chromosome scale with telomere ends for Pearlspot, Etroplus suratensis.

The pearlspot, Etroplus suratensis is a climate resilient cichlid fish that exhibits unusual adaptation to salinity. The fish is able to complete full life cycle in diverse salinity habitats ranging from fresh water to marine environments. High-quality primary and phased genome assemblies were generated for pearlspot fish using PacBio HiFi and Arima HiC sequencing technologies, for the first time.

Genome assembly, Full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus.

The mangrove red snapper, Lutjanus argentimaculatus, is a marine food fish of economic and aquaculture importance. The application of genomic selection-based breeding programs for this species is limited by the absence of a reference genome and transcriptome profiles. The current study attempted to fill this void by generating genomic and transcriptomic resources for red snapper.

Meta-analysis to Unravel Core Transcriptomic Responses in Penaeus vannamei Exposed to Biotic and Abiotic Stresses.

Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics.

Transcriptomic variations associated with salinity stress in Penaeus indicus.

Background: The Indian white shrimp, Penaeus indicus a native species of India, is important brackishwater aquaculture species. Shrimps are euryhaline in nature and they regulate osmotic and ionic concentrations by osmoregulatory process. However, variations in abiotic factors such as salinity result in stress to the shrimps during culture period affecting their growth and immunity.

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

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.

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling.

Background: Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers.

Prediction of Novel Probiotic Species Limiting Pathogenic Growth Using Constraint-Based Genome Scale Metabolic Modeling.

The prevalence of bacterial diseases and the application of probiotics to prevent them is a common practice in shrimp aquaculture. A wide range of bacterial species/strains is utilized in probiotic formulations, with proven beneficial effects. However, knowledge of their role in inhibiting the growth of a specific pathogen is restricted.

Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of sensu lato.

Splitting of the genus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera.

QTL for white spot syndrome virus resistance and the sex-determining locus in the Indian black tiger shrimp (Penaeus monodon).

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.

The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs.

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.

Biology, Host Range, Pathogenesis and Diagnosis of White spot syndrome virus.

White spot syndrome virus (WSSV) is the most serious viral pathogen of cultured shrimp. It is a highly virulent virus that can spread quickly and can cause up to 100 % mortality in 3-10 days. WSSV is a large enveloped double stranded DNA virus belonging to genus Whispovirus of the virus family Nimaviridae.

Application of nucleic-acid-based therapeutics for viral infections in shrimp aquaculture.

Viral infections are one of the major reasons for the huge economic losses in shrimp farming. The control of viral diseases in shrimp remains a serious challenge for the shrimp aquacultural industry, with major pathogens, such as the white spot syndrome virus, yellow head virus, Taura syndrome virus, hepatopancreatic parvovirus, and baculoviruses, being geographically widespread. In the absence of a true adaptive immune response system in invertebrates such as shrimp, one of the alternative and more specific approaches to counteract viral infections in shrimp could be the use of molecular-based gene transfer technologies, such as RNA interference (RNAi).