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The fish species Oplegnathus fasciatus exhibits an X 1 X 1 X 2 X 2 /X 1 X 2 Y sex determination mechanism. This species holds considerable economic value and displays pronounced sexual dimorphism in growth. Therefore, the development of a rapid and accurate method for sex identification is critical to enhancing breeding efficiency and maximizing production value. Using third-generation PacBio whole-genome sequencing, we identified a homologous region in the samd3/elf3 intergenic region of the X and Y chromosomes of O. fasciatus. Analysis of the whole-genome sequence revealed a large DNA insertion marker fragment within this region. Using specifically designed primers, two bands of 390 bp and 1008 bp were successfully amplified in males, whereas only a single 390 bp band was detected in females. This marker can be easily distinguished by agarose gel electrophoresis, greatly enhancing the efficiency and accuracy of sex identification. This study not only expands the molecular marker system for sex identification of O. fasciatus but also offers a valuable methodological reference for sex identification in other economically important fish species. These findings have significant implications for germplasm improvement and efficient selection in aquaculture., Competing Interests: Declarations. Conflict of Interest: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond., (© 2023 John Wiley & Sons Ltd.)

Lysozymes are crucial enzymes involved in the innate immune response against bacterial pathogens. In this study, we identified and characterized a goose-type lysozyme gene (SsLyG) from the black rockfish Sebastes schlegelii, an economically important aquaculture species. The deduced amino acid sequence of SsLyG contains 495 residues, which inculded a signal peptide, an immunoglobulin domain, and a goose egg-white lysozyme (GEWL) domain. Tissue expression analysis revealed the highest SsLyG levels in blood, and its transcription was significantly upregulated in the spleen and kidney upon bacterial and polyI:C challenges. Recombinant SsLyGE (rSsLyGE) exhibited lytic activity against Micrococcus lysodeikticus and concentration-dependent binding ability to Staphylococcus aureus and Micrococcus luteus. Furthermore, rSsLyGE promoted peripheral blood lymphocyte proliferation, enhanced macrophage respiratory burst activity, and increased reactive oxygen species production. RNA interference-mediated knockdown of SsLyG resulted in higher bacterial loads in the liver and spleen after Listonella anguillarum challenge, suggesting its role in early antibacterial defense. Collectively, these findings provide insights into the immune function of SsLyG and its potential application in developing antimicrobial strategies for aquaculture., Competing Interests: Declaration of competing interest The authors declare that they have no competing interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species., Objective: To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis., Methods: We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea., Results: In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (H d  = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise F ST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak., Conclusions: C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately., Competing Interests: Declarations. Conflict of interest: BH Yun, YH Kim, HS Han, and IC Bang declare that they have no conflict of interest. Ethical approval: For each sample was obtained under observe the guidance of the Korean Ministry of Environment and the Korea National Park Service., (© 2024. The Author(s) under exclusive licence to The Genetics Society of Korea.)

Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non-native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change-driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene., (© 2024 The Author(s). Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Planiliza haematocheilus, a teleostan species noted for its ecological adaptability and economic significance, thrives in both freshwater and marine environments. This study presents a novel chromosome-level genome assembly through Hi-C, PacBio CCS, and Illumina sequencing methods. The assembled genome has a final size of 651.58 Mb, with 24 chromosomes anchoring 91.94% of contigs. Contig N50 and scaffold N50 are respectively measured at 25.52 Mb and 28.59 Mb. Of the 22,476 protein-coding genes identified in the genome, 21,834 have functional annotations. BUSCO (Benchmarking Universal Single-Copy Orthologs) genome and gene annotation assessments yielded scores of 96% and 96.6%, respectively. The genome of P. haematocheilus revealed 228 expanded and 1433 contracted gene families. Comparative genomic analyses highlight adaptations and hypoxia tolerance, linked to protein synthesis, immune response, and metabolic regulation. The high-quality genome assembly supports advanced studies on gene expression patterns under different environmental stressors, contributing to genetic enhancement efforts for this economically important aquaculture species., Competing Interests: Declarations. Ethics Approval: All experimental procedures in our study with Planiliza haematocheilus were approved. Competing Interests: The authors declare no competing interests., (© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Silver arowana (Osteoglossum bicirrhosum) is a basal fish species with sexual monomorphism, while its sex determination mechanism has been poorly understood, posing a significant challenge to its captive breeding efforts., Results: We constructed two high-quality chromosome-level genome assemblies for both female and male silver arowana, with scaffold N50 values over 10 Mb. Combining re-sequencing data of 109 individuals, we identified a female-specific region, which was localized in a non-coding region, i.e., around 26-kb upstream of foxl2 gene (encoding forkhead box L2). Its strong interaction with the neighboring foxl2 on the same chromosome suggests foxl2 as a candidate sex-related gene in silver arowana. We subsequently propose a complex gene network in the sex determination process of silver arowana, with foxl2 acting as the central contributor. Transcriptome sequencing of gonads support our hypothesis that the regulation of foxl2 can be influenced by the spatial proximity of the female-specific fragment, thereby promoting ovarian function or inhibiting testicular function to stimulate gonadal differentiation. Furthermore, we found the sex chromosomes to be homomorphic with a potentially recent origin, as a linkage disequilibrium analysis proved minor recombination suppression., Conclusions: These results taken together serve as a crucial foundation for conducting extensive investigations on the evolution and differentiation of sex-determining mechanisms, as well as the emergence and development of sex chromosomes in various fishes., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Spotted scat, a marine aquaculture fish, has variable body color development stages during their ontogenesis. However, the regulatory mechanism of body color patterns formation was poorly understood. Thyroid hormones (TH) function as an important endocrine factor in regulating metamorphosis. In this study, exogenous thyroid hormones 3,5,3'-L-triiodothyronine (T3) and its inhibitor thiourea (TU) were used to treat spotted scat juveniles during the metamorphosis stage (from 60 to 90 dpf). The function and molecular mechanism of thyroid hormone signaling in regulating body color patterns formation was revealed, using the micro-observation of pigments cells distribution, colorimetric evaluation and carotenoids concentration measurement by spectrophotometry, and comparative transcriptome analysis., Results: Spotted scat body color patterns consisted of whole body black color, black bar, black and red spots, and its final pattern was formed through the metamorphosis. When spotted scat were treated with the inhibitor TU to disrupt thyroid hormone signaling, the levels of T3 and T4 were significantly decreased, the melanophores numbers were significantly increased, as well as the expression of genes involved in melanin synthesis and melanophore differentiation (tyr, tyrp1, dct, mitf, pmel, oca2, slc24a5, and erbb3) was significantly increased. Besides, the expression of genes associated with carotenoids and pteridine metabolism (apod, pnpla2, rdh12, stard10, xdh, abca1, retsat, scarb1, rgs2, and gch1) and carotenoids accumulation were stimulated, when thyroid hormone signaling was disrupted by TU. On the contrary, the levels of T3 and T4 were significantly elevated in spotted scat treated with T3, which could weaken the skin redness and reduce the number of black spots and melanophores, as well as the number and diameter of larval erythrophores. Notably, unlike melanophores and erythrophores, the differentiation of iridophore was promoted by thyroid hormones, gene related to iridophore differentiation (fhl2-l, fhl2, ltk, id2a, alx4) and guanine metabolism (gmps, hprt1, ppat, impdh1b) were up-regulated after T3 treatment, but they were down-regulated after TU treatment., Conclusions: Above results showed that thyroid hormone signaling might play critical roles in regulation pigments synthesis and deposition, thereby affecting pigment cells (melanophores, iridophores and erythrophores) formation and body color patterns. The mechanisms of hyperthyroid and hypothyroid on different pigment cells development were different. Excess thyroid hormone might impact the rearrangement of melanophore by regulating cell cycle, resulting in the abnormalities of black spots in spotted scat. Meanwhile, the excessed thyroid hormone could reduce the number and diameter of larval erythrophores, as well as weaken the skin redness of juvenile erythrophores, but they were enhanced by the disruption of thyroid hormone. However, the formation of iridophore differentiation and guanine synthesis genes expression were stimulated by thyroid hormones. These findings provide new insights for exploring the formation of body color patterns in fish, and help to elucidate the molecular mechanism of thyroid hormone in regulating pigment cell development and body coloration, and may also contribute to selective breeding of ornamental fish., Competing Interests: Declarations. Ethics approval and consent to participate: The experiment and animals were approved by the Institutional Animal Care and Use Committee (IA-CUS) of Guangdong Ocean University and complied with China’s laws and regulations on biological research. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Monitoring biodiversity on a large scale, such as in hydropower reservoirs, poses scientific challenges. Conventional methods such as passive fishing gear are prone to various biases, while the utilization of environmental DNA (eDNA) metabarcoding has been restricted. Most eDNA studies have primarily focused on replicating results from traditional methods, which themselves have limitations regarding representativeness and bias. In our study, we employed eDNA metabarcoding with three markers (12SrRNA, COI, and 16SrRNA) to evaluate the biodiversity of an 800 km2 reservoir. We utilized hydrodynamic modeling to determine water flow velocity and the water renewal ratio throughout the study area. Additionally, we conducted statistical comparisons-rarefaction curves and multivariate methods-among samples as an alternative approach to assess biodiversity representation. The eDNA identified taxa previously documented in the reservoir by traditional monitoring methods, as well as revealed 29 -nine fishes and 20 non-fish-previously unreported species. These results highlight the robustness of eDNA as a biodiversity monitoring technique. Our findings also indicated that by randomly sampling 30% of the original number of samples, we could effectively capture the same biodiversity. This approach enabled us to comprehend the reservoir's biodiversity profile and propose a straightforward, cost-effective monitoring protocol for the future based on eDNA., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Cortez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Japanese anchovy (Engraulis japonicus), a finfish with the largest biomass of a single species in the Yellow and East China Seas, plays an important pivotal role in converting zooplanktons into high trophic fish in the food web. As a result, the fish is regard as a key species in its habiting ecosystem. However, the lack of genomic resources hampers our understanding of its genetic diversity and differentiation, as well as the evolutionary dynamics. Here, we firstly report a complex chromosome-level genome assembly of E. japonicus with a large size of 1.4 Gb, with features of high repetitive sequences (54.9%), high heterozygosity (2.3%) and a number of protein-coding genes (24,405). The genome sequence exhibited a remarkable degree of completeness, valued 94.07% of the complete BUSCO. This work firstly reported the genome sequence of E. japonicus, offering the crucial resources for further studies on the genetic diversity and adaptive evolution of this species., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long. Consequently, it has prompted researchers to investigate gonadal development process of this fish. To gain further insight into the function of competing endogenous RNA (ceRNA) in the gonads of T. ovatus and the regulatory mechanism of the ceRNA network, whole transcriptome libraries were constructed from the testes and ovaries., Results: Overall, a total of 96 differentially expressed microRNAs (DE-miRNAs), 2,338 differentially expressed messenger RNAs (DE-mRNAs), 973 differentially expressed long non-coding RNAs (DE-lncRNAs), and 94 differentially expressed circular RNAs (DE-circRNAs) were identified. Additionally, a ceRNA network was constructed, and enrichment analysis confirmed the involvement of numerous pathways in reproduction and gonadal development, including the TGF-β signaling pathway and GnRH signaling pathway. The ceRNA network analysis revealed that the oni-let-7d-1-p3 and PC-3p-112794_13 may play significant roles in T. ovatus gonadal development. And we have observed a possible relationship related to gonadal development involving R-spondin-1 (Rspo1), oni-let-7d-1-p3, and MSTRG.14909.1 (lnc-TGFβR). Dual-luciferase gene reporter system and fluorescence in situ hybridization analyses preliminary verified the regulation relationship between Rspo1 and oni-let-7d-1-p3, as well as lnc-TGFβR and oni-let-7d-1-p3 in the cytoplasm of sertoli cells., Conclusion: It is hypothesized that the lnc-TGFβR functions as a sponge for oni-let-7d-1-p3, participating in regulating the process of testis development. These findings could enhance our understanding of ncRNAs in gonadal development. It also provides new insight into the function of ncRNAs and the regulatory relationship of ceRNA between males and females. These results might contribute to discussions on the regulation of ncRNA during gametogenesis., Competing Interests: Declarations. Ethics approval and consent to participate: All animal care and use procedures were approved by the Committee of the Ethics of Animal Experiments of the Ocean University of China, and were conducted in compliance with the Chinese Guidelines for the Care and Use of Laboratory Animals (GB/T 35892‐2018). We confirm that this study adheres to the ARRIVE guidelines. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H. otakii, achieved using PacBio long-read sequencing and Hi-C technology. The assembly yielded a genome size of 682.43 Mb with a contig N50 size of 2.39 Mb and a scaffold N50 size of 27.83 Mb. The completeness of genome assessed by BUSCO is 96.99%. A total of 22,334 protein-coding genes were predicted, with 21,619 (96.80%) functionally annotated across various protein databases. This genomic resource is a step forward in supporting the breeding, germplasm conservation, and enhancement of H. otakii, facilitating genetic studies and the development of strategies for disease resistance and growth optimization in aquaculture., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

This study investigated the efficacy of glycation with edible uronic acid-containing oligosaccharides via the Maillard reaction to enhance the anti-inflammatory effect of fish myofibrillar protein (Mf). Lyophilized Mf was reacted with pectin oligosaccharide (PO, half of the total protein weight) at 60 °C and 35 % relative humidity for up to 12 h to produce glycated Mf (Mf-PO). After pepsin and trypsin digestion, the anti-inflammatory effect was assessed by measuring the secretions of proinflammatory cytokines in LPS-stimulated RAW 264.7 macrophages, and the anti-inflammatory effect of Mf was enhanced by PO-glycation without marked lysine loss and browning. The effects on the expressions of genes related to the LPS-stimulated signaling pathway in macrophages were also examined. PO-glycation suppressed LPS-stimulated inflammation by suppressing expression of cd14 and enhancing suppressive effect of Mf on the TLR4-MyD88-dependent inflammatory signaling pathway. Therefore, as an edible reducing sugar, PO could be an effective bioindustrial material for developing anti-inflammatory Mf., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Wenzhao Li reports financial support was provided by Japan Science and Technology Agency. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Because of their noninvasive nature and high detection sensitivity, eDNA-based aquatic ecosystem surveys are useful for monitoring rare, elusive indicator species. Advancements in statistical techniques have expanded their use beyond simple population tracking to predict potential habitats based on the environmental conditions of sites detected eDNA. This study used species-specific molecular marker and targeted qPCR techniques to assess the distribution and habitat requirements of the endangered Gobiobotia naktongensis, a flagship fish species in Korean sandy river systems with increased public interest related to habitat restoration evaluations associated with dam construction. As a small and sand-burrowing species, G. naktongensis is difficult to identify using traditional sampling methods as its population size has declined because of the construction and operation of dams. However, eDNA investigations have detected genes from the species throughout the year, enabling the identification of stable population sites by comparing with those of historical sampling records. Logistic regression analysis of G. naktongensis eDNA absence/presence and environmental factors revealed that its habitat preferences are closely associated with streambed substrate structure, water quality, and food source diversity. eDNA analytical techniques are being actively used for species that are globally endangered and whose rarity makes population monitoring challenging. eDNA-based surveys are promising for species with small population sizes and species-specific ecological traits (e.g., benthic or sand-burrowing species), which have been limited in quantitative research approaches because of the low occurrence of eDNA in the water, because these methods can yield meaningful results with qualitative data alone., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Environmental DNA (eDNA) is revolutionizing how we investigate biodiversity in aquatic and terrestrial environments. It is increasingly used for detecting rare and invasive species, assessing biodiversity loss and monitoring fish communities, as it is considered a cost-effective and noninvasive approach. Some environments, however, can be challenging for eDNA analyses. Estuarine systems are highly productive, complex environments, but samples collected from these settings may exhibit PCR inhibition and a low fish read recovery. Here we present an approach for detecting fish in turbid, highly productive estuarine systems. The workflow includes bead-based extraction, inhibition removal, high fidelity and specificity DNA polymerase (Platinum SuperFi II) and multiplexing the universal MiFish primers. By applying this hybrid method to a variety of complex estuarine samples with known inhibition, we have more than doubled the number of recovered fish species while removing most of the off-target amplification., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005-2022) of barcoding of marine fishes identified from Australian territorial waters. Tissues targeted for sequencing with their matching physical specimens (and extracted DNA), obtained via a multi-agency sampling effort, are mostly maintained and curated by the CSIRO Australian National Fish Collection (ANFC) in Hobart, Australia. Species-level integrated taxonomy (assigned after combined morphological and genetic assessment) has been determined for 91% of the dataset. The library represents the most complete COI barcode reference dataset for marine fishes from Australian waters and is currently utilised for integrated taxonomy, (meta)barcoding and eDNA studies., Competing Interests: Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Transitions across ecological boundaries, such as those separating freshwater from the sea, are major drivers of phenotypic innovation and biodiversity. Despite their importance to evolutionary history, we know little about the mechanisms by which such transitions are accomplished. To help shed light on these mechanisms, we generated the first high-quality, near-complete assembly and annotation of the genome of the American shad (Alosa sapidissima), an ancestrally diadromous (migratory between salinities) fish in the order Clupeiformes of major cultural and historical significance. Among the Clupeiformes, there is a large amount of variation in salinity habitat and many independent instances of salinity boundary crossing, making this taxon well-suited for studies of mechanisms underlying ecological transitions. Our initial analysis of the American shad genome reveals several unique insights for future study including: (i) that genomic repeat content is among the highest of any fish studied to date; (ii) that genome-wide heterozygosity is low and may be associated with range-wide population collapses since the 19th century; and (iii) that natural selection has acted on the branch leading to the diadromous genus Alosa. Our analysis suggests that functional targets of natural selection may include diet, particularly lipid metabolism, as well as cytoskeletal remodeling and sensing of salinity changes. Natural selection on these functions is expected in the transition from a marine to diadromous life history, particularly in the tolerance of nutrient- and ion-devoid freshwater. We anticipate that our assembly of the American shad genome will be used to test future hypotheses on adaptation to novel environments, the origins of diadromy, and adaptive variation in life history strategies, among others., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Transposable elements (TEs) can make up more than 50% of any given vertebrate's genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of the mobilome over macroevolutionary timescales remains unclear. We investigated the degree to which the teleost genome duplication (TGD) shaped the diversification trajectory of the teleost mobilome. We integrate a new high coverage genome of Polypterus bichir with data from over 100 publicly available actinopterygian genomes to assess the macroevolutionary implications of genome duplication events on TE evolution in teleosts. Our results provide no evidence for a substantial shift in mobilome composition following the TGD event. Instead, the diversity of the teleost mobilome appears to have been shaped by a history of lineage-specific shifts in composition that are not correlated with commonly evoked drivers of diversification such as body size, water column usage, or latitude. Collectively, these results provide additional evidence for an emerging perspective that TGD did not catalyze bursts of diversification and innovation in the actinopterygian mobilome., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Interleukin 6 (IL-6) is one of the cytokines found to be multifunctional and biologically effective, regulating immune and inflammatory response by interacting with receptors to transmit signals. In this study, the full-length cDNAs of IL-6 (named as NaIL-6) and its receptors IL-6R and gp130 (named as NaIL-6Rα and NaIL-6Rβ) of Nibea albiflora were acquired and they possessed the typical symbolic motifs similar to its teleost orthologues in multiple sequence comparisons. The phylogenetic trees showed that NaIL-6 and its receptors clustered with their counterparts in bony fish, and had the closest affinity to Larimichthys crocea. Real-time PCR indicated that NaIL-6, NaIL-6Rα and NaIL-6Rβ were widely expressed in different tissues, among which NaIL-6 was highly expressed in the liver, NaIL-6Rα showed the highest expression in the kidney and NaIL-6Rβ was reflected in the liver. Following stimulation by Vibrio parahaemolyticus, Vibrio alginolyticus, or Polyinosinic-polycytidylic acid (Poly (I:C)) infection, the mRNA expression of all three genes were greatly up-regulated over time. The cell localization analysis showed that NaIL-6 distributed in cytoplasm and cell membrane, and NaIL-6Rα located on the cell membrane. After co-transfection of NaIL-6- mCherry and NaIL-6Rα-EGFP, they co-expressed as orange at the same position for their possibility of spatial interactions on the cellular membrane. By GST-Pull down with the purified target proteins, the association between NaIL-6-His and NaIL-6Rα-GST was confirmed, which may be utilized for further functional study. Taken together, the results indicated that the biological functions of NaIL-6 and its receptors NaIL-6Rα and NaIL-6Rβ involved in the immunologic mechanism in N.albiflora, which would provide a basis for the research of immune functions and signaling pathway of IL-6 and its receptors in fish., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Complete mitochondrial genomes have become markers of choice to explore phylogenetic relationships at multiple taxonomic levels and they are often assembled using whole genome short-read sequencing. Herein, using three species of sea chubs as an example, we explored the accuracy of mitochondrial chromosomes assembled using Oxford Nanopore Technology (ONT) Kit 14 R10.4.1 long reads at different sequencing depths (high, low and very low or genome skimming) by comparing them to 'gold' standard reference mitochondrial genomes assembled using Illumina NovaSeq short reads. In two species of sea chubs, Girella nigricans and Kyphosus azureus, ONT long-read assembled mitochondrial genomes at high sequencing depths (> 25× whole [nuclear] genome) were identical to their respective short-read assembled mitochondrial genomes. Not a single 'homopolymer insertion', 'homopolymer deletion', 'simple substitution', 'single insertion', 'short insertion', 'single deletion' or 'short deletion' were detected in the long-read assembled mitochondrial genomes after aligning each one of them to their short-read counterparts. In turn, in a third species, Medialuna californiensis, a 25× sequencing depth long-read assembled mitochondrial genome was 14 nucleotides longer than its short-read counterpart. The difference in total length between the latter two assemblies was due to the presence of a short motif 14 bp long that was repeated (twice) in the long read but not in the short-read assembly. Read subsampling at a sequencing depth of 1× resulted in the assembly of partial or complete mitochondrial genomes with numerous errors, including, among others, simple indels, and indels at homopolymer regions. At 3× and 5× subsampling, genomes were identical (perfect) or almost identical (quasiperfect, 99.5% over 16,500 bp) to their respective Illumina assemblies. The newly assembled mitochondrial genomes exhibit identical gene composition and organisation compared with cofamilial species and a phylomitogenomic analysis based on translated protein-coding genes suggested that the family Kyphosidae is not monophyletic. The same analysis detected possible cases of misidentification of mitochondrial genomes deposited in GenBank. This study demonstrates that perfect (complete and fully accurate) or quasiperfect (complete but with a single or a very few errors) mitochondrial genomes can be assembled at high (> 25×) and low (3-5×) but not very low (1×, genome skimming) sequencing depths using ONT long reads and the latest ONT chemistries (Kit 14 and R10.4.1 flowcells with SUP basecalling). The newly assembled and annotated mitochondrial genomes can be used as a reference in environmental DNA studies focusing on bioprospecting and biomonitoring of these and other coastal species experiencing environmental insult. Given the small size of the sequencing device and low cost, we argue that ONT technology has the potential to improve access to high-throughput sequencing technologies in low- and moderate-income countries., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Whether large-scale variation in lineage diversification rates can be predicted by species properties at the population level is a key unresolved question at the interface between micro- and macroevolution. All else being equal, species with biological attributes that confer metapopulation stability should persist more often at timescales relevant to speciation and so give rise to new (incipient) forms that share these biological traits. Here, we develop a framework for testing the relationship between metapopulation properties related to persistence and phylogenetic speciation rates. We illustrate this conceptual approach by applying it to a long-term dataset on demersal fish communities from the North American continental shelf region. We find that one index of metapopulation persistence has phylogenetic signal, suggesting that traits are connected with range-wide demographic patterns. However, there is no relationship between demographic properties and speciation rate. These findings suggest a decoupling between ecological dynamics at decadal timescales and million-year clade dynamics, raising questions about the extent to which population-level processes observable over ecological timescales can be extrapolated to infer biodiversity dynamics more generally., (© 2024 The Author(s). Ecology Letters published by John Wiley & Sons Ltd.)

Quantifying connectivity between endangered or threatened marine populations is critical information for management and conservation, especially where abundance and productivity differ among such populations. Spatial patterns of such connectivity depend not only on extrinsic factors such as oceanography and bathymetry but also on intrinsic species-specific factors such as life history, demography and the location of glacial refugia. Nevertheless, population structure is often inferred from related or ecologically similar species. For example, the population structure in most rockfish species (Sebastes spp.) in the Salish Sea and the US West Coast is currently inferred from genetic data of three species that are known to hybridise in Puget Sound. Here, we determined the population structure and connectivity in five Puget Sound Rockfish species (Black [Sebastes melanops], Yellowtail [S. flavidus], Redstripe [S. proriger], Greenstriped [S. elongatus], and Puget Sound Rockfish [S. emphaeus]) from over 12,000 restriction-site associated DNA sequencing (RADseq) loci. We found species-specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound rockfishes showed no genetic differentiation; Yellowtail and Greenstriped rockfishes were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure. Only Yellowtail Rockfish followed the federal DPS boundaries generally assumed for rockfish, further emphasizing the importance of species-specific management for the effective recovery and management of these rockfish populations and of marine species in general., (© 2024 His Majesty the King in Right of Canada and The Author(s). Molecular Ecology published by John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Fisheries and Oceans Canada. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Triplophysa bombifrons, a species of bony fish localized in China, has largely been understudied genetically, with limited data available beyond its mitochondrial genome. This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio long-read sequencing and Hi-C chromatin interaction mapping. The assembly reveals a genome structure comprising 25 chromosomes and an overall size of 655.95 Mb. The quality of this assembly is demonstrated by a scaffold N50 length of 24.25 Mb, and a genome completeness evaluation via BUSCO, which shows that 97.4% of the Vertebrata Benchmarking Universal Single-Copy Orthologs are present. Gene prediction methods including de novo, homology-based, and transcript-based, identified 34,211 genes, with 34,151 being functionally annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of T. bombifrons, as well as the molecular phylogenetics and evolutionary patterns in Triplophysa., Competing Interests: Competing interests: The authors declare that they have no competing interests., (© 2024. The Author(s).)

The albino northern snakehead (Channa argus) is an aquaculture species characterized by heritable albino body color, in contrast to the typical coloration. Additionally, there are gray- and golden-finned individuals, which exhibit distinct coloration in their caudal fins. We performed RNA-seq to profile the transcriptome of caudal fin tissues in albino gray-finned and golden-finned C. argus, contrasting these with normal morphs to elucidate the differences between the two groups. A total of 137,130 unigenes were identified in this study. Gene Ontology (GO) analysis showed that the identified DEGs were significantly enriched in cellular components related to cytoplasm. So far, 379 common DEGs have been identified in all three groups. Notably, we observed more DEGs in golden-finned individuals compared to gray-finned individuals. We also revealed that golden-finned individuals were enriched in collagen-related pathways compared with normal individuals. The enriched DEGs of collagen components include collagen I of COL1A1 and COL1A2, collagen II of COL2A1, collagen V of COL5A1 and COL5A2, collagen VI of COL6A1 and COL6A3, collagen IX of COL9A3, collagen X of COL10A1, collagen XI of COL11A2, collagen XII of COL12A1, collagen XVI of COL16A1, collagen XVIII of COL18A1 and decorin (DCN), all of which play a role in modulating the collagen matrix. In golden-finned albino fish, collagen-related genes were downregulated, suggesting that despite the abundance of collagen types in their caudal fin cells, gene expression was slightly limited. This work provides valuable genetic insights into collagen variation in albino C. argus, lays the foundation for research on collagen genes and is crucial for the development and utilization of fish-derived collagen as a biomaterial for tissue engineering and biomedical applications., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Amazon basin is the world's largest hydrographic basin, in terms of both its total area and its species diversity, with more than 2,700 species of fish. Despite this diversity, the data available on the fish fauna of the Amazon basin are still relatively scant and incomplete, in particular from the streams and floodplain lakes of the lower Amazon, which may contain a large proportion of the still undescribed species of the basin. Many of these species are expected to be of interest to the ornamental fish market. The investigation of the diversity of potential ornamental fish using molecular tools is even more limited. Given this scenario, the present study employed DNA barcoding to investigate the diversity of ornamental fish found in two streams and a floodplain lake of the lower Amazon. The mitochondrially encoded cytochrome c oxidase I (MT-CO1) molecular marker was used to identify the taxa, in combination with morphological keys. A total of 51 ornamental species were identified, representing 13 families and three orders. A majority of the species were found at only one of the sampling points, which indicates that the distribution of the species is influenced by ecological factors. The most speciose order was the Characiformes, followed by the Cichliformes and Siluriformes, while the family with the greatest diversity of species was the Acestrorhamphidae (31.3% of the total number of species), followed by the Cichlidae (27.4%), and the Lebiasinidae (9.8%). One specie was registered in the region of the lower Amazon for the first time, and evidence was found of the possible existence of species not formally described of Aphyocharax, Astyanax, Apareiodon and Hemigrammus., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 de Freitas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Alanine-rich, alpha-helical type I antifreeze proteins (AFPs) in fishes are thought to have arisen independently in the last 30 Ma on at least four occasions. This hypothesis has recently been proven for flounder and sculpin AFPs, which both originated by gene duplication and divergence followed by substantial gene copy number expansion. Here, we examined the origins of the cunner (wrasse) and snailfish (liparid) AFPs. The cunner AFP has arisen by a similar route from the duplication and divergence of a GIMAP gene. The coding region for this AFP stems from an alanine-rich region flanking the GTPase domain of GIMAPa. The AFP gene has remained in the GIMAP gene locus and has undergone amplification there along with the GIMAPa gene. The AFP gene originated after the cunner diverged from its common ancestor with the closely related spotty and ballan wrasses, which exhibit similar gene synteny but lack AFP genes. Snailfish AFPs have also recently evolved because they are confined to a single genus of this family. In these AFP-producing species, the AFP locus does not share any similarity to functional genes. Instead, it is replete with repetitive DNAs and transposons, several stretches of which could encode alanine tracts with a dominant codon (GCC) that matches the bias observed in the AFP genes. All four known instances of type I AFPs occurring in fishes are independent evolutionary events that occurred soon after the onset of Northern Hemisphere Cenozoic glaciation events. Collectively, these results provide a remarkable example of convergent evolution to one AFP type., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species., Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethics statement: Sampling for the present study focused on the European sardine from almost the entire species distribution range. Ethical or government approval, specific permissions or licenses for sample collection were not required for this study, as all specimens were collected as part of routine fishing procedures by fishermen of commercial fleets or scientific research campaigns. Fish are killed during the hauling of fishing gears due to differences in atmospheric pressure and fishing procedures. The experiments were conducted on dead animals, hence, no animal welfare or animal use permits were required for this study. Sardina pilchardus is not an endangered or protected species., (© 2024. The Author(s).)

The evolutionary origins of specialized organs pose significant challenges for empirical studies, as most such organs evolved millions of years ago. The Northern snakehead (Channa argus), an air-breathing fish, possesses a suprabranchial organ, a common feature of the Anabantoidei, offering a unique opportunity to investigate the function and evolutionary origins of specialized organs. In this study, a high-quality chromosome-level reference genome of C. argus was constructed using PacBio HiFi sequencing and Hi-C technology. The final genome assembly size is 712.14 Mb, with a scaffold N50 of 28.08 Mb. The assembled sequences were anchored to 24 pseudo-chromosomes and predicted 21,643 protein-coding genes. The genome comprises 27.70% repetitive elements and includes 3,588 (98.6%) complete BUSCOs, demonstrating superior contiguity and functional completeness compared to other published C. argus assemblies. This genome provides valuable genetic resources for exploring the evolution of the aquatic-aerial bimodal breathing system, including clarifying the evolutionary histories and adaptive strategies., Competing Interests: Competing interests: The authors declare no competing interests. Ethics statement: This work was approved by the Animal Research and Ethics Committees of Ocean University of China (Permit Number: 20141201). All the methods used in this study were carried out following approved guidelines., (© 2024. The Author(s).)

Background: Hypoxia triggers stress, leading to significant alterations in gene expression patterns, which in turn affect fish's growth and development. Real-time quantitative PCR (RT-qPCR) is a pivotal technique for assessing changes in gene expression. However, its accuracy is highly contingent upon the stable expression of reference genes. Ribosomal RNA ( 18s ), β-actin ( actb ), elongation factor 1-α ( ef1a ), α tubulin ( tuba ), and ribosomal protein L17 ( rpl17 ) are the widely used reference genes, but their expression stability in the tissues of black rockfish under hypoxic conditions remains unclear., Methods: The expression of genes was detected by RT-qPCR and the stability was assessed by Delta Ct, geNorm, NormFinder, and BestKeeper algorithms., Results: Results showed that tuba exhibited stable expression in liver, heart, gill tissues under normoxic conditions, and in the liver and head kidney under hypoxic conditions. Ef1a was identified as the most stably expressed gene in gill tissue under hypoxia. For hypoxic heart studies, rpl17 and tuba were recommended as reference genes. 18s showed high stability in spleen tissue under hypoxic conditions. Actb was the most stably expressed gene in spleen and head kidney tissues under normoxic conditions., Conclusions: The identified reference genes exhibited tissue-specific stability, and it was necessary to select appropriate reference genes based on the specific tissue type for gene expression studies under hypoxic conditions. These findings help in enhancing the accuracy of gene expression analysis in the mechanism of hypoxia for black rockfish.

Background: Interleukin 10 (IL-10) is uniquely positioned in the immune regulation of teleosts. Modifying the IL-10 pathway changes the teleost's disease susceptibility; however, there is no data on its post-transcriptional regulation. Trachinotus blochii is a high-value mariculture species., Methods: The full-length tbil-10 gene was generated through the Rapid Amplification of cDNA Ends-PCR. After the detailed sequence analysis, the identified features were compared with other IL-10 sequences. The gene expressions in healthy and challenged (Vibrio harveyi) fish were studied., Results: The sequence analysis showed an open reading frame of 564 bp and a 3' UTR (untranslated region) of 217 bp. The phylogram revealed an evolutionary distinction between marine and freshwater teleost IL-10. The shorter 3' UTR, additional conserved cysteines capable of forming stable disulphide bonds, and lesser mRNA instability moieties suggest the better structural stability of teleost IL-10 than tetrapods. Results identified 60 miRNA-mRNA duplexes that can regulate IL-10 3' UTR. Nine identified miRNAs are involved in immune response and seven are expressed in macrophages. The gills showed the highest gene expression in healthy fish. The study discovered two IL-10 mRNA transcripts that differed in 5' UTR lengths and thermodynamic ensemble's free energy. There was an increased expression of both tbil-10-mRNA transcripts from 2 to 48 h post-challenge which peaked at 24 h after the challenge, with higher expression of short mRNA transcript., Conclusions: The results gave insights into the structural, functional, post-transcriptional regulatory mechanisms, and expression characteristics of the IL-10 gene in T. blochii., Competing Interests: Declarations. Ethical approval: The ‘European Union’s Animal Experiments Directive 2010/63/E.U.’ and the ‘United Kingdom’s Animals (Scientific Procedures) Act (1986)’ were followed in the handling of live animals (2019). ICAR-CMFRI approved the methods (BT/AAQ/3/SP28267/2018). Consent to participate: Not applicable. Consent for publication: We confirmed that all the authors have read and approved the manuscript. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

The circumstances under which species diversify to genetically distinct lineages is a fundamental question in biology. Atlantic herring (Clupea harengus) is an extremely abundant zooplanktivorous species that is subdivided into multiple ecotypes that differ regarding spawning time and genetic adaption to local environmental conditions such as temperature, salinity, and light conditions. Here we show using whole genome analysis that multiple populations of piscivorous (fish-eating) herring have evolved sympatrically after the colonization of the brackish Baltic Sea within the last 8000 years postglaciation. The piscivorous ecotype grows faster, and is much larger and less abundant than the zooplanktivorous Baltic herring. Lesions of the gill rakers in the piscivorous ecotype indicated incomplete adaptation to a fish diet. This niche expansion of herring in the young Baltic Sea, with its paucity of piscivorous species, suggests that empty niche space is more important than geographic isolation for the evolution of biodiversity., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals., Results: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa., Conclusions: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation., Competing Interests: Declarations. Ethics approval and consent to participate: All the experiments were conducted in accordance with guidelines approved by the Animal Ethical and Welfare Committee of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou). Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Given the aggressive nature and robust survival capabilities of the alligator gar (Atractosteus spatula), if it was to exist in a new environment as an invasive species, it could cause significant disruption to the invaded ecosystem. Building on the continuity and completeness of the existing draft genome were not optimal, this study has updated a high-quality genome of the alligator gar at the chromosome level, which was assembled using Oxford Nanopore Technology and chromatin interaction mapping (Hi-C) sequencing techniques. In summary, the alligator gar genome in this study was 1.05 Gb in size with a contig N50 of 15.7 Mb and scaffold N50 of 56.8 Mb. We captured 98.26% of assembled bases in 28 pseudochromosomes. The completeness of the final chromosome-level genome reached 96.7%. Meanwhile, a total of 19,103 protein-coding genes were predicted, of which 99.83% could be predicted with functions. Taken together, the present high-quality alligator gar chromosome-level genome provides a valuable resource for exploring the underlying genomic basis to comprehend the functional genomics, chromosome evolution, and population management of this species., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Analysis of the content of the gut of fish helps in the understanding of their inter- and intra-specific interactions, fish behaviour, condition and energy intake. The stomach contents of the commercially important neritic tuna species of Sri Lanka, kawakawa (Euthynnus affinis), frigate tuna (Auxis thazard) and bullet tuna (Auxis rochei) were analysed to determine their feeding habits and to identify prey species., Methods and Results: The weighed stomachs of fish were dissected to reveal the types of prey found within. The prey was categorised into prey categories and each prey species was identified morphologically. Prey items which were partially digested were identified using DNA barcoding. The main prey category was small fish, followed by crustaceans and cephalopods. While the highest occurring prey category for E. affinis and A. rochei was fish, crustaceans dominated the A. thazard diet. DNA barcoding identified 11 prey items that were partially digested, which could not be identified to species-level morphologically. Of the prey items identified by DNA barcoding, four species of fish, three species of cephalopod and four species of crustaceans were identified. These prey item identifications confirmed that E. affinis, A. thazard and A. rochei are all nonspecific feeders., Conclusions: This exhibits the value of molecular tools in the identification of species which have lost their distinguishable features due to digestion. Further, it illustrates the predator-prey relationships between these species, aiding in the management of prey and predator populations, ensuring that both populations remain stable, helping in the maintenance of the balance of the ecosystem., Competing Interests: Declarations. Competing Interests: The authors declare no competing interests. Ethical approval: This is an observational study and no ethical approval is required., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Fish monitoring is essential for assessing the effects of natural and anthropic stressors on marine ecosystems. In this context, environmental DNA (eDNA) metabarcoding appears to be a promising tool, due to its efficiency in species detection. However, before this method can be fully implemented in monitoring programs, more studies are needed to evaluate its ability to assess the composition of fish assemblages compared with traditional survey methods that have been used for decades. Here, we used both eDNA metabarcoding and Underwater Visual Census (UVC) to assess the taxonomic and functional diversity (presence-absence data) of Mediterranean fish communities. We collected eDNA samples and performed UVC strip transects inside and outside four Marine Protected Areas in the Mediterranean Sea. Samples for eDNA analysis were collected by filtering seawater simultaneously at the surface and the bottom, and DNA was amplified using a combination of three sets of primers. We found that eDNA alone made an outstanding characterisation of fish composition with the detection of 95 % of the 60 taxa identified in this study, whereas UVC recovered only 58 % of them. Functional diversity was better evaluated with eDNA than with UVC, with the detection of a greater breadth of functional traits. eDNA was even better at characterising functional than taxonomic diversity, providing reliable information on ecosystem functioning with little sampling effort. Together these results suggest that eDNA metabarcoding offers great potential for surveying complex marine ecosystems. Combining eDNA metabarcoding and UVC in integrated monitoring programs would therefore improve monitoring strategies and enhance our understanding of fish communities, a key step promoting their conservation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Protein glutaminase (PG; EC 3.5.1.44) is a class of food-grade enzyme with the potential to significantly improve protein functionality. However, its low catalytic activity and stability greatly hindered industrial application. In this study, we employed structural-based engineering and computational-aided design strategies to target the engineering of protein glutaminase PG5, which led to the development of a combinatorial mutant, MT8, exhibiting a specific activity of 31.1 U/mg and a half-life of 216.2 min at 55 °C. The results indicated that the flexible region in MT8 shifted from the C-terminus to the N-terminus, with increased N-terminal flexibility positively correlating with its catalytic activity. Additionally, MT8 notably boosted fish myofibrillar proteins (MPs) solubility under the absence of NaCl conditions and enhanced their foaming and emulsifying properties. Key residues like Asp 31 , Ser 72 , Asn 121 , Asp 471 , and Glu 485 were crucial for maintaining PG5-myosin interaction, with Ser 72 and Asn 121 making significant energy contributions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Salinity gradients act as strong environmental barriers that limit the distribution of aquatic organisms. Changes in gene expression associated with transitions between freshwater and saltwater environments can provide insights into organismal responses to variation in salinity. We used RNA-sequencing (RNA-seq) to investigate genome-wide variation in gene expression between a hypersaline population and a freshwater population of the livebearing fish species Limia perugiae (Poeciliidae). Our analyses of gill gene expression revealed potential molecular mechanisms underlying salinity tolerance in this species, including the enrichment of genes involved in ion transport, maintenance of chemical homeostasis, and cell signaling in the hypersaline population. We also found differences in gene expression patterns associated with cell-cycle and protein-folding processes between the hypersaline and freshwater L. perugiae. Bidirectional freshwater-saltwater transitions have occurred repeatedly during the diversification of fishes, allowing for broad-scale examination of repeatable patterns in evolution. Therefore, we compared transcriptomic variation in L. perugiae with other teleosts that have made freshwater-saltwater transitions to test for convergence in gene expression. Among the four distantly related population pairs from high- and low-salinity environments that we included in our analysis, we found only ten shared differentially expressed genes, indicating little evidence for convergence. However, we found that differentially expressed genes shared among three or more lineages were functionally enriched for ion transport and immune functioning. Overall, our results-in conjunction with other recent studies-suggest that different genes are involved in salinity transitions across disparate lineages of teleost fishes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wilson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Understanding the influence of environmental pollutants on the assembly mechanisms of estuarine fish communities is vital for addressing conservation challenges in these biodiverse ecosystems. Although significant research has explored the toxic impacts of pollutants such as petroleum, heavy metals, and eutrophication on individual species and populations, their effects on community assembly processes and the differential responses of native versus non-native fish at the meta-community level remain inadequately understood. This study utilized environmental DNA (eDNA) metabarcoding to analyze fish community diversity across 28 subtropical estuaries in China, assessing how these pollutants affect community composition and assembly mechanisms. Results indicated that eDNA was 2.54 times more effective than traditional methods in species identification, while also enabling the detection of a higher number of non-native fish species and more diverse functional guilds within estuarine ecosystems. A significant distance decay pattern (p < 0.05) was observed among native fish, whereas non-native species exhibited non-significant patterns. Neutral and null models showed that non-native species had significantly higher migration rates (0.005939 vs 0.001757) and a greater contribution of stochastic processes (82.38 % vs 70.59 %) compared to native species. Additionally, distance-based redundancy analysis (db-RDA), variance partitioning analysis (VPA), and correlation analyses revealed that native species were strongly constrained by environmental factors, particularly oil, Hg, Zn, Pb, Cr 6+ , and NH 4 + , while non - native species displayed notable resilience to these pollutants. These findings highlight the potential for non-native species to disproportionately influence community dynamics and assembly through unrestricted random dispersal amid environmental disturbances. This research clarifies the contrasting ecological responses of native and non-native fish communities to anthropogenic pressures in estuarine environments, offering essential insights into ecosystem resilience and informing biodiversity conservation strategies in rapidly changing coastal ecosystems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Understanding how evolution and phenotypic plasticity contribute to variation in heat tolerance is crucial to predicting responses to warming. Here, we analyze 272 thermal death time curves of 53 fish species acclimated to different temperatures and quantify their relative contributions. Analyses show that evolution and plasticity account, respectively, for 80.5% and 12.4% of the variation in elevation across curves, whereas their slope remained invariant. Evolutionary and plastic adaptive responses differ in magnitude, with heat tolerance increasing to 0.54 °C between species and 0.32 °C within species for every 1 °C increase in environmental temperatures. After successfully predicting critical temperatures under ramping conditions to validate these estimates, we show that fish populations can only partly ameliorate the impact of warming waters via thermal acclimation, and this deficit in plasticity could increase as the warming accelerates., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Society for the Study of Evolution (SSE). All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

New technologies have resulted in a better understanding of blood and lymphatic vascular heterogeneity at the cellular and molecular levels. However, we still need to learn more about the heterogeneity of the cardiovascular and lymphatic systems among different species at the anatomical and functional levels. Even the deceptively simple question of the functions of fish lymphatic vessels has yet to be conclusively answered. The most common interpretation assumes a similar dual setup of the vasculature in zebrafish and mammals: a cardiovascular circulatory system, and a lymphatic vascular system (LVS), in which the unidirectional flow is derived from surplus interstitial fluid and returned into the cardiovascular system. A competing interpretation questions the identity of the lymphatic vessels in fish as at least some of them receive their flow from arteries via specialised anastomoses, neither requiring an interstitial source for the lymphatic flow nor stipulating unidirectionality. In this alternative view, the 'fish lymphatics' are a specialised subcompartment of the cardiovascular system, called the secondary vascular system (SVS). Many of the contradictions found in the literature appear to stem from the fact that the SVS develops in part or completely from an embryonic LVS by transdifferentiation. Future research needs to establish the extent of embryonic transdifferentiation of lymphatics into SVS blood vessels. Similarly, more insight is needed into the molecular regulation of vascular development in fish. Most fish possess more than the five vascular endothelial growth factor (VEGF) genes and three VEGF receptor genes that we know from mice or humans, and the relative tolerance of fish to whole-genome and gene duplications could underlie the evolutionary diversification of the vasculature. This review discusses the key elements of the fish lymphatics versus the SVS and attempts to draw a picture coherent with the existing data, including phylogenetic knowledge., (© 2024 The Author(s). Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools-including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)-that can accurately detect the population identity of individual fish. However, the biological relevance of such tools over longer periods of time remains unknown. Here, we demonstrate that diagnostic SNP panels designed for contemporary MSA in Atlantic herring have a millennium-long biological relevance and applicability. We assign the population identity of ancient Atlantic herring specimens-obtained through famously profitable historic fisheries-up to 1300 years old from eight archaeological sites across Europe. Analyzing contemporary and ancient whole-genome data, we obtain evidence for the long-term mixed-stock exploitation of Atlantic herring. Despite such mixed-stock exploitation, we exclusively identify autumn-spawning herring amongst these archaeological remains, indicative of a specific biological availability or cultural preference for certain herring ecotypes in the past. Moreover, our results show that herring demographic patterns were relatively stable until the dramatic disruptions and stock collapses during the 20th century. We find small but significant reductions in genetic diversity over time, indicating long-term evolutionary consequences from 20th-century stock declines. The long-term applicability of diagnostic SNP panels underscores their biological relevance and cost-effective application for the genetic monitoring of herring stocks and highlights the utility of ancient DNA to obtain insights in herring ecology and population dynamics., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)

Small dams are commonplace worldwide and impact local and regional aquatic diversity by altering habitats and disrupting dispersal networks. Quantifying the local and regional impacts of dams requires nearly comprehensive species occurrence data. We used environmental DNA (eDNA) metabarcoding to test theoretical predictions about the impacts of dams on local and regional bony fish diversity within the Chesapeake Bay Watershed, USA. We analyzed eDNA from 465 sampling points within 34 waterbodies documenting the distributions of 61 species. On average, dammed waterbodies had approximately half (48 %) as many species per site as undammed (lower alpha diversity) and more homogenous species composition (lower beta diversity). Native migratory species were less than one tenth (0.08) as likely to be detected at dammed sites than undammed sites, native resident (non-migratory) species were one third (0.34) as likely, whereas introduced species were 2.6 times more likely to be detected. Our sampling and bioinformatics methods were validated by a diverse mock community control. Our results suggest that dams in coastal waterways homogenize fish metacommunities, reduce local biodiversity through dispersal limitation and habitat alteration, and favor the dominance of lentic-adapted introduced species while potentially restricting the spread of introduced catfish. Decisions to construct or decommission dams should consider local and regional impacts on biodiversity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex-determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex-determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes., (Copyright © 2024 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.)

Human activities have transformed coastal environments by introducing numerous artificial structures that impact local ecosystems. Our study investigated fish species diversity in the mussel farm (MF) and the surrounding natural reef habitat (NH) around Gouqi Island in the East China Sea (ECS). Gouqi Island, which hosts the largest mussel farm in ESC, is also a critical region for marine fish activity. We monitored fish species diversity across four seasons for the first time using eDNA technology in December (winter) 2022, March (spring), June (summer), and September (autumn) 2023. We recorded a total of 55 fish species across 49 genera, 33 families, and 10 orders. Alpha diversity analysis revealed that species diversity peaked in summer throughout the year. Diversity in the mussel farming area was significantly higher than in the natural reef habitat. Principal Component Analysis (PCA) and Analysis of Similarities (ANOSIM) confirmed significant differences in community composition between the two habitats (p < 0.01), with a more stable community structure in the mussel farm. This indicates that the mussel farming area supports a distinct fish community compared to the surrounding natural waters. The dominant fish family in the mussel farm was Sciaenidae, which includes several economically valuable species and could be a target for resource conservation. Additionally, the mussel farm hosted numerous migratory fish species exhibiting clear seasonal patterns, suggesting that the farm serves as an important ecological corridor utilized by these species throughout their life cycles., Competing Interests: Declaration of competing interest The authors declare that they have no known financial interests or personal relationships that might influence the work reported in this study., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Channa asiatica is an economically valuable fish species and excellent model for studying hypoxic tolerance. However, the underlying genetic and molecular mechanisms are poorly understood. In this study, we assembled a high-quality C. asiatica genome (23 chromosomes, totaling 722 Mb) using a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing. Repetitive elements accounted for 28.39%of the C. asiatica genome, and 23,949 protein-coding genes were predicted, with 96.63 % of these functionally annotated. Moreover, a comparative genomic analysis of 12 fish genomes showed that gene families associated with oxygen binding and transport were expanded in C. asiatica. In addition, transcriptome analysis revealed that multiple oxidative stress pathways were activated when C. asiatica was exposed to air. In conclusion, this study provided high-quality genome assembly and transcriptome data, both serving as critical resources for researching the genetic basis of hypoxic tolerance in C. asiatica., Competing Interests: Declaration of competing interest All authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Spotted knifejaw (Oplegnathus punctatus) is a significant marine fish species that exhibits pronounced sexual dimorphism, with males generally exhibiting greater weight and growth rates than females. Therefore, the farming of O. punctatus with a high proportion of males is beneficial for improving the quality and efficiency of the O. punctatus aquaculture industry. Furthermore, the development of a rapid technique in sexing O. punctatus fry will facilitate the selection and breeding of superior male varieties of O. punctatus. In this study, genome-wide scanning, comparative genomics, and structural variation analysis methods were employed to identify and extract the homologous region of the inter-alpha-trypsin inhibitor heavy chain 4 (itih4b) gene on the X and Y chromosomes from the complete genome sequence of O. punctatus. This analysis revealed the presence of a large segment of DNA insertion markers on the Y chromosome in the region. Itih4b plays an important role in the mechanisms that regulate inflammatory and immune responses in multicellular organisms. The method described here involved the design of a pair of primers to amplify two bands of 532 bp and 333 bp in males (individuals with DNA insertion variants in the intron of the itih4b gene). In females (individuals without DNA insertion), only one band of 333 bp could be distinguished by agarose gel electrophoresis. This method shortened the time required to accurately characterize intronic DNA insertion variants and genetic sexes in O. punctatus, thereby improving detection efficiency. This study has significant value for the large-scale breeding of O. punctatus all-male seedlings and provides a reference point for the study of intron variation regulation and RNA shearing in the itih4b gene., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The conventional water filtration approach for collecting environmental DNA (eDNA) has critical limitations. The collection of eDNA via passive eDNA samplers (PEDS) has been proposed as an alternative to the water filtration method. Here, we developed a novel and rapid eDNA sampling approach and evaluated the extent to which this method enhances eDNA sampling efficiency. We drove boats along transects across nine large natural lakes and deployed PEDS either by briefly submerging them at each sampling location ("angling") or towing them in the water ("trolling"). One liter of water was also collected at each location and processed via the filtration method. Fish biodiversity was determined by metabarcoding analysis of eDNA extracts. Despite a short total submersion time (42-66 min of "angling") and substantially fewer samples (PEDS: 3-6 samples; filtration: 21-33 samples per lake), PEDS generally detected more fish species in each lake as well as per sample compared with filtration. Detection probabilities for fish species were significantly higher for PEDS compared with the filtration method. PEDS are also superior to the filtration method since sampling requires less equipment, labor, time, and costs. Our innovative sampling strategy is thus effective and could be used for the eDNA biomonitoring of large water systems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

To compare and analyze the differences in immunological response between the two color morphs of Channa argus, a fish cohort was divided into four groups: black C argus + PBS (B-PBS), black C argus + Aeromonas hydrophila (B-Ah), white C. argus + PBS (W-PBS), and white C. argus + A hydrophila (W-Ah). The B-PBS and W-PBS groups received 100 μL PBS, while the B-Ah and W-Ah groups received 3.6 × 10 5  CFU/mL A. hydrophila in the same volume. The death rate in each group was noted, changes in plasma biochemical indicators and the expression of liver immune-related genes were examined, and transcriptome techniques were used to compare the differences between the two colors of C. argus following stress. No mortality occurred in the B-PBS and W-PBS groups. Mortality in the W-Ah and B-Ah groups showed an upward and then downward trend after A. hydrophila injection. The highest mortality occurred within 24 h and was higher in the W-Ah group than in the B-Ah group. MDA levels in the B-Ah and W-Ah groups increased and then decreased, while SOD and T-AOC showed the reverse tendency. The W-Ah and W-PBS groups differed significantly in MDA at 3, 12, and 24 h, SOD from 6 to 96 h, and T-AOC between 6 and 48 h. Plasma MDA and T-AOC levels at 12 h and SOD levels at 24 and 48 h differed significantly between the B-PBS and B-Ah groups. In both the W-Ah and B-Ah groups, the expression levels of IL-1β and IL-8 in the liver showed a temporal pattern with an initial increase followed by a decrease, reaching peak levels after 24 h, while IL-10 showed the reverse pattern. Transcriptome analysis of the liver revealed significant differences between the two C. argus colors. Differential genes in black C. argus were mainly enriched in steroid biosynthesis, glycolysis/gluconeogenesis, and glutathione and propanoate metabolism pathways 24 h after infection. In contrast, differential genes in white C. argus were mainly enriched in pathways such as oxidative phosphorylation, pancreatic secretion, and protein digestion and absorption 24 h after infection. After A. hydrophila infection, white C. argus had higher mortality, more severe oxidative stress and inflammatory responses, and lower antioxidant capacity than black C. argus., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)