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Abstract Remora albescens, also known as white suckerfish, recognized for its distinctive suction-cup attachment behavior and medicinal significance. In this study, we produced a high-quality chromosome-level genome assembly of R. albescens through the integration of 23.87 Gb PacBio long reads, 64.54 Gb T7 short reads, and 88.63 Gb Hi-C data. Initially, we constructed a contig-level genome assembly totaling 605.30 Mb with a contig N50 of 23.12 Mb. Subsequently, employing Hi-C technology, approximately 99.68% (603.38 Mb) of the contig-level genome was successfully assigned to 23 pseudo-chromosomes. Through the integration of homologous-based predictions, ab initio predictions, and RNA-sequencing methods, we successfully identified a comprehensive set of 22,445 protein-coding genes. Notably, 96.36% (21,629 genes) of these were effectively annotated with functional information. The genome assembly achieved an estimated completeness of 98.1% according to BUSCO analysis. This work promotes the applicability of the R. albescens genome, laying a solid foundation for future investigations into genomics, biology, and medicinal importance within this species.

Abstract Echeneis naucrates, as known as live sharksucker, is famous for the behavior of attaching to hosts using a highly modified dorsal fin with oval-shaped sucking disc. Here, we generated an improved high-quality chromosome-level genome assembly of E. naucrates using Illumina short reads, PacBio long reads and Hi-C data. Our assembled genome spans 572.85 Mb with a contig N50 of 23.19 Mb and is positioned to 24 pseudo-chromosomes. Additionally, at least one telomere was identified for 23 out of 24 chromosomes. Furthermore, we identified a total of 22,161 protein-coding genes, of which 21,402 genes (96.9%) were annotated successfully with functions. The combination of ab initio predictions and Repbase-based searches revealed that 15.57% of the assembled E. naucrates genome was identified as repetitive sequences. The completeness of the genome assembly and the gene annotation were estimated to be 97.5% and 95.4% with BUSCO analyses. This work enhances the utility of the live sharksucker genome and provides a valuable groundwork for the future study of genomics, biology and adaptive evolution in this species.

Global biodiversity loss is one of the most serious environmental crises of the 20th and 21st centuries. Fish diversity, an important component of biodiversity, is also in decline. The conservation of fish diversity is therefore essential for ecosystem management and the sustainable use of resources. Most current aquatic biodiversity surveys rely on conventional methods. The emergence and application of environmental DNA (eDNA) technology has triggered unprecedented innovations in aquatic organism investigation and monitoring. eDNA metabarcoding refers to the selection of appropriate universal primers for different target taxa and the identification of multiple target species in environmental samples via PCR amplification combined with high-throughput sequencing. The Zhoushan Archipelago, located in the northeastern waters of Zhejiang Province, consists of 2 085 islands with a total area of 22 216 square kilometers. Located at the confluence of the Yangtze River, the Qiantang River, the Yongjiang River, and the Taiwan Warm Current, the Zhoushan Archipelago forms a unique and complex hydrological environment, which provides a rich source of nutrients and a suitable habitat for fish. In recent years, the large-scale exploitation of marine resources and marine pollution have led to a serious loss of fish diversity near the Zhoushan Archipelago. To restore fish diversity, conservation efforts have been implemented by the government and researchers, including stricter fishing bans and ecological fish stock enhancement and release. However, the lack of reliable tools to understand the species and assess biodiversity is the most critical issue in conservation efforts. Trawl sampling and morphological identification are the primary fish diversity assessment methods. However, these conventional methods are often inefficient, time-consuming, selective, and destructive. The extensive rocky reefs in the Zhoushan Archipelago make it difficult to use conventional fishery resource survey methods efficiently. Therefore, simple and accurate methods for species diversity monitoring are needed. In this study, Xixuan Island, an offshore island in Zhoushan, was taken as a reference. Four different sampling stations were designed, and a total of 12 water samples were collected in February, May, and November 2019. The species composition and diversity characteristics of offshore fish communities around Xixuan Island were described, and the spatial and temporal differences in fish diversity were evaluated. A total of 33 fish species belonging to 12 orders, 26 families, and 32 genera were detected. Among them, Perciformes has the most abundant species, with 19 species, accounting for approximately 57.6% of all species detected. The diversity and evenness indices of the different sampling seasons were significantly different (P < 0.05), indicating that season may be one of the factors affecting the diversity of offshore fish around Xixuan Island. The results of the combined temporal and spatial analysis showed that more fish species were detected during the breeding season at sampling sites far from the main island side of Zhoushan. By comparing the results with the conventional fishery resources survey, we found a large variation in the dominant species in different seasons, which may be related to the limited sampling site numbers. Temperature and longitude may be important factors affecting the fish diversity around Xixuan Island. The result of enriching the dominant species in each season by heat trees differed significantly from those of traditional surveys, indicating that eDNA cannot completely substitute the conventional survey methods; however, it can be applied as an auxiliary method to monitor fishery resources, improve detection efficiency, and reduce interference to ecosystems. This study not only provides novel methods for the fishery resources survey in offshore Zhoushan but also provides technical support for the subsequent investigation and evaluation of fish diversity and its protection and management.

Astrocytes are the most abundant glial cells in the central nervous system; they participate in crucial biological processes, maintain brain structure, and regulate nervous system function. Exosomes are cell-derived extracellular vesicles containing various bioactive molecules including proteins, peptides, nucleotides, and lipids secreted from their cellular sources. Increasing evidence shows that exosomes participate in a communication network in the nervous system, in which astrocyte-derived exosomes play important roles. In this review, we have summarized the effects of exosomes targeting astrocytes and the astrocyte-derived exosomes targeting other cell types in the central nervous system. We also discuss the potential research directions of the exosome-based communication network in the nervous system. The exosome-based intercellular communication focused on astrocytes is of great significance to the biological and/or pathological processes in different conditions in the brain. New strategies may be developed for the diagnosis and treatment of neurological disorders by focusing on astrocytes as the central cells and utilizing exosomes as communication mediators.

The classification of the Uranoscopidae species is controversial and the Ichthyscopus pollicaris belonging to Uranoscopidae was first reported in 2019. In the present study, the whole genome sequence of I. pollicaris were generated by PacBio and Illumina platforms for the first time. After de novo assembly and correction of the high-quality PacBio data, a 527.25 Mb I. pollicaris genome with an N50 length of 11.25 Mb was finally generated. Meanwhile, 170.41 Mb repeating sequence, 21,263 genes, 784 miRNAs, 2,225 tRNAs, 3004 rRNAs, and 1422 snRNAs were annotated in I. pollicaris genome. Furthermore, 3,168 single-copy orthologous genes were applied to reconstructed the phylogenetic relationship between I. pollicaris and other 11 species. The draft genome sequences have been deposited in NCBI database with the accession number of PRJNA1071810.

The construction of high-quality genomes is fundamental for molecular studies of species. Currently, there are no published genome sequences within the Uranoscopidae family, and research on the genomic characteristics of this family is lacking. In this study, genomic analyses of seven species from the Uranoscopidae family which captured from the southeastern coast of China were conducted using next-generation sequencing technology. The results revealed that the genomic characteristics of the seven species are relatively similar. The genome sizes of the seven Uranoscopidae species ranged from 536.00 Mb to 652.49 Mb, with repeat sequence proportions between 20.09% and 36.64%, and heterozygosity levels ranging from 0.41% to 0.88%. The assembled draft genomes exhibited GC contents of these species ranging from approximately 42.14% to 43.53%. Furthermore, the mitochondrial sequences for the seven species were assembled, with sizes ranging from 14,966 to 18,446 bp. The evolutionary relationships between different species were depicted through the mapping of conserved genes, whole-genome variances and mitochondrial genome sequences. Besides, the historical effective population sizes of all species experienced rapid expansion after the Last Interglacial Period, with three species undergoing bottleneck effects. In conclusion, this study provides a reference for the subsequent construction of high-quality genomes for species within the Uranoscopidae family and offers a rich data resource for further evolutionary research.

As the population continues to age, there is a growing need for elderly care services. In China, home care is widely embraced as a preferred method of caring for the elderly, and it has a promising commercial outlook. The strategic allocation of Elderly Care Service Personnel (ECSP) is a crucial component of the operational procedures for home care services. By strategically assigning elderly service personnel, it is possible to enhance the satisfaction and simultaneously minimize expenses. The issue of rationalizing the assignment of ECSP in the face of restricted resources is a genuine challenge that requires a solution, given the many types of elderly service demands and the skill requirements and time limits of certain projects. This study presents a strategy for assigning personnel on an hourly basis, taking into account time frame limits. This method involves several steps. Firstly, it involves assessing the specific service needs of the elderly, including the required door-to-door service time, service level, and gender preferences. Secondly, it calculates the service satisfaction and service operation cost of the Home Care Service Platform (HCSP) separately. Finally, it constructs a multi-objective elderly service personnel assignment method. This method aims to minimize the ECSP 's travel time and wasted time, maximize the satisfaction of the elderly by considering priority levels and ECSP scores, and minimize the operation cost of the HCSP. A model is developed to assign ECSP for elderly individuals, with the goal of minimizing travel time and wasted time, maximizing elderly satisfaction by considering priority and service personnel rating, and minimizing operating costs for the HCSP. Additionally, if there are unserved elderly individuals, an optimized path model is constructed using a cross-modified genetic algorithm to obtain the optimal matching result. Ultimately, an arithmetic example is employed to demonstrate the practicality and efficiency of the strategy put forth in this research. The findings demonstrate that the model presented in this research possesses distinct advantages in comparison to other conventional models.

Abstract Background Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. Results To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. Conclusions Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.

Pampus belongs to the Perciformes, Stromateoidei, and Stromateidae and are widely distributed throughout the Indian Ocean and the Western Pacific. In this study, we employed next-generation sequencing to generate comprehensive genomic data for Pampus punctatissimus and Pampus echinogaster and subsequently compared the obtained genomic information with the published data of Pampus argenteus. P. echinogaster was identified to be the largest genome size (602 Mb), heterozygosity (1.38%), and repetitive sequence ratio (33.06%), while similar genome sizes between P. punctatissimus (540 Mb) and P. argenteus (550 Mb) were observed. A total of 402,921 and 628,298 SSRs were identified for P. punctatissimus and P. echinogaster, respectively. Additionally, 1,876, 638, and 394 single-copy homologous genes were identified from P. punctatissimus, P. echinogaster, and P. argenteus, respectively. The KEGG enrichment results of the unique single-copy genes to the three species were significantly different in genetic information processing, protein processing, and metabolic functions. The complete mitochondrial genomes of P. punctatissimus and P. echinogaster were successfully assembled, and the resulting phylogenetic relationships align with the currently reported taxonomic status of species in the Stromateoidei. Additionally, population size analysis using PSMC revealed that P. punctatissimus experienced one bottleneck effect, while P. echinogaster underwent two bottleneck events during the Pleistocene Glacial Epoch.

Modeling postprocessing methods can improve the accuracy of quantitative precipitation forecasts. At present, postprocessing methods for precipitation based on statistical analysis are mainly used to correct the precipitation rates or to estimate the precipitation probability. It usually ignores the spatial displacement errors of the precipitation area forecast, thus resulting in low forecast scores. In this study, a new spatial postprocessing method based on rain cluster matching is developed to correct the spatial errors of the precipitation area forecast, in order to improve the forecasting accuracy. With the identification and separation of rain clusters, this method applies the Bayesian multi-objective tracking approach and compares the model forecasting and observed rain clusters at the current time window, so as to obtain the displacement and intensity errors between the model forecasting results and the observations. Finally, these discrepancies are used to correct the model output in the coming time window. With the method proposed in this study, the precipitation forecast based on ECMWF ensemble predication system for summer precipitation processes during 2018—2019 in North China are corrected and tested. Using the CMPAS hourly precipitation analysis dataset as observations, the test results show that, after correction, the mean TS score of the precipitation forecasts at coming time window increases from 0.333 to 0.369, with the correlation coefficient increasing from 0.260 to 0.327, and the mean absolute error decreasing from 2.788 mm to 2.541 mm. We suggest that the method proposed in this study can effectively improve the accuracy of precipitation forecasts.

Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10−6 to 8.77 × 10−6, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.

IntroductionThe cultured Lota lota can meet the market demand in the context of the decline of wild resources, but the disease in the high-density culture process also deserves attention. Therefore, understanding the immune regulation mechanisms of L. lota will be the basis for obtaining high benefits in artificial culture.MethodsTo explore the viral response mechanism of L. lota, RNA-seq was applied to identify the transcriptomic changes of the liver and spleen in L. lota by poly (I:C) stress.ResultsThe DEGs (liver: 2186 to 3123; spleen 1542 to 2622) and up-regulated genes (liver: 1231 to 1776; spleen 769 to 1502) in the liver and spleen increased with the prolongation (12h to 48h) of poly (I:C)-stimulation time. This means L. lota needs to mobilize more functional genes in response to longer periods of poly (I:C)-stimulation. Despite the responses of L. lota to poly (I:C) showed tissue-specificity, we hypothesized that both liver and spleen of L. lota can respond to poly (I:C) challenge may be through promoting apoptosis of DNA-damaged cells, increasing the activity of immune-enhancing enzymes, and increasing energy supply based on DEGs annotation information.ConclusionsOur results demonstrate the transcriptional responses of L. lota to poly (I:C)-stimulation, and these data provide the first resource on the genetic regulation mechanisms of L. lota against viruses. Furthermore, the present study can provide basic information for the prevention of viral diseases in L. lota artificial culture process.

Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophis japonicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C. japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C. japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C. japonicus is closely related with Anarrhichthys ocellatus, Cebidichthys violaceus, and Pholis gunnellus. The results provide more thorough genetic information of C. japonicus and a theoretical basis and reference for further genome-wide analysis.

It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.

The goldstripe ponyfish is a small tropical economic fish in the Leiognathidae family. The genome of this fish was assembled as 24 chromosomes with a total length of 577.66 Mb and 54.81 Mb unanchored contigs using HiFi and Hi-C sequencing technologies. There are 256.7 Mb of repeat elements, which cover 40.59% of the genome, and 21,506 coding genes, which cover 47.68%. According to phylogenetic analysis, the goldstripe ponyfish is closely related to the Sillaginidae family’s Chinese sillago. The distance between goldstripe ponyfish and Chinese sillago in the hierarchical clustering of gene family contractions and expansions is also the shortest, indicating a similarity even greater than that between croakers of the same family (Sciaenidae). The goldstripe ponyfish and Chinese sillago share 25 identical contracted gene families, the majority of which are immune recognition receptors, such as innate immunity-related C-type lectin and butyrophilin families, as well as acquired immunity-related T-cell receptor region V and the surface glycoprotein CD4, implying that these two fishes’ immune systems may adopt similar evolutionary strategy at the genomic level. Additionally, the positively selected genes of the Chinese sillago and the goldstripe ponyfish were enriched in biological functions involved in the cell cycle, such as telomeres, which may account for the disparities in body size and lifespan between the two species.

Coupled with geological and geographical history, climatic oscillations during the Pleistocene period had remarkable effects on species biodiversity and distribution along the northwestern Pacific. To detect the population structure and demographic history of Odontamblyopus lacepedii, 547-bp fragments of the mitochondrial DNA control region were sequenced. A low level of nucleotide diversity (0.0065 ± 0.0037) and a high level of haplotype diversity (0.98 ± 0.01) was observed. The Maximum Likelihood (ML) and Bayesian Inference phylogenetic trees showed no significant genealogical structure corresponding to sampling locations. The results of AMOVA and pairwise FST values revealed some significant genetic differentiation among populations, and the isolation by distance (IBD) analysis supported that the genetic differentiation was associated with the geographic distances. The demographic history of O. lacepedii examined by neutrality tests, mismatch distribution analysis, and Bayesian Skyline Plots (BSP) analysis suggested a sudden population expansion, and the expansion time was estimated to be around the Pleistocene. We hypothesize that the climate changes during the Pleistocene, ocean currents, and larval dispersal capabilities have played an important role in shaping contemporary phylogeographic pattern and population structure of O. lacepedii.

Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

Sleep-stage classification is essential for sleep research. Various automatic judgment programs, including deep learning algorithms using artificial intelligence (AI), have been developed, but have limitations with regard to data format compatibility, human interpretability, cost, and technical requirements. We developed a novel program called GI-SleepNet, generative adversarial network (GAN)-assisted image-based sleep staging for mice that is accurate, versatile, compact, and easy to use. In this program, electroencephalogram and electromyography data are first visualized as images, and then classified into three stages (wake, NREM, and REM) by a supervised image learning algorithm. To increase its accuracy, we adopted GAN and artificially generated fake REM sleep data to equalize the number of stages. This resulted in improved accuracy, and as little as one mouse’s data yielded significant accuracy. Due to its image-based nature, the program is easy to apply to data of different formats, different species of animals, and even outside sleep research. Image data can be easily understood; thus, confirmation by experts is easily obtained, even when there are prediction anomalies. As deep learning in image processing is one of the leading fields in AI, numerous algorithms are also available.

Abstract Background Understanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure. Results A total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses. Conclusion The high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising.

Harpadon nehereus forms one of the most important commercial fisheries along the Bay of Bengal and the southeast coast of China. In this study, the genome-wide survey dataset first produced using next-generation sequencing (NGS) was used to provide general information on the genome size, heterozygosity and repeat sequence ratio of H. nehereus. About 68.74 GB of high-quality sequence data were obtained in total and the genome size was estimated to be 1315 Mb with the 17-mer frequency distribution. The sequence repeat ratio and heterozygosity were calculated to be 52.49% and 0.67%, respectively. A total of 1,027,651 microsatellite motifs were identified and dinucleotide repeat was the most dominant simple sequence repeat (SSR) motif with a frequency of 54.35%. As a by-product of whole genome sequencing, the mitochondrial genome is a powerful tool to investigate the evolutionary relationships between H. nehereus and its relatives. The maximum likelihood (ML) phylogenetic tree was constructed according to the concatenated matrix of amino acids translated from the 13 protein-coding genes (PCGs). Monophyly of two species of the genus Harpadon was revealed in the present study and they formed a monophyletic clade with Saurida with a high bootstrap value of 100%. The results would help to push back the frontiers of genomics and open the doors of molecular diversity as well as conservation genetics studies on this species.

Trichiuridae fish are economically important species and are widely distributed across the nearshore to the open ocean. In the present study, the genomic survey sequencing method was used to analyze the genomic characteristics of five Trichiuridae fish. The calculated genome size was 913 Mb, 868 Mb, 871 Mb, 747 Mb, and 670 Mb for Trichiurus japonicus, Trichiurus nanhaiensis, Trichiurus brevis, Lepturacanthus savala, and Eupleurogrammus muticus, respectively. The average GC content of the five Trichiuridae fish ranged from 39.59% to 42.05%, and the repeat sequence content ranged from 33.21% to 45.87%. The heterozygous ratio of E. muticus was the highest, and that of L. savala was the smallest. The proportion of microsatellite motifs showed a decreasing trend with the increase in repeat numbers: the dinucleotide repeats were dominant, followed by the trinucleotide repeats, tetranucleotide repeats, pentanucleotide repeats, and hexanucleotide repeats. The mitochondrial genomes of five Trichiuridae species were excavated from the genome data, and the ML tree revealed that T. japonicus, T. nanhaiensis, T. brevis, L. savala, and E. muticus formed into one clade. E. muticus showed earlier expansion than the other four species and had a significant population decline at the Last Glacial period by pairwise sequentially Markovian coalescent (PSMC) analysis. This is the first report to sequence and characterize the whole genomes of five Trichiuridae species.

Environmental DNA (eDNA) is becoming a potentially valuable survey technique to monitor marine organisms, especially when the research spans wide-ranging temporal or spatial dimensions. Pampus echinogaster plays an important role in China’s marine fisheries. However, the stock of P. echinogaster is gradually declining, so the fishery protection and management of P. echinogaster are becoming crucial. To achieve the non-invasive and large-scale monitoring of P. echinogaster, we developed a specific quantitative real-time PCR (qPCR) method based on eDNA technology. Results showed that positive signals of P. echinogaster eDNA were successfully detected at 36 sites (82% of the total) in the East China Sea. Significant differences in eDNA concentrations between the southern and northern stations in the East China Sea suggested differences between the life histories of P. echinogaster in these two sea areas. The hotspot was found around the central areas of the East China Sea, especially around the Taizhou seawater (Jiaojiang Estuary). Vertical distribution showed that the eDNA hotspots were primarily concentrated in the middle and upper layers (0–40 m). The distribution results of eDNA hotspots were similar to those of previous findings through motor–trawl capture, indicating the validity of the eDNA results. The relationship between environmental factors and the eDNA concentration showed that PO43-− was significantly correlated with the P. echinogaster eDNA concentration. Overall, our study indicated that the eDNA approach was an effective survey method and can be used as a monitoring tool. We advocate this monitoring approach as supplementary means to guide the management and conservation of large-scale sea areas and thus enable the initially surveying to provide the best information about species-specific distribution.

Understanding fish stock distribution is crucial in the context of sustainable fishery development. Traditional approaches such as net catching, mark recapturing, and visual counting are often time-consuming, less effective, and prone to subjective bias. Recently, environmental DNA (eDNA) technology has made up for the shortcomings of traditional fishery resource survey methods and has been widely used for species monitoring, biodiversity assessment, and biomass estimation. In this study, the eDNA method was used to analyze the potential distribution range of the black sea bream (Acanthopagrus schlegelii) in the East China Sea. The black sea bream-specific primers and probe were designed and applied in the current study. Results showed high black sea bream eDNA concentrations in Dasha fishing ground, Yangtze Estuary fishing ground, and Zhoushan fishing ground. Higher concentrations of black sea bream eDNA were found in water depths approximately 30–40 m. The eDNA hotspots were mainly concentrated at 29°N–33°N, 122°E–125°E, but no significant differences in horizontal or vertical distributions were observed. Temperature is a critical factor in the presence and black sea bream eDNA among environmental variables in the correlation analysis. In addition, a linear formula between environmental factors and the black sea bream eDNA concentration of black sea bream was predicted, which may be helpful for future fishery resource surveys. To summarize, the present paper provides a new idea for marine resource surveys. It also affords a method and theoretical basis for applying the eDNA technology in fishery surveys, which is expected to become an essential tool for fishery resource surveys in the future.

The yellow drum (Nibea albiflora) is a marine teleost fish with strong disease resistance, yet the understanding of its immune response and key functional genes is fragmented. Here, RNA-Seq was used to investigate the regulation pathways and genes involved in the immune response to infection with lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (poly (I:C)) on the spleen of the yellow drum. There were fewer differentially expressed genes (DEGs) in the LPS-infected treatment group at either 6 or 48 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly significantly enriched in c5-branching dibasic acid metabolic and complement and coagulation cascades pathways. The yellow drum responded more strongly to poly (I:C) infection, with 185 and 521 DEGs obtained under 6 and 48 h treatments, respectively. These DEGs were significantly enriched in the Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, Jak-STAT signaling pathway, NOD-like signaling pathway, and cytokine–cytokine receptor interaction. The key functional genes in these pathways played important roles in the immune response and maintenance of immune system homeostasis in the yellow drum. Weighted gene co-expression network analysis (WGCNA) revealed several important hub genes. Although the functions of some genes have not been confirmed, our study still provides significant information for further investigation of the immune system of the yellow drum.

Acanthogobius ommaturus is a large, fast-growing annual fish widely distributed in coastal and estuarine areas. The adults will die after breeding, and its life cycle is only 1 year. The first chromosome-level genome assembly of A. ommaturus was obtained by PacBio and Hi-C sequencing in this study. The final genome assembly after Hi-C correction was 921.49 Mb, with contig N50 and scaffold N50 values of 15.70 Mb and 40.99 Mb, respectively. The assembled sequences were anchored to 22 chromosomes by using Hi-C data. A total of 18,752 protein-coding genes were predicted, 97.90% of which were successfully annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results for genome and gene annotations were 93.6% and 84.6%, respectively. A. ommaturus is phylogenetically closely related to Periophthalmodon magnuspinnatus and Boleophthalmus pectinirostris, diverging approximately 31.9 MYA with the two goby species. The A. ommaturus genome displayed 597 expanded and 3,094 contracted gene families compared with the common ancestor. A total of 1,155 positive selected genes (PSGs) (p < 0.05) were identified. Based on comparative genomic analyses, we obtained several expanded genes such as acsbg2, lrp1, lrp6, and znf638 involved in lipid metabolism. A total of twenty candidate genes were identified under positive selection, which associated with lifespan including ercc6, igf1, polg, and tert. Interspecific collinearity analysis showed a high genomic synteny between A. ommaturus and P. magnuspinnatus. The effective population size of A. ommaturus decreased drastically during 200–100 Ka because of Guxiang ice age and then increased gradually following warm periods. This study provides pivotal genetic resources for in-depth biological and evolutionary studies, and underlies the molecular basis for lipid metabolism.

As molecular mediators, long noncoding RNAs (lncRNAs) are essential for multiple biological processes, such as activating immune response genes and regulating the inflammatory process. The draft genome has been sequenced in yellow catfish (Pelteobagrus fulvidraco), but the expression profile and role of lncRNAs in this fish are still unclear. To identify the immunity-associated lncRNAs in the head kidney of yellow catfish, lncRNA sequences were acquired after Aeromonas hydrophila infection. After high-throughput sequencing, 202 differentially expressed lncRNAs were obtained, including 131 upregulated and 71 downregulated lncRNAs. The functional annotation of cis- and trans-regulatory target genes revealed that many DE-lncRNAs were involved in multiple immunity-associated GO terms and KEGG pathways, such as C-C motif chemokine 3 and interferon regulatory factor 1. Moreover, some lncRNAs might give rise to miRNA. The present study not only revealed the immunomodulatory lncRNAs in head kidney, but also provided a new perspective on the immune response mechanism. The results will facilitate subsequent studies in this species.

Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic–Indo–West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic–Indo–West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.

Salinity variation affects the physiological processes of fish. This study analyzed the transcriptome of the gill tissue of Argyrosomus japonicus to determine the significantly differentially expressed genes (DEGs) of A. japonicus under salinity changes. Transcriptome analysis of nine samples yielded 55.873 Gb of clean data, 64,912 transcripts, and 29,567 unigenes, and 83.62% of the transcripts and 81.89% of the unigenes were annotated. Compared with the control group, the high- and low-salt groups showed 1,731 and 695 DEGs, respectively. Gene Ontology enrichment analysis revealed that the DEGs were significantly enriched in transportation, metabolism, and stress response. Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that the DEGs were significantly enriched in some signaling pathways. Several key genes (KRT1, KRT2, ATP1A, LDH, PFN, ACTB_G1, TUBB, GZMB, MHC2, CCL19, EPX, ANXA5, ACBP, EHF, BHMT, COL1A, and RHOA) were related to salinity adaptation. When environmental salinity fluctuated, genes related to stress, immunity, ion transport, and metabolism became more sensitive. These results suggest that the adaptation of A. japonicus under salinity changes is a complex process that involves multiple genes acting together.

Toll-like receptor (TLR) is a cluster of type I transmembrane proteins that plays a role in innate immunity. Based on the marbled rockfish (Sebastiscus marmoratus) genome database, this study used bioinformatics methods to identify and analyze its TLR gene family members. The results showed that there were 11 TLR gene family members in Sebastiscus marmoratus (SmaTLR), which could be divided into five different subfamilies. The number of amino acids encoded by the Smatlr genes ranged from 637 to 1206. The physicochemical properties of the encoded proteins of different members were also computed. The results of protein structure prediction, phylogenetic relation, and motif analysis showed that the structure and function of the SmaTLRs were relatively conserved. Quantitative Real-Time PCR (qRT-PCR) analysis revealed the expression patterns of SmaTLRs in the gill, liver, spleen, head kidney, kidney, and intestine. SmaTLRs were widely detected in the tested tissues, and they tended to be expressed higher in immune-related tissues. After polyriboinosinic polyribocytidylic acid (poly(I:C)) challenge, SmaTLR14, SmaTLR3, SmaTLR5S, SmaTLR7, and SmaTLR22 were significantly upregulated in the spleen or liver. The results of this study will help to understand the status of TLR gene family members of marbled rockfish and provide a basis for further study of the functional analysis of this gene family.

The evolutionary relationships of lungfish can provide crucial information on the transition from Sarcopterygii to tetrapods. Phylogenomics is necessary to explore accurate internal phylogenetic relationships among all lungfish species. In the context of the lack of genome-wide genetic information for Protopterus amphibious, we are the first to systematically report the transcriptome of P. amphibius and these sequences can be used to enrich the genome-wide genetic information of lungfish. Meanwhile, we also found significant differences in the expression levels of 3,189 genes between the lung and heart of P. amphibious. Based on phylogenomics, 1,094 shared orthologous genes were identified and then applied to reconstruct the internal phylogenetic structure of lungfish species. The reconstructed phylogenetic relationships provide evidence that lungfish is the sister group of terrestrial vertebrates and that Neoceratodus forsteri is the most primitive lungfish. Moreover, the divergence time between the most primitive lungfish and other lungfish species is between 186.11 and 195.36 MYA. Finally, 43 protein metabolism-related, stress response-related, and skeletogenesis-related genes were found to have undergone positive selection and fast evolution in N. forsteri. We suspected that these genes possibly helped ancient fish adapt to the new terrestrial environment and ultimately contributed to its spreading to land.

Temperature is a crucial environmental factor affecting the survival and growth of aquatic organisms. However, the global warming caused by the growth of greenhouse gas emission has severely affected the sustainable development of global nature ecosystem. The change in water temperature has caused a disorder in the aquatic ecosystems. Lota lota lota is a unique member of cold-freshwater codfish; it has an important economic value like its marine relatives. It is also a good model for studying the molecular mechanisms of temperature adaptability of fish. In this study, RNA sequencing based on the Illumina HiSeq™ 2500 platform was used to reveal gene expression at the transcriptome level. Transcriptome profiles were generated from liver and brain samples from fish exposed to (0 °C, 17 °C and 28 °C). A total of 30,958 annotated differentially expressed genes (DEGs) were identified in all comparisons, with more DEGs in high-temperature groups (1668) than in low-temperature groups (1110). GO analysis was divided into three extensive categories and 55 subcategories. A series of candidate genes and pathways associated with temperature responsiveness was detected, mainly including heat-shock protein (HSP) family, fatty acid desaturase (FAD) and antigen processing and presentation. The expression levels of HSP70 were highest amongst those of the HSP family members in the high-temperature groups, implying that HSP70 was an efficient biomarker of high temperature challenge in L. lota lota. An obvious upward trend in the expression of FAD was conducive to regulating fatty acid composition and maintaining membrane fluidity under low-temperature stress. In addition, evidence indicated that elevated temperature had a large influence on immune function and heat stress could upregulate the immune-related pathways in L. lota lota.

Poly (I:C) can work as an immunostimulant and a viral vaccine; however, its functional mechanism in aquatic animals needs to be further investigated. In this study, comparative transcriptomic analyses were performed to investigate the effects of poly (I:C) on Argyrosomus japonicus at 12 h and 48 h postinjection. A total of 194 and 294 differentially expressed genes were obtained in the liver and spleen, respectively. At 12 h, poly (I:C) injection could significantly influence the function of the metabolism-related pathways and immune-related pathways in the liver through the upregulation of the genes GST, LPIN, FOXO1, CYP24A1, ECM1, and SGK1, and the downregulation of the genes IL-1β, CXC19, TNFAIP3, and IRF1. At 48 h, poly (I:C) could enhance the liver energy metabolism by upregulating the genes TXNRD and ECM1, while it also induced some injury in the cells with the downregulation of the genes HBA and CYP24A1. In the spleen, poly (I:C) could regulate the fish immunity and inflammatory response by upregulating the genes DDIT4, C3, EFNA, and MNK, and by downregulating the genes ABCA1, SORT1, TNF, TLR2, IL8, and MHCII at 12 h, and at 48 h, the poly (I:C) had a similar influence as that in the liver. Intersection analyses demonstrated that CYP24A1 and ECM1 were the main functional genes that contributed to the health of the liver. Ten and four genes participated in maintaining the health of the two tissues after 12 h and 48 h, respectively. In summary, our results provided a new insight into ploy (I:C) application in A. japonicus, and it also helped us to better understand the fish response mechanism to the viral vaccine injection.

The complete mitochondrial genome of the Hexagrammos agrammus is presented in this study. The mitochondrial genome is 16,512 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition were similar to those of most other vertebrates. The nucleotide compositions of the heavy strand are 17.27% of G, 26.10% of T, 26.85% of A, and 29.78% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The phylogenetic analysis by neighbour-joining (NJ) method showed that H. agrammus has the closer relationship with Hexagrammos otakii and Hexagrammos lagocephalus in the phylogenetic relationship.

Abstract Background Flathead fishes of the genus Platycephalus are economically important demersal fishes that widely inhabit the continental shelves of tropical and temperate sea waters. This genus has a long history of taxonomic revision, and recently four Platycephalus species (Platycephalus sp. 1, Platycephalus sp. 2, P. indicus, and P. cultellatus) in the northwestern Pacific Ocean (NWP) have been recognized and redescribed. However, many aspects of their systematics and evolutionary history are unclear. Results A total of 411 individuals were sampled from 22 different sites across their distributions in the NWP. Three mitochondrial loci were sequenced to clarify the phylogeny and phylogeographic history of the fishes. The results showed significant differentiation of four Platycephalus species in the NWP with well-supported clades in which Platycephalus sp. 1 and Platycephalus sp. 2 were the closest, clustered with P. cultellatus, while their genetic relationship with P. indicus was the furthest. There were significant genealogical branches corresponding to P. indicus but not to other Platycephalus lineages. We further examined the phylogeographic patterns of 16 Platycephalus sp. 1 populations along the coastlines of China and Japan. A total of 69 haplotypes were obtained, with 23 shared among populations. One dominant haplotypic group, with a modest lineage structure and low levels of haplotype diversity and nucleotide diversity, was observed among Platycephalus sp. 1 populations. The demographic history reconstruction suggested a Platycephalus sp. 1 population expansion event dating back to the late Pleistocene. Conclusions Distributional rang variations may be the crucial factors shaping the genetic relationships of the genus Platycephalus. Reproductive schooling and potential egg/larval dispersal ability, coupled with the effects of ocean currents, are responsible for the present phylogeographic pattern of Platycephalus sp. 1.

Sebastiscus marmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S. marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S. marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S. marmoratus.

The complete mitochondrial genome of Sillaginopsis panijus has been determined for the first time using Sanger Dideoxy DNA sequencing. The mitogenome is a circular molecule of 16,529 bp in length. It contains 37 mitochondrial genes (13 protein-coding genes, two ribosomal RNA, and 22 transfer RNA) and a control region as other bony fishes. In the phylogenetic analysis using 12H-strand protein-coding genes, monotypic S. panijus is situated separately from the genus Sillago. The present phylogeny supports its taxonomic position according to morphology and will be helpful for evolutionary analysis.

Due to difficulty in recognition, many true species have been covered under the synonyms of wide-spread species. To justify the identification of a widely distributed species, Sillago sihama from the Bay of Bengal, Bangladesh, an integrated approach including morphology and DNA barcoding was used. Two unrecognized species of Sillago, i.e., Sillagomuktijoddhai sp. nov. and S. mengjialensis sp. nov., were identified from the coastal area of Bangladesh. S. muktijoddhai sp. nov. has marked differences in the body color, anal fin color, number of gill rakers, snout length, and swimbladder. S. mengjialensis sp. nov. has notable differences in the anal fin color, snout length, and swimbladder and is distinguished from S. muktijoddhai sp. nov. by the body color and swimbladder. The morphological characters of 14 documented Sillago species with two posterior extensions of the swimbladder were referenced and distinguished to accredit the two new species. Genetic analyses of partial mitochondrial cytochrome oxidase subunit I and 16S ribosomal RNA also supported the validity of the new species. This study has increased the number of recognized species of Sillago in the world and confirmed the prevailing misidentification of these two new species in Bangladesh as so-called S. sihama. Moreover, the study confirmed the misidentification of S. mengjialensis sp. nov. in Indonesia as S. sihama and the identification of unknown Sillago sp.1 in India.

The Pleistocene climate oscillations have been proven to have profound influences in the evolutionary processes of marine species and left significantly tractable footprints in genomes of marine fauna. However, such history remains unknown for the Japanese grenadier anchovy Coilia nasus, a relatively large fish found in marine, freshwater and brackish water. In order to provide insight into the phylogeographic pattern and historical demography of C. nasus, we employed the mtDNA D-loop and Cyt b as molecular markers to estimate the genetic variation among populations of C. nasus. We took samples from 18 populations throughout the distribution of C. nasus. Partial sequences of mtDNA D-loop (n = 424) and Cyt b (n = 129) were obtained. Four phylogeographic lineages were revealed by the mtDNA D-loop analysis. Frequency changes of the four lineages throughout the species’ distribution indicated limited genetic exchange among three major geographic regions. Patterns of isolation-by-distance were detected among the populations. Neutrality test, mismatch distribution, and network analyses consistently showed that all the four lineages had populations with relatively stable over time and then subjected to sudden expansion during the late-Pleistocene era (c. 20,000–75,000 years ago). The phylogeographic and demographic history of C. nasus was highly influenced by climatic fluctuations in the Pleistocene. Geographic isolation resulted from Pleistocene climatic fluctuations might have profound impacts on the distribution pattern of genetic variation of C. nasus. Our result also indicated that the population expansion event for C. nasus occured along with habitat continuous expansion during the inter-glacial period.

The effect of impingement cooling using a dual synthetic jet actuator (SJA) with improvement of exit configuration has been investigated experimentally. A hump with cross section of a half-elliptic shape was attached to the flat between the two exits of the SJA. Due to Coanda effect, spread of the synthetic jet was enhanced. Two different humps with height to half width ratios of e = 1.0 and 1.5 have been tested. An infrared camera was utilised to record the temperature of the cooled plate. Statistical results of the temperature have been discussed. With humps, average temperature of the impinged area decreased about 2.6 °C and 0.6 °C corresponding to e = 1.0 and 1.5. Standard deviation of the temperature in the impinged area was almost unchanged. Effective cooled area on the plate was enlarged significantly. For e = 1.0 and 1.5, the effective cooled area with temperature below 20 °C increased by 1.1 and 0.5 times. It means that the improvement is very helpful to applications of electrothermal cooling that involve large cooled area.

Species distribution monitoring and biomass assessment are crucial for fishery management and resource conservation. However, traditional methods such as motor trawling are costly and less effective than the novel environmental DNA (eDNA) approach. This study employs eDNA approach to investigate horizontal and vertical distributions of small yellow croaker (Larimichthys polyactis), an economically important species, in the East China Sea. The analysis of 171 eDNA samples collected from 44 stations using the species-specific primers and Taqman probe suggests a presence of small yellow croaker at 28 sampling layers in 44 stations. Significant differences in croaker eDNA concentrations were revealed among sampling stations and layers, consistent with previous findings through motor-trawl capture offshore and nearshore ichthyoplakton surveys, indicating small yellow croaker exhibits strong regional distribution and layer preference. In addition, we found a high eDNA concentration of small yellow croaker in the surface waters beyond the motor-trawl prohibition line, which confirms spawning grounds have been expanded from nearshore to offshore areas. Such expansion of spawning grounds could be a response by small yellow croaker to stressors such as overfishing, climate change, and nearshore environment contamination. To identify environmental variables potentially associated with small yellow croaker presence and absence, we conducted a correlation analysis between eDNA concentration and environmental variables, and the results provide a guideline for further investigation of fishery resources in the future. In conclusion, this study demonstrates the power of the eDNA approach in monitoring small yellow croaker at extensive geographic scales. The developed protocols and the findings are expected to assist in long-term monitoring and protection programs and benefit sustainable fishery in small yellow croaker.

Understanding patterns of population diversity and structuring among marine populations is of great importance for evolutionary biology, and can also directly inform fisheries management and conservation. In this study, genotyping-by-sequencing was used to assess population genetic diversity and connectivity of Sebastiscus marmoratus. Based on 130 individuals sampled from 10 locations in the northwestern Pacific Ocean, we identified and genotyped 17 653 single-nucleotide polymorphisms. The patterns of genetic diversity and population differentiation suggested that the Okinawa Trough might be the ancestral centre of S. marmoratus after the Last Glacial Maximum. A shallow genetic structure was observed among sampled populations based on the implemented structuring approaches. Surprisingly, we detected genetic homogeneity in two population pairs (i.e. Xiamen–Niigata and Zhuhai–Iki Island), in which populations have large geographical and latitudinal intervals. Population structure and allele frequency distribution based on outlier loci also mirrored the observed genetic homogeneity in the above-mentioned population pairs. Integrated with biological, environmental and genomic data, our results provide possible genetic evidence for parallel evolution. Our study also provides new perspectives on the population structure of S. marmoratus, which could have important implications for sound management and conservation of this fishery species.

Pampus argenteus is an economically important fish that is often erroneously identified as Pampus echinogaster. No population genetic analyses have been performed on the true P. argenteus species. Here, the mitochondrial control region (CR) was used to evaluate the population genetics and elaborate the historical demography of the Silver pomfret collected from six geographical locations in China, Pakistan, and Kuwait. A high level of genetic diversity was demonstrated in this species. Analysis of molecular variance (AMOVA) revealed that the genetic divergence was mainly derived from within the populations (P < 0.05). A historical demographic analysis indicated that the Silver pomfret experienced a recent population expansion during the late Pleistocene. The phylogeographical structure revealed two obvious lineages that diverged in the late Pleistocene, during which the Silver pomfret populations historically experienced exotic divergence and mixed again with differentiated populations. Currently, Silver pomfret populations have insufficient time to attain migration-drift equilibrium. Population genetic data of the Silver pomfret can provide preliminary genetic knowledge for its fishery management.

The 137 individuals of Johnius grypotus were collected from seven localities from the Bohai Sea to the East China Sea. A 549 base pair (bp) fragment of the hypervariable region of the mtDNA control region was sequenced to examine genetic diversity and population structure. The populations of J. grypotus showed high haplotype diversity (h) with a range from 0.7500 to 0.9740 and low nucleotide diversity (π) with a range from 0.0024 to 0.0067. Low and non-significant genetic differentiation was estimated among populations except for North Yellow Sea population, which has a significant genetic difference with other populations. The demographic history examined by mismatch distribution analyses and Bayesian skyline plot (BSP) analyses revealed that a sudden population expansion occurred almost 20 to 40 thousand years before. Relatively recent population expansion in the last glacial period, large dispersal of eggs or larvae carried by coastal current, and the homogeneity of living environment may have an important influence on the population genetic pattern.

The yellow drum (Nibea albiflora) is an important marine economic fish that is widely distributed in the coastal waters of the Northwest Pacific. In order to understand the molecular regulatory mechanism of the yellow drum under salinity stress, in the present study, transcriptome analysis was performed under gradients with six salinities (10, 15, 20, 25, 30, and 35 psu). Compared to 25 psu, 907, 1109, 1309, 18, and 243 differentially expressed genes (DEGs) were obtained under 10, 15, 20, 30, and 35 psu salinities, respectively. The differential gene expression was further validated by quantitative real-time PCR (qPCR). The results of the tendency analysis showed that all DEGs of the yellow drum under salinity fluctuation were mainly divided into three expression trends. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the PI3K-Akt signaling pathway, Jak-STAT signaling pathway as well as the glutathione metabolism and steroid biosynthesis pathways may be the key pathways for the salinity adaptive regulation mechanism of the yellow drum. G protein-coupled receptors (GPCRs), the solute carrier family (SLC), the transient receptor potential cation channel subfamily V member 6 (TRPV6), isocitrate dehydrogenase (IDH1), and fructose-bisphosphate aldolase C-B (ALDOCB) may be the key genes in the response of the yellow drum to salinity stress. This study explored the transcriptional patterns of the yellow drum under salinity stress and provided fundamental information for the study of salinity adaptability in this species.

In this study, we used next-generation sequencing to obtain the complete mitochondrial genome of Jaydia lineata. This mitochondrial genome, consisting of 16,510 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 848 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. The overall base composition shows 26.71% of T, 28.46% of C, 27.24% of A and 17.58% of G, with a slight A + T rich feature (53.95%). The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Lepturacanthus savala is a commercially important marine fish belonging to the family Trichiuridae, with a wide distribution in the Indian-Western Pacific coastal waters. In this study, the complete mitochondrial genome of L. savala has been determined by primer walking methods. The mitogenome is 17,146 bp in length containing 13 protein-coding genes, 2 ribosomal RNA genes, 21 transfer RNA genes, a control region, and an origin of light-chain replication region. The base composition is 28.9% for A, 29.0% for C, 15.7% for G, and 26.4% for T. The maximum-likelihood tree based on whole mitogenome showed that it is the closest related species of Trichiurus.

The complete mitochondrial genome of Acanthogobius stigmothonus is first sequenced in this study. This genome was 16,666 bp in size and contained 37 classic genes, including 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. The gene organization and nucleotide composition were the same with those found in most other Gobiidae fishes. Among 37 genes, 28 were encoded by the heavy strand, while nine were encoded by the light strand. The total nucleotide composition of this genome was 27.4% for adenine (A), 17.6% for guanine (G), 28.2% for cytosine (C), and 26.8% for thymine (T), with a high A + T content of 54.2%. This study will provide a better understanding of population genetic diversity of A. stigmothonus and offer useful information for future studies concerning Gobiidae mitogenome evolution.

In this study, we obtained the complete mitochondrial genome of Hapalogenys analis using whole genome sequencing. With the exception for control region, this mitochondrial genome, consisting of 16,355 base pairs (bp), contains 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 21 transfer RNAs (tRNAs). This mitochondrial genome also lacks a tRNA-Pro gene after tRNA-Thr gene. The overall base composition shows 25.45% of T, 29.73% of C, 28.68% of A and 16.14% of G, with a slight A + T rich feature (54.13%). Sanger sequencing is needed to confirm the accuracy of control region, as well as the lack of tRNA-Pro gene. The mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.