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Abstract 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.

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.

Measurement(s) Whole Genome Sequencing • Chromosome assembly by Hi-C data • Whole Transcriptome Sequencing Technology Type(s) PacBio Sequel System • Hi-C • Illumina HiSeq. 2500 • Illumina NovaSeq. 6000 Sample Characteristic - Organism Takifugu ocellatus

Objective To investigate the frequency of CD36 deletion and gene mutation in voluntary blood donors of Zhongshan city, and to explore the possibility of establishing local CD36 negative platelet donor bank. Methods Platelet CD36 antigen was detected by ELISA in 1 654 voluntary blood donors.Some of the negative samples were confirmed by flow cytometry, and genotyping was also performed. Results Platelet CD36 antigen was negative in 27 cases, accounting for 1.6% (27/1654), among which 1.6% (18/1149) were males and 1.8% (9/505) were females.No significant difference was noticed between males and females in CD36 antigen deletion cases (P>0.05). Fifteen CD36 negative samples were randomly selected, genotyped and sequenced, with type I deletion in 1 case[ 6.7% (1/15)], type Ⅱ deletion in 14 cases[ 93.3% (14/15)], and gene mutation in exon 3-14 detected in 8 cases. Conclusion The frequency of platelet CD36 antigen deletion in Zhongshan is comparable to that in other southern regions of China.The establishment of CD36 negative platelet donor bank is conductive to improve the effectiveness of platelet transfusion.

Abstract Background Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea. Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker. Results In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of C. irritans, in this study, by comparing transcriptome data from different tissues of L. crocea, we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of L. crocea gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein–protein interaction (PPI) network analysis identified 3 hub genes including NFKBIA, TNFAIP3 and CEBPB, and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method. Conclusions In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of L. crocea post C. irritans and the molecular mechanism of pathogenesis for cryptocaryonosis. Highlights Skin and gills are important sources of pro-inflammatory molecules, and their gene expression patterns are tissue-specific after C. irritans infection. 15 DEGs and 5 DE lncRNAs were identified as hub regulatory elements after C. irritans infection The HIF-1 signaling pathway and the complement and coagulation cascade pathway may be key tissue-specific regulatory pathways in gills and skin, respectively.

Takifugu bimaculatus is a new breed of pufferfish that has emerged in the recent twenty years. As a euryhaline species, the habitat of T. bimaculatus ranges from the Yangtze River estuary to the South China Sea. It is always mix-bred with Penaeus monodon and Ruditapes philippinarum. The strong adaptability to temperature and salinity makes it become a candidate species for Takifugu aquaculture in south china. But the slower growth rate and smaller body size limit the further development and promotion of the T. bimaculatus breeding industry. In addition, the sexual maturity of the three years hinders the efficiency of traditional breeding methods. With the increasing demand of market, selecting and breeding new strains with excellent growth-related traits by the markers-assistance selection (MAS) and genome selection (GS) will accelerate the T. bimaculatus breeding industrial upgrading. In this study, 5 traits were employed to represent the growth, including body length (BL), body weight (BW), body length gain (BLG), body weight gain (BWG), and condition factor (K) at 8, 20 and 32-month after hatch. 167 individuals of a full-sib family were genotyped by Whole-genome Resequencing (WGS) and 122,573 SNPs were identified on 22 chromosomes. 9 genome-wide significant SNPs were identified to be associated with different growth-related traits through the Genome-wide association study by Mixed Linear Model (MLM). Surrounding these SNPs, we identified 17 growth-related candidate genes, including mstn1, igfbp5, igfbp2b, igf1r, fgfr3, fgf10 and tgfbr3. These genes are involved in the muscle growth, Insulin-like growth factor (IGF) pathway, Transforming growth factor-β (TGF-β) pathway and Fibroblast growth factor (FGF) pathway. Besides, 10 genome-wide significant SNPs and 5 candidate genes were identified to be associated with K, including pth2r, myh7b, gdf10, hspb8a and midnb, which are involved in osteoblast differentiation, adipogenesis and heat stress response. These results above will contribute to the understanding of the genetic basis of growth and provide several reliable molecular markers for the MAS and GS in T. bimaculatus breeding project.

The Rock Bream (Oplegnathus fasciatus) is an economically important rocky reef fish of the Northwest Pacific Ocean. In recent years, it has been cultivated as an important edible fish in coastal areas of China. Despite its economic importance, genome-wide adaptions of domesticated O. fasciatus are largely unknown. Here we report a chromosome-level reference genome of female O. fasciatus (from the southern population in the subtropical region) using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 120 contigs with a total length of 732.95 Mb and a contig N50 length of 27.33 Mb. After chromosome-level scaffolding, 24 chromosomes with a total length of 723.22 Mb were constructed. Moreover, a total of 27,015 protein-coding genes and 5,880 ncRNAs were annotated in the reference genome. This reference genome of O. fasciatus will provide an important resource not only for basic ecological and population genetic studies but also for dissect artificial selection mechanisms in marine aquaculture.

The common carp is derived from recent whole genome duplication and represents a model for polyploid genome evolution, rare in vertebrates. Here, the authors generate and analyse chromosome-level reference genomes for common carp, and describe subgenome gene expression changes.

As a typical marine adaptive radiation species, most Takifugu species are widely distributed in East Asian offshore, which have diversified morphological characteristics and different ecological habits. The phylogenetic relationship and population structure of the Takifugu species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of Takifugu genus, explore the introgression and natural hybridization between different Takifugu species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 Takifugu samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between Takifugu bimaculatus and Takifugu flavidus, Takifugu oblongus, and Takifugu niphobles, Takifugu rubripes, and Takifugu obscurus, Takifugu xanthoptreus, and Takifugu ocellatus. Further admixture analysis indicated the divergence of T. obscurus population and the bidirectional gene flow between T. bimaculatus and T. flavidus. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between T. bimaculatus and T. flavidus at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of syt1, zar1 and tgfbr1 related to the semilunar reproduction rhythm in T. niphobles, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of T. niphobles specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For Takifugu species, our research provides reliable genetic resources and results for the phylogeny, introgression, hybridization and adaptive evolution, and could be used as a guide for the formulation of the protection and proliferation release policies.

Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker.

High-density single-nucleotide polymorphism (SNP) genotyping array is an essential tool for genetic analyses of animals and plants. Large yellow croaker (Larimichthys crocea) is one of the most commercially important marine fish species in China. Although plenty of SNPs have been identified in large yellow croaker, no high-throughput genotyping array is available. In this study, a high-throughput SNP array named NingXin-I with 600K SNPs was developed and evaluated. A set of 82 large yellow croakers were collected from different locations of China and re-sequenced. A total of 9.34M SNPs were identified by mapping sequence reads to the large yellow croaker reference genome. About 1.98M candidate SNPs were selected for further analyses by using criteria such as SNP quality score and conversion performance in the final array. Finally, 579.5K SNPs evenly distributed across the large yellow croaker genome with an average spacing of 1.19 kb were proceeded to array production. The performance of NingXin-I array was evaluated in 96 large yellow croaker individuals from five populations, and 83.38% SNPs on the array were polymorphic sites. A further test of the NingXin-I array in five closely related species in Sciaenidae identified 26.68–56.23% polymorphic SNP rate across species. A phylogenetic tree inferred by using the genotype data generated by NingXin-I confirmed the phylogenetic distance of the species in Sciaenidae. The performance of NingXin-I in large yellow croaker and the other species in Sciaenidae suggested high accuracy and broad application. The NingXin-I array should be valuable for quantitative genetic studies, such as genome-wide association studies (GWASs), high-density linkage map construction, haplotype analysis, and genome-based selection.

Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.

Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC) that recruits the replicative helicase MCM(2-7) via Cdc6 and Cdt1. We find that the three origins in the single chromosome of the archaeon Sulfolobus islandicus are specified by distinct initiation factors. While two origins are dependent on archaeal homologs of eukaryal Orc1 and Cdc6, the third origin is instead reliant on an archaeal Cdt1 homolog. We exploit the nonessential nature of the orc1-1 gene to investigate the role of ATP binding and hydrolysis in initiator function in vivo and in vitro. We find that the ATP-bound form of Orc1-1 is proficient for replication and implicates hydrolysis of ATP in downregulation of origin activity. Finally, we reveal that ATP and DNA binding by Orc1-1 remodels the protein’s structure rather than that of the DNA template.

Chitinolytic enzymes have an important physiological significance in immune and digestive systems in plants and animals, but chitinase has not been identified as having a role in the digestive system in molluscan. In our study, a novel chitinase homologue, named Ca-Chit, has been cloned and characterized as the oyster Crassostrea angulate. The 3998bp full-length cDNA of Ca-Chit consisted of 23bp 5-UTR, 3288 ORF and 688bp 3-UTR. The deduced amino acids sequence shares homologue with the chitinase of family 18. The molecular weight of the protein was predicted to be 119.389 kDa, with a pI of 6.74. The Ca-Chit protein was a modular enzyme composed of a glycosyl hydrolase family 18 domain, threonine-rich region profile and a putative membrane anchor domain. Gene expression profiles monitored by quantitative RT-PCR in different adult tissues showed that the mRNA of Ca-Chit expressed markedly higher visceral mass than any other tissues. The results of the whole mount in-situ hybridization displayed that Ca-Chit starts to express the visceral mass of D-veliger larvae and then the digestive gland forms a crystalline structure during larval development. Furthermore, the adult oysters challenged by starvation indicated that the Ca-Chit expression would be regulated by feed. All the observations made suggest that Ca-Chit plays an important role in the digestive system of the oyster, Crassostrea angulate.

Speckle noise is a granular interference that degrades image quality in coherent imaging systems, including underwater sonar, Synthetic Aperture Radar (SAR), and medical ultrasound. This study aims to enhance speckle noise reduction through advanced deep learning techniques. We introduce the Deep Gradient-Guidance Network (DGGNet), which features an architecture comprising one encoder and two decoders—one dedicated to image recovery and the other to gradient preservation. Our approach integrates a gradient map and fractional-order total variation into the loss function to guide training. The gradient map provides structural guidance for edge preservation and directs the denoising branch to focus on sharp regions, thereby preventing over-smoothing. The fractional-order total variation mitigates detail ambiguity and excessive smoothing, ensuring rich textures and detailed information are retained. Extensive experiments yield an average Peak Signal-to-Noise Ratio (PSNR) of 31.52 dB and a Structural Similarity Index (SSIM) of 0.863 across various benchmark datasets, including McMaster, Kodak24, BSD68, Set12, and Urban100. DGGNet outperforms existing methods, such as RIDNet, which achieved a PSNR of 31.42 dB and an SSIM of 0.853, thereby establishing new benchmarks in speckle noise reduction.