Dynamic epigenomic landscape and gene regulatory networks during embryonic development in Pacific white shrimp (Litopenaeus vannamei) as revealed by histone modification profiling using CUT&Tag.

Background: The Pacific white shrimp (Litopenaeus vannamei) is the most widely farmed shrimp species globally, yet the epigenetic regulation underlying its embryonic development remains largely unexplored. Histone modifications are known to orchestrate gene expression during early development in model organisms, but their role in crustaceans is poorly understood.

Results: In this study, we present the first comprehensive histone modification landscape during L.

The discovery of disease resistance-related factors based on exoskeleton components in the Pacific white shrimp Litopenaeus vannamei.

Shrimp are globally important aquaculture species and a valuable source of protein; the sustainable development of shrimp farming faces serious challenges, however, due to a variety of diseases that affect this species. Acute hepatopancreatic necrosis disease (AHPND), caused by specific Vibrio parahaemolyticus strains (VpAHPND), leads to rapid, large-scale mortality in shrimp, especially the Pacific white shrimp Litopenaeus vannamei. Without effective vaccines or immune stimulants, gaining a thorough understanding of shrimp innate immunity is vital to achieve AHPND control.

Role of multi-omics in aquaculture genetics and breeding: current status and future perspective.

Aquaculture, a fast-growing sector, plays an important role in the supply of nutrient-rich food for humans. Selective breeding is a promising approach to ensure the development and sustainability of intensive aquaculture systems by achieving cumulative and permanent improvements in desirable traits. The advancement of omics technologies offers unprecedented opportunities for genetic improvement, especially in the prioritization of SNPs to be used in the genomic selection and editing of economically important traits.

Molecular and Physiological Responses of to Nitrogen and Phosphorus Stress.

Environmental stressors such as nitrogen and phosphorus play a critical role in regulating the growth and physiological functions of , a key species in aquaculture. This study investigates the effects of nitrogen and phosphorus stress on shrimp growth, oxidative stress, tissue damage, and molecular mechanisms. Exposure to increasing concentrations of nitrogen and phosphorus significantly reduced growth rates.

Acute nitrite exposure causes gut microbiota dysbacteriosis and proliferation of pathogenic Photobacterium in shrimp.

Nitrite exposure has become a significant concern in the aquaculture industry, posing a severe threat to aquatic animals such as shrimp. While studies have reported the adverse effects of nitrite on shrimp growth, the part played by the gut microbiota in shrimp mortality resulting from nitrite exposure is poorly understood. Here, the effects of nitrite on shrimp gut bacterial community were investigated using 16S rRNA amplicon sequencing, bacterial isolation, genomic analysis, and infection experiments.

Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach.

The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( ).

The leopard coral grouper ( ) is a species of significant economic importance. Although artificial cultivation of has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.

Proteome analysis of outer membrane vesicles from Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease.

A specific strain of Vibrio parahaemolyticus (VpAHPND) causes acute hepatopancreatic necrosis disease (AHPND), leading to significant losses in shrimp aquaculture. Outer membrane vesicles (OMVs) are naturally secreted by Gram-negative bacteria, and their significant roles in host-pathogen interactions and pathogenicity have been recognized. In the present study, OMVs were isolated from VpAHPND by differential-ultracentrifugation and used for proteomics analysis.

Signatures of selection in underpinning its rapid adaptation to laboratory conditions.

The dwarf surf clam, , is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions.

Deqformer: high-definition and scalable deep learning probe design method.

Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study.

Symbiotic hemolymph bacteria reduce hexavalent chromium to protect the host from chromium toxicity in Procambarus clarkii.

Hexavalent chromium (Cr(VI)) is a cytotoxic heavy metal pollutant that adversely affects all life forms. Interestingly, the crustacean Procambarus clarkii exhibits a relatively high tolerance to heavy metals. The underlying mechanisms remain unclear.

Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae.

Background: Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments.

Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation.

Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies.

Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle.

Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates, such as the flight evolution of birds. However, whether similar evolutionary processes exist in invertebrates remains poorly understood. Derived from the second-largest animal phylum, scallops are a special group of bivalve molluscs and acquire the evolutionary novelty of the swimming lifestyle, providing excellent models for investigating the coordinated genome and lifestyle evolution.

Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture.

It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for genetic data analysis in aquatic species of farming interest.

Effects of Low-Frequency (0.5 Hz) and High-Frequency (10 Hz) Repetitive Transcranial Magnetic Stimulation on Neurological Function, Motor Function, and Excitability of Cortex in Ischemic Stroke Patients.

Background: Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive neuromodulation technique. The purpose of our study is to explore the effects of low-frequency (0.5 Hz) and high-frequency (10 Hz) rTMS on neurological function, motor function, and excitability of cortex in Chinese ischemic stroke patients.

High-quality reannotation of the king scallop genome reveals no 'gene-rich' feature and evolution of toxin resistance.

The king scallop, is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been published for , however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids.

Genome-Wide Association Study Reveals as the Candidate Gene for Thermal Tolerance in Bay Scallop ().

The increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop () was introduced into China in 1982 and has developed into a vast aquaculture industry in northern China.

Genomic Insights into the Origin and Evolution of Molluscan Red-Bloodedness in the Blood Clam Tegillarca granosa.

Blood clams differ from their molluscan kins by exhibiting a unique red-blood (RB) phenotype; however, the genetic basis and biochemical machinery subserving this evolutionary innovation remain unclear. As a fundamental step toward resolving this mystery, we presented the first chromosome-level genome and comprehensive transcriptomes of the blood clam Tegillarca granosa for an integrated genomic, evolutionary, and functional analyses of clam RB phenotype. We identified blood clam-specific and expanded gene families, as well as gene pathways that are of RB relevant.

The complete mitochondrial genome and phylogenetic analysis of sp. J (Mollusca: Hiatellidae).

The genus is one of most abundant and widespread marine bivalves. To date, its intra-generic phylogeny remains disputed and mitogenome information is therefore much needed. Here, we first report the complete circular mitogenome of sp.