Aquaculture has become one of the fastest-growing sources of animal protein worldwide, however, climate change is increasingly threatening its productivity and sustainability through more frequent marine heatwaves and episodic cold spells. Phenotypic plasticity may provide rapid, within-generation buffering against such environmental fluctuations, yet the molecular basis of plastic thermal tolerance in aquaculture fishes remains incompletely understood. Here, we integrated transcriptome (RNA-seq) and whole-genome bisulfite sequencing (WGBS) analyses in liver tissues of large yellow croaker (Larimichthys crocea) acclimated to 11 degrees C (cold-acclimated) and 30 degrees C (heat-acclimated). We identified 642 differentially expressed genes (DEGs) in the heat-acclimated group and 293 DEGs in the cold-acclimated group, with stronger fold changes under cold acclimation. Gene Ontology and KEGG analyses highlighted carbohydrate metabolism, endocrine signaling, and stress response pathways. Whole-genome DNA methylation analysis identified 15,813 and 16,508 differentially methylated regions (DMRs) in the heat-and cold-acclimated group, respectively, with 176 (Heat) and 81 (Cold) differentially methylated genes (DMGs) overlapping with DEGs. Key candidates included gck, bpgm, and midn, suggesting potential links between methylation dynamics and the transcriptional regulation of glucose metabolism and hormone responses. Our results suggest that both transcriptional and epigenetic plasticity are associated with thermal tolerance in L. crocea, providing molecular insights into climate adaptation. This work enriches our understanding of plasticity mechanisms in marine aquaculture species and identifies candidate biomarkers for selective breeding and management under global climate change.

Large yellow croaker is an economically important carnivorous marine aquaculture fish in China with high protein requirements. Current fish meal - based feeds face issues like high cost and resource depletion, while plant protein sources have potential but also controversies. To explore this, a 120 - day feeding trial was conducted with a standard commercial feed (CF) and a modified feed (PF) where 70% of fish meal was replaced by plant protein. Results showed no significant growth performance differences between the two groups. Transcriptome analysis identified 557 and 308 differentially expressed genes in the liver and intestine respectively. GO and KEGG enrichment analyses indicated their association with immune response, lipid metabolism, and signal transduction. Five key genes related to metabolism and immune regulation were also found. These findings underscore the potential of integrating plant protein into fish diets, which could significantly enhance sustainable practices in global aquaculture while reducing reliance on fish meal. Emphasizing this transition is crucial for fostering environmental sustainability and supporting the future of aquaculture.

Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp.

Takifugu genus has been brought to the fore in scientific and practical research due to its compact genome, explosive speciation progress and economic value. Here we updated the chromosome-level genome of Takifugu bimaculatus by an ultra-high-density linkage map, a classic and accurate way of chromosome assembly. The map constituted a robust assembly frame, with 92.2% (372.77 Mb) of the draft genome cumulatively placed. With intraspecies and interspecies comparative genomic analysis, we developed a criterion to quantify the differences between assemblies and established a novel way to integrate information from multiple assemblies. The integrated assembly rectified potential mis-assemblies, greatly improving the genome contiguity and correctness. Our results rendered profound information on the genetic recombination of T. bimaculatus and provided new insights into effective genome assembly. The consolidated assembly will be a contributory tool of T. bimaculatus and broadly across the Takifugu by providing a convincing reference for genomic research.

Large yellow croaker is a marine fish with high industrial value. Its traditional breeding in China is established through mass selection and family-based selective breeding. Pedigree records are essential in aquaculture for estimating genetic merits when family-based breeding is applied. Pedigree records can be traced through indi-vidual tagging, which is costly and not practical for small fish. Alternatively, the parentage of an individual can be tracked by using DNA markers. Single nucleotide polymorphisms (SNPs) have been widely used in aqua -culture for parentage assignments due to their even distribution across the genome and are highly adaptive for robust genotyping of a large number of animals. This study aimed to develop an informative SNP panel for paternity assignment in large yellow croaker and evaluate its accuracy using individuals (n = 635) with known pedigrees. A total of 635 samples randomly selected from 11 families and a mixed group were genotyped using the "NingXin-III 55 K" SNP array. High-quality SNPs with high polymorphism were targeted. The informative-ness of the final SNP panel was assessed based on genetic diversity (observed (Hobs) and expected heterozygosity (Hexp) and marker parameters such as discrimination power (DP), probability of exclusion (PE), and poly-morphism information content (PIC)). The final panel consisted of 141 highly informative SNPs (DP: 0.610-0.625, PE: 0.111-0.125, PIC: 0.361-0.375). The cumulative probability of exclusion (CPE) for the selected panel (CPE > 0.999999989) met the standard criteria for animal DNA testing (CPE > 0.999). A successful parentage assignment for 635 individuals was performed using the selected SNPs with a probability >99.99%. In addition, the results were validated with principal component analysis and phylogenetic tree. The findings prove that the developed SNP panel enables accurate parentage assignment in the breeding population of large yellow croaker.

Common carp are among the oldest domesticated fish in the world. As such, there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection. Hebao red carp (HB, Cyprinus carpio wuyuanensis), an indigenous strain in China, is renowned for its unique body morphology and reddish skin. To reveal the genetic basis underlying the distinct skin color of HB, we constructed an improved high-fidelity (HiFi) HB genome with good contiguity, completeness, and correctness. Genome structure comparison was conducted between HB and a representative wild strain, Yellow River carp (YR, C. carpio haematopterus), to identify structural variants and genes under positive selection. Signatures of artificial selection during domestication were identified in HB and YR populations, while phenotype mapping was performed in a segregating population generated by HB×YR crosses. Body color in HB was associated with regions with fixed mutations. The simultaneous mutation and superposition of a pair of homologous genes ( mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB. Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids. This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.

Consideration of the thermal adaptation of species is essential in both evolutionary biology and climate-change biology because it frequently leads to latitudinal gradients of various phenotypes among populations. The spotted sea bass (Lateolabrax maculatus) has a broad latitudinal distribution range along the marginal seas of the Northwest Pacific and thus provides an excellent teleost model for population genetic and climate adaptation studies. We generated over 8.57 million SNP loci using whole-genome resequencing from 100 samples collected at 14 geographic sites (five or ten samples per site). We estimated the genetic structure of the sampled fish and clustered them into three highly differentiated populations. The genetic differentiation pattern estimated by multivariable models combining geographic distance and sea surface temperature differences suggests that isolation by distance and isolation by environment both have significant effects on this species. Further investigation of genome-wide evolutionary signatures of climate adaptation identified many genes related to growth, muscle contraction, and vision that are under positive natural selection. Moreover, the contrasting patterns of natural selection in high-latitude and low-latitude populations prompted different strategies of trade-offs between growth rate and other traits that may play an essential role in adaptation to different local climates. Our results offer an opportunity to better understand the genetic basis of the phenotypic variation in eurythermal fishes inhabiting different climatic regions.

The large yellow croaker ( Larimichthys crocea ) is one of the most economically valuable marine fish in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades. The stock division and species distribution, which have important implications for ecological protection, germplasm recovery, and fishery resource management, have been debated since the 1960s. However, it is still uncertain even how many stocks exist in this species. To address this, we evaluated the fine-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers. Compared with the widely accepted stock boundaries proposed in the 1960s, our results revealed that a climate-driven habitat change probably occurred between the Naozhou (Nanhai) Stock and the Ming-Yuedong (Mindong) Stock. The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait, accompanied by highly asymmetric introgression. In addition, we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas. The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes, whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations. These findings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker, providing a basis for conservation, fisheries management and further evolutionary biology studies.

In order to promote the genetic selective breeding of large yellow croaker, we designed and developed the liquid single nucleotide polymorphism (SNP) array named NingXin-III that based on the genotyping by target sequencing (GBTS) technology and 55 K high-throughput solid chip-based array (NingXin-II SNP array) of large yellow croaker. NingXin-III SNP array contains 98.85% of the loci on the NingXin-II SNP array, and 1535 new loci, totaling 54,990 loci, which are evenly distributed on 24 chromosomes of large yellow croaker. Based on the NingXin-III SNP array, 89 samples from two batches of large yellow croaker were genotyped, and the results showed that the genotyping success rate of NingXin-III SNP array in both batches was over 97.4%, the average genotype concordant rate of individuals in different batches was 99.56%, and the average genotype concordant rate of duplicate individuals in the same batch was 99.7%. A comparison of the genotyping results of the shared loci on NingXin-II and NingXin-III showed that the average genotype concordant rate of common loci between them reached over 96%. In summary, NingXin-III SNP array has a high genotyping accuracy, high reproducibility and no batch effect, which can completely replace NingXin-II SNP array. NingXin-III SNP array will provide important technical support for genetic improvement of important economic traits of large yellow croaker.

The growth rate of allotetraploid common carp (Cyprinus carpio) is sex dimorphic. Thus, intervention for controlling sex is crucial for farming this fish. However, few studies have investigated the spatiotemporal interaction of interaction of various genes related to sex determination/early gonadal differentiation in carp. In this study, comparative gonadal transcriptomic analyses were conducted during 4 key sex differentiaton stages for common carp of both sexes including sex determination stage, pre-gonadal, gonadal differentiation, and maturation stages. Altogether, 305.66 Gb raw reads were obtained form 48 libraries. Differentially expressed genes (DEGs) associated with sex differentiation and gonadal development were identified at each time point. Male-specific DEGs including dmrt1, amh, hmga2, sox3, dmrt2, wnt2b, and wnt9b, and female-biased DEGs including foxl2, cyp19a1a, zp3, zp4, and gper1 were identified. The trend analysis of the key genes of sex determination and gonadal differentiation indicated that 35 dph or earlier is the male sex determination period, 90–100 dph is the key window period of male sex differentiation, and 90–100 dph may be the key window period of female sex differentiation. Functional enrichment analysis showed that DEGs at the testicular undifferentiated stages were mainly enriched in androgen receptor signaling, while DEGs from the onset of testicular differentiation to maturity were enriched in male sex differentiation, spermatogenesis, and male gonadal development. In genetic females, DEGs at the undifferentiated ovarian stage are mainly enriched in insulin-like growth factor (IGF) transport, whereas DEGs from the onset of ovarian differentiation to maturation are mainly enriched in ovarian steroidogenesis and oocyte meiosis. Protein-protein interaction (PPI) analysis revealed that 8 DEGs, including Foxl2, Src, Ncor1, and Smad4, were identified as hub proteins. Additionally, plasma 17β-estradiol and 11-Ketotestosterone levels were sexually dimorphic in C. carpo. The study provide insights into the genetic network of the underlying mechanisms of early sex determination and gonadal differentiation in C. carpo for intervening all-female production in better way.

Grain-sized moxibustion (GS-Moxi) and suspended moxibustion (S-Moxi) represent the two typical local heat therapies in Traditional Chinese Medicine (TCM) and have been extensively used in treating gastric ulcers (GU) in China. However, the difference in biological response between the two moxibustion therapies in treating GU remains unclear. Here we investigated the therapeutic effect and potential mechanistic difference underlying the two moxibustion methods. Ethanol-induced GU model was established and was treated with GS-Moxi or S-Moxi at ST36 and ST21 for 5 days separately. And then, gastric histopathological examination, immunohistochemical staining for repair factors (EGFR, VEGF, Ki67), and 1H NMR-based metabolomics analysis of plasma and stomach of rats were conducted. We found GS-Moxi and S-Moxi effectively alleviated gastric damage and significantly increased the expression of related repair factors. However, S-Moxi corrected aberrant energy metabolism and lipids metabolism in GU rats but had little effect on neurotransmitter-related metabolism, while GS-Moxi regulated energy metabolism and neurotransmitter-related metabolism in GU rats but had no effect on lipids metabolism. We further proposed that the main target of S-Moxi may be liver and vasculature, whereas GS-Moxi specially targeted the stomach via regulating nervous system. This study strongly verified the outstanding gastroprotective effects of moxibustion and enriched our understanding of the varied biological responses triggered by different moxibustion methods.

The environment contains a large extent of chemical information, which could be detected as olfactory sense. Olfactory in vertebrates plays important roles on many aspects during life time, including localizing prey or food, avoiding predators, mating behavior and social communication. Considering the essential role of olfactory receptors in the specific recognition of diverse stimuli, understanding the evolutionary dynamics of olfactory receptors in teleost means a lot, especially in the allotetraploid common carp, who has undergone the fourth whole-genome duplication event. Here, we identified the whole set of olfactory receptor genes in representative teleosts and found a significant contraction in common carp when compared with other teleosts. Odorant receptor genes (OR) occupy the most among four groups of olfactory receptors, including 33 functional genes and 16 pseudogenes. Furthermore, 6 trace amine-associated receptor (TAAR) genes (including 1 pseudogene), 7 odorant-related-A receptor genes, and 10 olfactory C family receptor genes (including 3 pseudogenes) were identified in common carp. Phylogenetic and motif analysis were performed to illustrate the phylogenetic relationship and structural conservation of teleost olfactory receptors. Selection pressure analysis suggested that olfactory receptor groups in common carp were all under relaxed purifying-selection. Additionally, gene expression divergences for olfactory receptor genes were investigated during embryonic development stages of common carp. We aim to determine the abundance of common carp olfactory receptor genes, explore the evolutionary fate and expression dynamics, and provide some genomic clues for the evolution of polyploid olfactory after whole-genome duplication and for future studies of teleost olfactory.

Heat tolerance is an important ability for fish to cope with increased temperature. Large yellow croaker (Larimichthys crocea) is one of the most economically important mariculture fish in China. However, the sustainable development of large yellow croaker aquaculture has long been hampered by extremely high temperature in summer, which is further intensified by the ever-increased global warming. To relieve mass death caused by extreme heat events, it is essential to improve the heat tolerance of this species, which will benefit from a comprehensive understanding of the genetic basis underlying heat tolerance. Here, using a 650 K high density SNP array, we conducted a genome-wide association study (GWAS) on acute heat tolerance (AHT) of large yellow croaker. As a result, 5 significant single nucleotide polymorphisms (SNPs) on 4 chromosomes were identified, indicating the polygenic control characteristics of this trait. A clear peak on Chr19 was found and most of the nearby genes showed differential expression during heat stress, indicating the potential relevance of this region with AHT. Based on the 5 identified SNPs, we predicted 30 candidate genes including heat shock factor protein 1, DnaJ homolog subfamily B member 4, protein Hikeshi, protein disulfide-isomerase A3 etc. Further comparative and validation analysis suggested the importance of blood vessel regulation, heat shock response and endoplasmic reticulum stress response in mediating the interindividual AHT variation of large yellow croaker. These results provide insights into the genetic basis of AHT in fish and will be helpful for heat-tolerance improvement of large yellow croaker by marker-assisted selection.

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

ABSTRACTThe diploidPoropuntius huangchuchieniin the cyprinid family, which is distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp. Therefore, theP. huangchuchienigenome is essential for polyploidy evolution studies in Cyprinidae. Here, we report a chromosome-level genome assembly ofP. huangchuchieniby integrating Oxford Nanopore and Hi-C technology. The assembled genome size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed thatP. huangchuchienidiverged fromCyprinus carpioat approximately 12 Mya. Genome comparison betweenP. huangchuchieniand the B subgenome ofC. carpioprovided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified betweenP. huangchuchieniandC. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genomic and genetic analyses. The high-quality genomic dataset created forP. huangchuchieniprovides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.

当前我国儿童亚健康状态的人群比例已超过70％.由于亚健康状态并不纳入临床疾病的范畴,只表现为个人身心感受的不适,因此常常被忽略.近年来,我国医学领域的专家学者对疾病的研究逐渐从临床疾病转向非疾病的亚健康状态.然而,多数研究只集中于成人,对儿童亚健康状态的研究尚不完善.基于中医阴阳、脏腑、气血理论,结合小儿的生理和病理特点,总结和归纳少儿临床常见的亚健康状态表现,建立少儿亚健康状态的中医辨识体系和中医防治方案,以期降低儿童亚健康状态的比例,预防疾病的发生发展.

本文基于中医学八纲辨证理论,并根据厦门大学医学院杨宗保教授多年的临床经验总结出人体15大亚健康状态类型,分别为:气虚、血虚、津亏、精虚、气滞、血瘀、痰湿、风寒、寒湿、虚寒、风热、脏热(包括肺热、肝火、心火、胃火、大肠火)、湿热(包括脾胃湿热、肝胆湿热、大肠湿热、膀胱湿热、湿热痹症)、虚热、过敏状态.

OBJECTIVE:To investigate the effect of refined moxibustion on expression of gastric mucosal epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF), and changes of metabolite profiles in gastric ulcer (GU) rats, so as to analyze its mechanism underlying improvement of GU.METHODS:Male SD rats were randomized into control, model, acupoint moxibustion groups (n=6 per group). The GU model was induced by cold-restraint stress. The ignited refined moxa was applied to bilateral "Liangmen" (ST21) and "Zusanli" (ST36) for 3 cones/acupoint, once daily for 7 days. Then, we employed 1H NMR-based metabolomics approach to analyze the metabolic profiles of serum and stomach tissue samples. The conventional histopathological changes of the gastric mucosa were observed by H.E. stain and the expressions of EGFR and VEGF in the gastric mucosa were detected by immunohistochemistry.RESULTS:Compared to the control group, the expression levels of EGFR and VEGF were significantly increased in the model group (P<0.01, P<0.05), and further notably up-regulated in the acupoint moxibustion group (P<0.001, P<0.01). Results of H.E. staining showed damage of the folds of gastric mucosa, disordered arrangement of the glands, infiltration of inflammatory cells and unclear structure of gastric mucosa in the model group, which was relatively milder in the acupoint moxibustion group. 1H-NMR technical analysis showed that in comparison with the control group, 11 and 11 metabolites in the stomach extract and plasma were increased, 10 in the gastric tissue and 3 in the plasma were decreased in the GU model group; while in comparison with the model group, 17 differently expressed metabolites in the gastric extract and 10 metabolites in the plasma restored to their levels of control group after the acupoint moxibustion intervention. These metabolites participate in 12 metabolic pathways including glycine, serine and threonine metabolism, glutathione metabolism, glycine metabolism, alanine, aspartic acid and glutamic acid metabolism, purine metabolism, glyoxylic acid and digarboxylic acid metabolism, biosynthesis of aminoacyl-tRNA, amino sugar and nucleotide sugar metabolism, cysteine and methionine metabolism, citrate cycle, pyruvate metabolism, and the mutual conversion of pentose and glucuronate，suggesting their involvement in moxibustion-induced improvement of GU.CONCLUSION:Refined moxibustion at ST21 and ST36 can up-regulate the expression of EGFR and VEGF in the gastric mucosa and lessen gastric mucosal injury, which may be related to its effects in reducing GU-induced metabolic disorders, including sugar, purine, amino acid, and phospholipid metabolism and antioxidant defense system.