Larimichthys crocea (the large yellow croaker) is one of the most economically significant marine fish in East Asia. While chromosome-scale genome assemblies for three female (XX) geographical populations (Mindong, South China Sea, and Daiqu) were available, the lack of a high-quality male (XY) reference genome has hindered the exploration of male-specific sequences and the molecular mechanisms underlying sex determination. Here, we present the male T2T reference genome for the Mindong population of L. crocea by integrating Oxford Nanopore ultra-long, PacBio HiFi, and Hi-C sequencing. The assembly totals 747.28 Mb with a contig N50 of 31.79 Mb. We further achieved telomere-to-telomere (T2T) assembly and haplotype partitioning of the X and Y sex chromosomes. Telomeric repeats (TTAGGG) were identified at both termini of all 23 autosomes and two sex chromosomes. Moreover, centromeric regions exhibited significant enrichment of six major transposable elements, including DNA MULE, LTR Gypsy, DNA CMC-EnSpm, RC Helitron, LTR ERV1, and DNA TcMar-Tc2, with 76.19–93.42% of their total copies localized to centromeres. Together with a 42 bp tandem repeat (Cen-42), these elements form the centromeric architecture characterized by higher-order repeats (HORs). The T2T genome assembly exhibits high technical quality, with a BUSCO completeness of 99.6% and a base accuracy (QV) exceeding 59.75. The genome annotation yielded 29,933 protein-coding genes, providing a comprehensive map of the male-specific regions. This gap-free male reference genome provides a definitive genetic resource for studying sex-biased traits, sex chromosome evolution, and precision molecular breeding in L. crocea.

Body shape evolution in vertebrates frequently involves modifications in vertebral number or patterns of vertebral fusion, with distinct lineages displaying divergent trajectories. This study investigated the morphological and genetic basis of body shape variation between Hebao red carp (HB, Cyprinus carpio wuyuanensis) and Yellow River carp (YR, Cyprinus carpio haematopterus). Although both subspecies share an identical vertebral count (35), the compressed morphology of HB was attributable to skeletal anomalies, including vertebral shortening and fusion. Genome-wide association and population genetic analyses were performed on F1 and F2 hybrid cohorts to identify loci associated with this phenotype. A total of 231 selective sweep regions were detected across chromosomes A06, A08, A16, B05, and B06, with a prominent locus on chromosome A08 (15.99-16.39 Mb) strongly correlated with body shape traits. Transcriptomic analysis revealed haplotype-dependent expression of rflna within this interval, implicating rflna in axial skeletal patterning. Functional validation using CRISPR/Cas9-mediated knockout of rfln in zebrafish (Danio rerio) induced vertebral malformations, including axial shortening, kyphosis, fusion, and a rounded abdominal profile. These results delineate the morphological and molecular framework governing axial remodeling in HB and highlight a conserved regulatory role for rflna in teleost skeletal development.

Understanding how collective behavior emerges from individual interactions is a fundamental challenge in biology, with practical implications for managing socially complex species like the economically important large yellow croaker (Larimichthys crocea). While animal groups are known to exhibit different collective states, how group size-an intrinsic property-governs the stability and selection of these states, particularly through its interaction with other key factors like individual speed, remains an open question. By comparing an agent-based model (ABM) with empirical data, we demonstrate that group size exerts a profound and non-monotonic influence on schooling dynamics, contingent on locomotor activity. The empirical data were derived from observations of shoals containing 10 and 20 individuals in an open circular arena (radius: 90 cm, water depth: 30 cm). The ABM was then employed to explore a wider gradient of group sizes (N = 20, 50, 100, 300, and 1000). Under low-speed conditions, order increases monotonically with size, with very large schools (N = 1000) stabilizing in a polarized state. Strikingly, this relationship reverses under high-speed conditions: polarization peaks at an intermediate size (N = 100) but significantly declines in the largest groups (N >= 300), which regress to the transitional state and shift toward milling. This critical reversal challenges the prevailing assumption of simple monotonic scaling in collective systems. Our findings establish group size as a key governing parameter whose interaction with individual speed determines collective outcomes. The results demonstrate that the interplay between group size and individual speed serves as a general mechanism giving rise to non-monotonic scalability, where physical and informational constraints overwhelm local ordering beyond a critical group-size-and-speeddependent threshold.

Animal personality, a core component of phenotypic diversity, significantly influences survival, reproduction, and environmental adaptation in animals. Despite its economic and ecological importance in China, the personality traits and their genetic basis remain poorly understood for the large yellow croaker (Larimichthys crocea). In this study, we repeatedly screened individual croakers for exploration (number venturing into a novel environment) and sociability (preference to a conspecific shoal), while also measuring growth performance and conducting a genome-wide association study (GWAS). Key findings include: (1) Consistent inter-individual differences in both exploration and sociability across trials; (2) A notable trend emerged regarding behavioral interaction effects on growth, where individuals exhibiting high exploration-low sociability demonstrated a significantly higher body weight gain rate (BWGR) than those with high exploration-high sociability; and (3) Identification of 4 significant single nucleotide polymorphism (SNP) associated with exploratory behavior via GWAS, pinpointing 28 candidate genes (including ERBB4, ADAM10, LPL, Kansl1, and fh). This study is the first to characterize the population distribution of exploratory and sociability in large yellow croaker, reveal their interaction effect on growth performance, and identify potential genetic loci underlying exploratory behavior. These results provide a crucial theoretical foundation for understanding the behavioral ecology and genetic architecture of fish personality, offering insights to optimize intensive aquaculture management.

Consumer preference for slender-bodied large yellow croaker (Larimichthys crocea) has made body shape an economically important trait in aquaculture. In this study, we integrated geometric morphometrics and genome-wide association analysis (GWAS) to investigate the genetic architecture of body shape variation in large yellow croaker. A composite morphological index combining caudal peduncle height and condition factor effectively classified individuals into two distinct morphotypes: slender (SL) and stout (ST). Geometric morphometric analyses confirmed significant shape differences between SL and ST individuals across age groups. Notably, SL fish exhibited significantly higher critical swimming speeds than ST fish, likely due to their more streamlined body profiles and thinner trunks. GWAS using the binary trait identified multiple significant SNPs on chromosome 17 in the male population, leading to the detection of 54 candidate genes. Among them, tmem38b, ric1, sema4d, tbx3, herc1, grp, and pgam2 are potentially involved in skeletal development and may contribute to the observed body shape divergence. Functional enrichment further highlighted pathways related to cell signaling, morphogenesis, and amino acid metabolism. These findings offer novel insights into the genetic basis of body shape variation in large yellow croaker and provide valuable markers for future marker-assisted selection in breeding programs.

The large yellow croaker (Larimichthys crocea), a cornerstone of China’s marine aquaculture, faces survival challenges in offshore farming due to intensified water currents. To elucidate the genetic basis of swimming performance, a key adaptive trait, we integrated meta-analysis of genome-wide association studies (meta-GWAS) with selection signature analysis across three populations. A genomic selection (GS) program targeting critical swimming speed (Ucrit) was implemented, in which parents with the highest and lowest genomic estimated breeding values (GEBVs) formed selective (SL) and control (CL) lines, respectively. Three populations were analyzed: juveniles from SL (JS) and CL (JT), and adults from SL (AS). Swimming tests showed that JS exhibited 19.5% higher absolute Ucrit than JT (27.99 vs. 23.43 cm·s⁻¹, p < 0.05), with adult Ucrit reaching 61.80 cm·s⁻¹ . Despite genetic differentiation between JS and JT (supported by phylogenetic and linkage disequilibrium analyses), meta-GWAS identified two quantitative trait loci (QTLs), SPC4_1 and SPC4_2, on chromosome 4. Selection scans revealed 97 regions under positive selection, with SPC4_1 showing signatures of recent artificial selection and harboring key genes such as CACNA1E (calcium signaling), GNA11/GNA15 (G-protein coupling), LPL (lipid metabolism), and PODN (connective tissue development). Enriched KEGG pathways included metabolic, biosynthetic, and signal transduction processes, underscoring their potential involvement in swimming performance. This study pioneers the integration of meta-GWAS and selection signature analysis in marine fish, highlights candidate genomic regions responsive to short-term GS. The identified QTLs and candidate genes represent promising targets for future functional validation, providing a foundation for subsequent improvements in offshore aquaculture performance.

Triploid, a key strategy for reproductive control, its comprehensive effects for Larimichthys crocea remain to be elucidated. This study achieving 100% triploid via cold treatment. Using offspring from a single parental pair and rearing in adjacent, non-replicated net pens within an integrated cage system, providing a controlled comparison between triploid and diploid siblings under synchronized environmental conditions. Hatching rates did't differ (p = 0.15). At 20 months post-hatch (mph), diploid reproductive season: stage V in testes ovaries, triploids exhibited impaired gametogenesis: testes stage III; ovaries stage I, leading higher carcass yield (92.93 +/- 0.83% vs. 90.33 +/- 3.35%, p < 0.01), reduced gonadosomatic index (0.58 +/- 0.23 vs. 3.45 +/- 3.14, p < 0.001), 27.05% enhanced body weight uniformity. However, a phenotypic trade-off was observed. Triploid weight was comparable to diploid males (p = 0.71) but lower than diploid females (406.33 +/- 129.26 g; p < 0.05), suggesting triploidization eliminates the female-specific growth advantage by suppressing sexual dimorphism rather than generalized growth impairment. Furthermore, triploids showed similar resistance to Cryptocaryon irritans (p = 0.059) at 132 days post-hatch (dph), lower tolerance to Vibrio alginolyticus (14.82% vs. 21.76%, p < 0.05) at 151 dph, and lower relative swimming speed (BL/s) (2.50 +/- 0.39 vs. 3.12 +/- 0.42, p < 0.05) at 13 mph. These results indicate triploidization balances gains in reproductive control, carcass yield, uniformity against loss of sex-specific growth increments, bacterial disease resistance, and swimming stamina, providing a practical framework for evaluating the commercial and ecological suitability of triploid L. crocea.

Artificial domestication imposes sustained directional selection on cultured populations, driving genomic differentiation and the accumulation of traits favored under anthropogenic breeding regimes. Yet, how genomes respond to long-term selection and how genetic gain accumulates across successive generations remain poorly resolved. Here, we systematically characterized phenotypic improvement, selection response, population genetic structure, genetic diversity, and genomic signatures of selection across multiple generations of artificial domestication in Larimichthys crocea. The results showed that survival after Cryptocaryon irritans challenge increased from G0 to G4, with the selected population showing higher survival than the control. Genomic estimated breeding value based on survival time increased from 70.6 in G0 to 98.0 in G4, corresponding to a cumulative relative gain of 38.8

The utilization of plant protein in aquafeeds to reduce dependence on fishmeal has become an important strategy for improving the sustainability of marine aquaculture. This study investigated the effects of low-fishmeal plant protein diets on growth performance and gut–liver molecular responses in large yellow croaker. A total of 2,048 fish were fed two diets for 206 days: a commercial-like control diet containing 280 g/kg fishmeal (C group) and a low-fishmeal diet containing 100 g/kg fishmeal with increased inclusion of plant protein sources (P group). Growth trials indicated that fish in the C group had significantly higher weight gain rate and specific growth rate than those in the P group (p < 0.001). Transcriptomic analysis identified 546 and 724 differentially expressed genes (DEGs) in the hindgut and liver, respectively. Hindgut DEGs were mainly enriched in pathways associated with lipid metabolism, immune responses, and signal transduction, whereas liver DEGs were primarily involved in lipid metabolism, immune regulation, and apoptosis. Several pathways, including fat digestion and absorption, complement and coagulation cascades, taurine and hypotaurine metabolism, antigen processing and presentation, and cytokine–cytokine receptor interaction, were enriched in both tissues, suggesting coordinated gut–liver regulation. Representative genes involved in lipid metabolism and immune regulation, including apob, scarb1, c3, b2m, and ccr9, exhibited tissue-specific and coordinated expression changes. PPI network analysis further identified c3, scarb1, vwf, and apob as key regulatory nodes potentially involved in coordinated metabolic and immune adaptation. Collectively, these findings provide new insights into the molecular mechanisms underlying gut–liver adaptation to plant-based diets in marine fish.

Large yellow croaker (Larimichthys crocea) is one of the main marine aquaculture species in China, but has faced considerable losses due to Cryptocaryon irritans infection. In this study, we successfully established a C. irritans-susceptible population of large yellow croaker by genomic selection technology. We then compared the immune genetic mechanisms of this susceptible population with those of a large yellow croaker population from eastern Fujian in response to C. irritans infection. GWAS identified 44 significant SNPs across 11 QTL regions on different chromosomes associated with C. irritans infection, with most located on chromosomes 1 and 24. Notably, the QTL region on chromosome 1 overlapped with the resistance QTL region mapped in the C. irritans-resistant population previously established by our team, underscoring its crucial role in conferring resistance to C. irritans infection. RNA-Seq analysis revealed significant differences in immune responses between the two groups, with the susceptible group specifically activating the Jak / Stat signaling pathway and upregulating interleukin-related genes, including il11a, il-5r and il-20r. A combined analysis of the GWAS and RNA-Seq data revealed that cspg4 was located in the overlapping QTL region on chromosome 1 associated with resistance. Upon infection, the expression of cspg4 was significantly higher in the susceptible group compared to the control group. As a downstream factor of interleukins, cspg4 may regulate interleukin expression by activating the Jak / Stat pathway, thereby influencing the body’s normal immune defense functions. These findings provide new insights into the mechanisms of host-parasite immune responses and highlight potential therapeutic targets.

L-amino acid oxidase (laao) is a key immune factor capable of producing reactive oxygen species (ROS) and has been demonstrated to possess significant antibacterial and immunomodulatory functions in a variety of organisms. In recent years, increasing attention has been paid to the role of laao in the immune defense of fish against Cryptocaryon irritans infection. In this study, the laao of large yellow croaker (Larimichthys crocea) was successfully cloned, and its structural and functional characteristics were systematically analyzed. The full-length ORF of large yellow croaker was 1578 bp, encoding 526 amino acids. Structural prediction indicated that the protein possesses typical features of a secretory protein, including a distinct signal peptide region and three potential N-glycosylation sites. The Laao of large yellow croaker shows high conservation at key catalytic residues compared with those of Danio rerio and Bothrops pauloensis. Molecular docking further revealed a clear substrate preference, with hydrophobic amino acids exhibiting the strongest binding affinity, whereas polar substrates showed weaker interactions. Phylogenetic analysis revealed that laao is highly conserved among teleosts, showing the highest sequence similarity to Collichthys lucidus (96.57 %) and Nibea albiflora (81.57 %). The tissue expression analysis demonstrated that laao exhibits a tissue-specific expression pattern in large yellow croaker, being mainly expressed in the gills, fins, kidneys, and spleen, with the lowest expression in the brain. Following C. irritans infection, laao expression in the gills and spleen responded rapidly, reaching a peak at 24 h post-infection. However, although laao expression peaked in the skin as early as 12 h post-infection, its expression level was relatively low. The transcriptomic data before and after infection also confirmed that laao was activated upon C. irritans challenge, showing differential expression with an overall upregulation trend. The qRT-PCR results further demonstrated that overexpression of laao significantly altered the expression patterns of immune-related genes (hif1, tnf-α, il-8, il-1β and stat3) were downregulated, while jak1 was upregulated-suggesting that laao may participate in host immune regulation by suppressing inflammatory signaling and activating cytokine-mediated pathways. In summary, this study reveals the structural features of laao and its response characteristics during C. irritans infection, providing a theoretical basis for further understanding the role of large yellow croaker laao in fish immune defense and for developing novel immune prevention and control strategies.

The yellow boxfish ( Ostracion cubicus) exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics, including a fused dermal plate. Contradictory evolutionary evidence hinders true classification of O. cubicus. To clarify its evolutionary position within Tetraodontiformes, a chromosome-level genome assembly was generated, representing the most contiguous and complete genome to date for this lineage. Notably, O. cubicus possessed the largest genome within the order Tetraodontiformes, primarily due to extensive transposable element expansion. Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups (Ostraciidae-Molidae, Tetraodontidae, and Balistidae-Monacanthidae). Comparative genomic evidence indicated that O. cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa. Although overall genomic architecture was largely conserved, certain genetic and environmental changes may have contributed to its phenotypic adaptations, including climate cooling during the Miocene-Pliocene Transition, recent DNA and long interspersed nuclear element (LINE) transposon bursts, lineage-specific chromosomal rearrangements, and gene family expansion. Many positively selected genes and rapidly evolving genes were associated with skeletal development, including bmp7, egf7, and bmpr2. Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation, such as postn, scpp1, and components of the TGF-β signaling pathway. A derived amino acid substitution in eda, coupled with protein structural modeling, suggested potential molecular convergence in dermal plate formation among teleosts. These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O. cubicus, offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.

The yellow boxfish ( Ostracion cubicus) exhibits a combination of derived morphological traits specialized for coral reef environments and ancestral characteristics, including a fused dermal plate. Contradictory evolutionary evidence hinders true classification of O. cubicus. To clarify its evolutionary position within Tetraodontiformes, a chromosome-level genome assembly was generated, representing the most contiguous and complete genome to date for this lineage. Notably, O. cubicus possessed the largest genome within the order Tetraodontiformes, primarily due to extensive transposable element expansion. Phylogenetic analysis based on 19 whole genomes and 131 mitochondrial genomes resolved Tetraodontiformes into three major sister groups (Ostraciidae-Molidae, Tetraodontidae, and Balistidae-Monacanthidae). Comparative genomic evidence indicated that O. cubicus diverged early from the common ancestor of modern Tetraodontiformes and retained the highest number of HOX genes among surveyed taxa. Although overall genomic architecture was largely conserved, certain genetic and environmental changes may have contributed to its phenotypic adaptations, including climate cooling during the Miocene-Pliocene Transition, recent DNA and long interspersed nuclear element (LINE) transposon bursts, lineage-specific chromosomal rearrangements, and gene family expansion. Many positively selected genes and rapidly evolving genes were associated with skeletal development, including bmp7, egf7, and bmpr2. Transcriptomic comparisons between carapace and tail skin revealed various candidate genes and pathways related to carapace formation, such as postn, scpp1, and components of the TGF-β signaling pathway. A derived amino acid substitution in eda, coupled with protein structural modeling, suggested potential molecular convergence in dermal plate formation among teleosts. These findings provide novel insights into the genomic and developmental basis of carapace evolution and coral reef-adaptation in O. cubicus, offering a strong case for evolutionary balance between genomic conservation with regulatory innovation to achieve coral reef specialization.

Swimming performance is critical to the survival of fish, influencing behaviors such as foraging, predator avoidance, and habitat selection. However, most previous studies have focused on a single type of swimming performance, with limited attention to the integration and interrelation of different swimming performances within the same individual. In this study, we systematically evaluated the relationships among critical swimming speed (Ucrit), burst swimming speed (Uburst), and endurance time in the large yellow croaker (Larimichthys crocea), and investigated the physiological basis underlying individual variation in swimming performance. Using three distinct swimming test protocols, we comprehensively evaluated various types of swimming performance in the same fish. Our findings revealed that the distributions of Ucrit, Uburst, and endurance time approximated normality, with Ucrit displaying significant positive correlations with both Uburst and endurance duration. Histological observations revealed qualitative structural differences in red muscle between groups. Superior swimmers (SS) exhibited more orderly and compact red muscle myofibrils and better-preserved mitochondrial morphology, whereas inferior swimmers (IS) showed disrupted myofibrillar organization and mitochondrial damage. Moreover, these SS individuals exhibited significantly higher activities of key metabolic enzymes (phosphofructokinase, pyruvate kinase, lactate dehydrogenase, and citrate synthase) in white muscle tissue. Together, these results indicate that muscle structural characteristics and metabolic enzyme capacities contribute to individual variation in swimming performance. Our findings highlight that swimming performance is a complex integrative trait shaped by multiple interacting physiological factors, and provide a theoretical foundation for improving the health, welfare, and sustainability of offshore aquaculture practices for large yellow croaker.

The large yellow croaker is one of the most important marine aquaculture species in China, yet its intensive farming industry faces challenges from various pathogens, particularly white spot disease caused by Cryptocaryon irritans. This study aimed to address the issue of white spot disease through genetic breeding. We implemented two consecutive generations of genomic selection (GS) of large yellow croaker against Cryptocaryon irritans, resulting in three continuous generations for subsequent analyses. Challenge tests demonstrated significantly higher 96-h survival rates in the selected generations compared to corresponding controls, with increases of 18.5% and 79.7%, respectively. Survival analysis confirmed that the two selected generations exhibited significantly stronger resistance to C. irritans. By merging the genotype files across generations, a comprehensive dataset containing 1844 individuals and 28,637 SNPs was created. Genomic Estimated Breeding Values (GEBVs) showed steady increases across the three consecutive generations, while genetic structure analysis revealed progressive population differentiation resulting from the two rounds of GS. Through genome-wide selection signature scanning, we identified five positive selection regions (PSRs) distributed across four chromosomes. These regions were enriched for multiple biological pathways related to energy metabolism, immune response, and cell death, including the HIF-1 signaling pathway, NOD-like receptor signaling pathway, and apoptosis. Within these pathways, we identified key candidate genes, including crebbp in the HIF-1 signaling pathway and traf2 involved in immune regulation, both significantly associated with resistance to C. irritans. Our results validate the effectiveness of GS in selective breeding of large yellow croaker against C. irritans and demonstrate that just two consecutive generations of GS can induce substantial differentiation in genetic structure. This approach facilitates the identification of candidate genes and biological pathways associated with disease resistance.

In diploid organisms, deleterious recessive alleles represent a significant component of genetic mutations and often result in lethal effects when in a homozygous state. Large yellow croaker (Larimichthys crocea), a critical marine aquaculture species in China, has shown signs of inbreeding depression due to its limited natural distribution along the coasts of Fujian, Guangdong, and Zhejiang provinces, combined with intensive artificial propagation practices. Identifying loci with deleterious recessive homozygous genotypes is therefore crucial for sustainable industry development. In this study, 1844 large yellow croaker across three consecutive generations were analyzed, resulting in the preliminary identification of 131 loci with missing recessive homozygous genotypes. After excluding false positives through parentage analysis, large-scale validation was conducted using genotype data from 4663 individuals from the MinDong population and 830 individuals from the Daqu population. Ultimately, 22 loci with complete absence of homozygous recessive genotypes were identified across 7337 individuals. The average minor allele frequency (MAF) of these loci was 0.16. Except for LG17_2296176 and LG17_4414232, which exhibited moderate linkage disequilibrium, the remaining 20 loci were largely independent with no observed linkage disequilibrium. Annotation of the 22 loci identified 12 associated genes, including vegfa, sntg2, tcf7, kif2a, lage3, ano10, mpdu1, and others. These genes are involved in key biological processes such as signal transduction regulation, cytoskeletal organization, neural function, and glycan synthesis. To further verify the reliability of the loci with missing recessive homozygous genotypes, heterozygous parental fish carrying 6 randomly selected loci were paired to establish independent families. None of the offspring exhibited recessive homozygous genotypes at these loci, supporting the accuracy of the prior identification. By analyzing genotype data from large yellow croaker populations, this study identifies key loci with missing recessive homozygous genotypes. These findings may offer guidance for selective breeding strategies aimed at minimizing lethal mutations, thereby enhancing population fitness and supporting the sustainable development of the aquaculture industry.

The gut microbiota is becoming increasingly important in enhancing aquaculture productivity. However, there are fewer studies on the effect of host genetic background on the gut microbiota of cultured fish. In the current study, we aimed to determine whether the genetic background of large yellow croaker influences differences in gut microbial composition and growth. To address this objective, we conducted a comparative experiment involving the nearshore cage culture of a selected line (SL) of large yellow croaker, which was subjected to genetic selection for swimming performance, alongside a control line (CL). Both lines were reared under identical environmental and dietary conditions for a duration of six weeks. We employed 16S rRNA gene sequencing technology to analyze the gut microbial composition of the large yellow croaker, and utilized bioinformatics methods to assess the abundance and diversity of the gut microbiota. The findings revealed that the core gut microbiota of both lines primarily comprised Proteobacteria, Firmicutes, and Bacteroidetes. However, a significant disparity in gut microbiota abundance was observed between SL and CL following nearshore cage culture. Additionally, the survival rate of SL reached 64.8 %, significantly higher than the 37.3 % observed in CL. The feed conversion efficiency of SL reached 47.7 %, significantly higher than that of CL (28.6 %). These results underscore the influence of host genetic background on driving differences in gut microbial community composition and production phenotypes. This research offers intriguing insights into the interconnectedness of gut microbiota, fish genetics, and production phenotypes.

Decapterus maruadsi is one of the representative offshore fish in the Western Pacific. Since the last century, it has become a commercially valuable marine fishery species in the Western Pacific region. Despite its high economic value, there is still a lack of high-quality reference genome of D. maruadsi in germplasm resource evaluation research. Here we report a chromosome-level reference genome of D. maruadsi based on Nanopore sequencing and Hi-C technologies. The whole genome was assembled through 169 contigs with a total length of 723.69 Mb and a contig N50 length of 24.67 Mb. By chromosome scaffolding, 23 chromosomes with a total length of 713.58 Mb were constructed. In addition, a total of 199.49 Mb repetitive elements, 33,515 protein-coding genes, and 6,431 ncRNAs were annotated in the reference genome. This reference genome of D. maruadsi will provide a solid theoretical basis not only for the subsequent development of genomic resources of D. maruadsi but also for the formulation of policies related to the protection of D. maruadsi .

Large yellow croaker (Larimichthys crocea) has been demonstrated to be divided into three geographical stocks from south to north along the coast of China, including Nanhai, Mindong, and Daiqu. Although multiple versions of L. crocea have been published, no high-quality Nanhai and Daiqu genomes have been assembled, hampering the assessment of the fine-scale genetic structure and adversely affecting wild stock conservation, fishery management, and germplasm exploitation of large yellow croaker. To fill the gap, we sequenced the genomes of three L. crocea stocks using a combination of PacBio and Hi-C technologies. We assembled each genome (~712 Mb) into 24 chromosomes with a contig N50 of 19.46-29.71 Mb and an integration efficiency of 88.13-92.80%. Furthermore, 26,851-28,133 protein-coding genes were predicted. The reference genomes of three geographical stocks of L. crocea provide vital resources for future research on the conservation and utilization of genetic diversity.

Visceral white spot disease (VWND) caused by Pseudomonas plecoglossicida poses a major threat to the sustainable development of large yellow croaker (Larimichthys crocea) aquaculture. Genome-wide association analysis (GWAS) and RNA-seq research indicated that LcCD82a play an important role in resistance to visceral white spot disease in L. crocea, but the molecular mechanism of LcCD82a response to P. plecoglossicida infection is still unclear. In this study, we cloned and validated the Open Reading Frame (ORF) sequence of LcCD82a and explored the expression profile of LcCD82a in various tissues of L.crocea. In addition, two different transcript variants (LcCD82a-L and LcCD82a-S) of LcCD82a were identified that exhibit alternative splicing patterns after P. plecoglossicida infection, which may be closely related to the immune regulation during pathogenetic process of VWND. In order to explore the function of LcCD82a, we purified the recombinant protein of LcCD82a-L and LcCD82a-S. The bacterial agglutination and apoptosis function analysis showed that LcCD82a may involve in extracellular bacterial recognition, agglutination, and at the same time participate in the process of antigen presentation and induction of cell apoptosis. Collectively, our studies demonstrate that LcCD82a plays a crucial role in regulating apoptosis and antimicrobial immunity.