Trachidermus Research Articles

Comparative transcriptomic analysis of ovary and testis reveals sex-related genes in roughskin sculpin Trachidermus fasciatus

Comparative transcriptomic analysis of ovary and testis reveals sex-related genes in roughskin sculpin Trachidermus fasciatus

Molecular characterization and functional analysis of peroxiredoxin 1 (Prx1) from roughskin sculpin (Trachidermus fasciatus).

Peroxiredoxin1(Prx1), also known as natural killer enhancing factor A (NKEF-A), is a crucial antioxidant involving in various cellular activities and immune response against bacterial and viral infection in fish. In the present study, a full-length Prx1 cDNA sequence (TfPrx1) was firstly cloned from roughskin sculpin (Trachidermus fasciatus), which was composed of 1044bp nucleotides encoding a peptide of 199 amino acids with a molecular weight of 22.35kDa and a theoretical pI of 6.42, respectively. The predicted peptide was a typical 2-cys Prx containing two conserved characteristic motifs 43FYPLDFTFVCPTEI56 and 170GEVCPA175 with the two conserved peroxidatic and resolving cysteine residuals forming disulfide bond. Quantitative real-time PCR analysis showed that TfPrx1 was ubiquitously expressed in all tested tissues with the highest expression in the intestine. It could be significantly induced following LPS injection and heavy metal exposure. Recombinant TfPrx1 (rTfPrx1) displayed insulin disulfide reduction and ROS-scavenging activity in a concentration-dependent manner, and further exhibited DNA and cytoprotective effects under oxidative stress. These results suggested that TfPrx1 protein may play an important role in fish immune protection from oxidative damage.

Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing.

The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.

Status of aquatic organisms resources and their environments in Yangtze River system (2017–2021)

The Yangtze River is the mother river of China. To promote the aquatic ecosystem protection of the great river, the Project of Yangtze Fisheries Resources and Environment Investigation (2017–2021) supported by the Ministry of Agriculture and Rural Affairs, P. R. China carried out by 24 institutes and universities that located in the Yangtze River basin surveys the status of (1) fish species composition and spatial distribution, (2) current fish abundance, (3) endangered fishes, (4) Yangtze finless porpoise, (5) aquatic eco-environments, (6) water-level fluctuation areas, (7) capture fisheries and recreational fisheries of the Yangtze River mainstream and 10 of its main tributaries, including Yalong River, Heng River, Min River (including Dadu River), Chishui River, Tuo River, Jialing River, Wu River, Han River, Dongting Lake and Poyang Lake. The results showed that there were 443 fish species (belonging to 163 genus, 37 families, and 18 orders) before 2017, but only 323 fish species (including 15 new recorded exotic species) were recorded in the project of 2017–2021. Among them, Cyprinus carpio, Carassius auratus, Hypophthalmichthys molitrix, Pelteobagrus fulvidraco, Coilia brachygnathus, Silurus asotus, Saurogobio dabryi, Ctenopharyngodon idellus, Pelteobagrus nitidus, Hemiculter leucisculus, Siniperca chuatsi, Coreius heterodon, Culter alburnus, Parabramis pekinensis, and Aristichthys nobilis were the dominant species across the whole Yangtze River system. It is estimated that there were 886 million individuals weighing 124.8 million kg, merely equivalent to 27.3% of the resources in 1950s, 30.9% of the resources in 1960s, or 58.7% of the resources in 1980s. In the new list of protected fishes that recorded in the Yangtze River system, only 15 of 29 were collected in this project of 2017–2021. Psephurus gladius has been affirmed to be Extinct by International Union for Conservation of Nature (IUCN). The wild individuals of Tenualosa reevesii and Luciobrama macrocephalus have disappeared for many years and maybe have been extinct already. Acipenser dabryanus has been affirmed to be Extinct in the Wild by IUCN. The natural propagations of A. sinensis, Myxocyprinus asiaticus and Trachidermus fasciatus have been interrupted for many years. The populations of Yangtze finless porpoise in the Yangtze River mainstream, Dongting Lake and Poyang Lake have steadily rising sizes and expanding distributions in 2017–2021. Parts of them migrate from one region to another with the seasons, which would result in the fluctuation of Yangtze finless porpoise population within some regions. The conventional indicators of water quality in the Yangtze River system were good and conformed to the water quality criteria of fishery in 2017–2021. In the last 40 years, the maximum surface water area in the Yangtze River basin extended to approximately 63,360 km2, the minimum surface water area covered approximately 26,396 km2, and the seasonal water-level fluctuation areas occupied approximately 36,964 km2. Compared with 1984–2000 period, the 2001–2020 period witnessed an overall decreasing trend in the frequency of surface water occurrence within about 25,869 km2 of aquatic areas. From 1984 to 2000 period to 2001–2020 period, permanent surface water has decreased by nearly 8,750 km2. In 2017, the fishermen were mainly 40–60 years old and their educational levels were mainly lower than junior high school. In 2017, most anglers were older than 40 and used hand rod and/or sea rod. Their average catch of each time was mainly less than 1 kg. Results suggested that the fishing ban in key waters of the Yangtze River basin is not only an ecological project of aquatic ecosystem conservation, but also a livelihood project for the fisherman to embrace industrial transformation and improve their living conditions. After the implementation of the fishing ban, the fisheries resources would gradually recover, and the Yangtze finless porpoise population size would also see a steady increase. However, the endangered species would remain threatened for a long time. The degraded waterbodies and water-level fluctuation areas would be the key restrictive factors for future aquatic ecosystem recovery in the Yangtze River basin. Since this survey was carried out before the fishing ban, the current results could provide a baseline for future evaluation of the effect of the Yangtze River fishing ban.

Molecular characterization and antibacterial activities of a goose-type lysozyme gene from roughskin sculpin (Trachidermus fasciatus)

Lysozymes, acting as antimicrobial molecules, play a vital role in the host's innate immune response to pathogen infections. In the present study, a g-type lysozyme gene termed Tf-LyzG from roughskin sculpin, Trachidermus fasciatus was firstly reported. The deduced amino acid sequence of Tf-LyzG contained 188 residues and possessed conserved catalytic residues (Glu71, Asp84, and Asp95). Gene expression analysis revealed that Tf-LyzG was widely distributed in the tested eleven tissues with the highest expression in the gill and could be significantly induced post lipopolysaccharide (LPS) challenge. The lysozyme activity of the purified recombinant protein (rTf-LyzG) was found to be most active at pH 5.5 and 37 °C. rTf-LyzG exhibited a wide spectrum of potent bacteriolytic activity against four Gram-positive bacteria and six Gram-negative bacteria. It also displayed a high affinity to polysaccharides on bacteria surfaces including LPS, lipoteichoic acid (LTA), and peptidoglycan (PGN). rTf-LyzG was capable of binding and agglutinating all nine bacteria. Flow cytometry assay further revealed that rTf-LyzG could disrupt the membrane of Micrococcus lysodeikticus which is confirmed by scanning electron microscope (SEM) analysis that reveals blebs around the bacterial cell membrane. In summary, these data indicate that Tf-LyzG is of great importance in the fish immune response against pathogens invasion.

A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation.

The cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here, we generated a high-quality, chromosome-scale genome assembly (521.26Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93Mb and a scaffold N50 of 24.06Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosome-scale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.

Spring Ichthyoplankton Assemblage Structure in the Yangtze Estuary Under Environmental Factors

Estuaries, where fresh and salty water converge, provide abundant nutrients for ichthyoplankton. Ichthyoplankton, including fish eggs, larvae, and juveniles, are important fishery recruitment resources. The Yangtze Estuary and its adjacent waters comprise a typical large-scale estuary and supply many important fish spawning, feeding, and breeding areas. In this study, 1,291 ichthyoplankton individuals were collected in the Yangtze Estuary in spring, from 2013 to 2020. The aims of the study were to provide detailed information on characteristics of the ichthyoplankton assemblage, explore interannual variation, and evaluate the effects of environmental variables on the temporal variation in assemblage structure. Twenty-six species in seventeen families were identified. The dominant species were Coilia mystus, Chelidonichthys spinosus, Engraulis japonicus, Hypoatherina valenciennei, Larimichthys polyactis, Salanx ariakensis, Stolephorus commersonnii, and Trachidermus fasciatus. The ichthyoplankton assemblage changed significantly over time, and Chelidonichthys spinosus became one of the dominant species. Canonical correspondence analysis showed that temperature and chlorophyll a were the key factors affecting the assemblage structure in the Yangtze Estuary in spring.

Molecular characterization and functional analysis of Trx and Trp14 in roughskin sculpin (Trachidermus fasciatus).

Thioredoxins (Trxs) are a family of small and highly conserved proteins which play crucial roles in the maintenance and regulation of the cellular redox homeostasis. In this study, the full-length cDNAs of thioredoxin 1 (TfTrx1) and thioredoxin-related protein of 14kDa (TfTrp14) were isolated from roughskin sculpin (Trachidermus fasciatus). TfTrx1 is 662bp in length with a 336-bp open reading frame (ORF) that encodes for a peptide with 111 amino acids, and TfTrp14 consists of 1066bp with a 372-bp ORF that is translated to 123 amino acids. TfTrx1 and TfTrp14 contain highly conserved catalytic site motif CGPC and CPDC, respectively. Tissue distribution analysis indicated that both genes were broadly expressed in all examined tissues with the highest expression of TfTrx1 in the blood and TfTrp14 in the brain. In post-LPS and heavy metal challenge, the mRNA of both genes was significantly increased in the skin, liver, spleen, and brain at various times. The results of western blot detection displayed that the time of the induced maximum protein expression was 6-h post-LPS injection in the skin and liver, which were slightly delayed compared with that of 2h at mRNA level. The recombinant TfTrp14 and TfTrx1 proteins were expressed in E. coli BL21 (DE3). The increase of the fluorescence intensity in rTfTrx1 and rTfTrp14 suggested the redox state changes in the microenvironment around tryptophan residues. Both of the recombinant proteins exhibited concentration-dependent disulfide reductase activity towards insulin, and the catalytic activity of rTfTrx1 was much higher than that of rTfTrp14.

Cloning and expression analysis of <italic>HSC</italic>70 gene in <italic>Trachidermus fasciatus</italic>

Among heat shock proteins, heat shock protein 70(HSP70) is highly conserved in biological evolution, widely found in archaea, plants and animals, and plays an important role in biological resistance to external stimuli, folding and packaging of proteins, presenting antigens and cell proliferation and differentiation. It can be divided into two categories. One type can be induced to express rapidly and in large quantities under different stress conditions, but will be restored to the basic level under normal environment, so they are usually called induced HSP70. The other type has no stress induction process and is expressed constitutively, which is called heat shock homologous protein 70 (HSC70).In this study, a heat shock homologous protein (TfHsc70) was cloned from <italic>Trachidermus fasciatus</italic> by expressing sequence tag (EST) and rapid cDNA end amplification (RACE) technique. It was 2 138 bp with a theoretical molecular weight of 71.1 kDa and an isoelectric point of 5.27,and included an open reading frame (ORF) of 1 947 bp, a 5′-terminal untranslated region (UTR) of 78 bp, and a 3′-terminal UTR of 95 bp with a stop codon (TAA). Sequence alignment showed that <italic>TfHsc</italic>70 contained three conserved sequence tags of the HSP70 family (GIDLGTTY, DLGGGTFD and VLVGGSTRIPKIQK) and an ATP-GTP binding site motif (AEAYLGKT).Compared with the heat shock homologous protein 70 (HSC70) of many fishes, amphibians and reptiles, it was found that the similarity of HSC70 was 88.89%-97.09%. Quantitative real-time PCR (qRT-PCR) demonstrated that the <italic>TfHsc</italic>70 mRNA was expressed in blood, heart, liver, stomach, intestine, spleen, kidney, brain, and gill of <italic>Trachidermus fasciatus</italic>, and the expression level of the <italic>TfHsc</italic>70 mRNA was the highest in the brain. But it was almost undetectable in the skin. When using lipopolysaccharide (LPS) to stimulate <italic>Trachidermus fasciatus</italic>, the expression of <italic>TfHsc</italic>70 significantly increased in skin, blood and liver at 2 h, and was slightly upregulated in gill and spleen, but <italic>TfHsc</italic>70 showed initial down-regulation followed by a gradual up-regulation in the brain. This was due to the sensitivity of different tissues to LPS. Based on the analysis of the protein sequence of TfHsc70 and the expression of <italic>TfHsc</italic>70 mRNA, it was shown that TfHsc70 was a member of HSP70 family of heat shock proteins, and it might play an important role in innate immunity of <italic>Trachidermus fasciatus</italic>. In conclusion, the research explored the sequence characteristics and expression of <italic>TfHsc</italic>70 mRNA in <italic>Trachidermus fasciatus</italic>, which laid a foundation for the study of innate immunity in <italic>Trachidermus fasciatus</italic> and other fish.

Molecular characterization and functional analysis of the bactericidal permeability-increasing protein/LPS-binding protein (BPI/LBP) from roughskin sculpin (Trachidermus fasciatus)

Bactericidal permeability-increasing protein (BPI) and lipopolysaccharide (LPS) binding proteins (LBP) both play important roles in innate immunity against bacterial infection. Herein, we identified a novel full-length cDNA sequence of BPI/LBP from Trachidermus fasciatus (designated as TfBPI/LBP). The full-length cDNA sequence of TfBPI/LBP was 1594bp, which contains an open reading frame (ORF) of 1422bp encoding a secreted protein with 473 amino acid residues. Similar to BPI/LBPs from other teleost and mammals, the peptide of TfBPI/LBP contains an N-terminal BPI/LBP/CETP domain with an LPS-binding motif and a C-terminal BPI/LBP/CETP domain BPI2. Multiple alignments and phylogenetic analysis supported that TfBPI/LBP was a new member of the vertebrate BPI/LBP family. TfBPI/LBP gene was ubiquitously expressed in all detected tissues, with the most abundant in the liver, and could be significantly induced in the skin, blood, liver, spleen post LPS challenge. The recombinant N-terminal domain of TfBPI/LBP (designated as rTfBPI/LBPN) was successfully expressed in Escherichia coli. Sugar binding assay showed that rTfBPI/LBPN could bind to LPS, peptidoglycan (PGN), and lipoteichoic acid (LTA), with the highest affinity to LPS. The results of bacteria binding and agglutinating assay revealed that rTfBPI/LBPN could bind and agglutinate to all of the 9 kinds of bacteria we used. Moreover, membrane integrity analysis indicated that rTfBPI/LBPN could increase the membrane permeability of bacteria. These results suggested that BPI/LBP may play crucial roles in host defense against microorganisms, possibly through non-selective bacterial recognition and induction of membrane penetration.

Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome.

Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.

A non-exhaustive survey revealed possible genetic similarity in mitochondrial adaptive evolution of marine fish species in the northwestern Pacific.

Mitochondrial coding genes involved in the oxidative phosphorylation pathway play vitally important roles in energy production and thermal adaptation. Investigating the underlying molecular mechanism of mitochondrial adaptive evolution is crucial for understanding biodiversity and ecological radiation. In this study, we collated population genetic studies of marine fish species in the northwestern Pacific based on mitochondrial cytochrome b gene sequences, to investigate whether similar patterns could be detected in mitochondrial adaptive evolution. After filtering, nine studies containing eight marine fish species (Ammodytes personatus, Boleophthalmus pectinirostris, Larimichthys polyactis, Mugil cephalus, Pampus argenteus, Platycephalus sp.1, Sebastiscus marmoratus, and Trachidermus fasciatus) belonging to eight different families were retained. Multiple codon-based approaches were used to identify potential sites under selection in each species. By comparison, our results showed that the posterior part of the mitochondrial cytochrome b gene (particularly codon 372 and its neighboring sites) seemed to be involved in the adaptive evolution process, suggesting potential genetic similarity among distantly related species. We also summarized four types of adaptive patterns in the reviewed species, and suggest that the level of genetic differentiation and mitochondrial adaptive evolution might be correlated. Further studies are needed to confirm such relationship by detecting RNA-level evidence and investigating more species and samples.

Effects of osmotic stress on the expression profiling of aquaporin genes in the roughskin sculpin (Trachidermus fasciatus)

Aquaporins (AQPs) are a family of integral membrane proteins that have been shown to be important for osmoregulation in many vertebrates. To identify potential stress resistance-related aqp genes in salinity adaptation of the roughskin sculpin Trachidermus fasciatus, we investigated the time-course expression dynamics of seven aquaporin genes (aqpl, 4, 7, 8, 10, 11 and 12) in three osmoregulatory tissues (kidney, gill and intestine) and one metabolic tissue (liver). The fish were subjected to two different acute osmotic treatments (seawater-to-freshwater transfer respectively achieved in 1 h and 24 h, namely, E-acute and acute group). The expression profiling of the seven aqp genes were performed using quantitative real-time PCR (qRT-PCR). At the time of all sampling time points (0 h, 12 h, 24 h and 48 h), no expression of aqp4 was found in the gill, liver and intestine; no expression of aqp7 was found in the gill and liver. Significant differences of aqp expression were determined in the four target tissues, and the mRNA levels were largely variable among gene members and tissues. Similar patterns of the time-course expression were detected in most of the aqp genes in T. fasciatus between the two acute groups, except that only one gene (aqpl2) in the kidney and three genes (aqp7, aqp8 and aqp10) in the intestine revealed different expression patterns. These results suggest that the expression response of aqp genes was similar under osmotic changes with different rates.

Characteristics of Fish Fauna Data in jin Island, Korea

The fish community in the Jin Island (Jindo, Jisan, Munnae, Yulri, 1/25,000 scale) was investigated with the data collected through the 3rd National Ecosystem Survey from April to October in 2012. During the period, 25 species belonging to 7 families were collected. There were 11 biological resources subject to the approval of outbound transfer, including Squalidus gracilis majimae, Abbottina rivularis, Aphyocypris chinensis, Hemiculter eigenmanni, Rhodeus ocellatus, Iksookimia hugowolfeldi, Iksookimia koreensis, Trachidermus fasciatus, Monopterus albus, Macropodus ocellatus and Oryzias latipes. The dominant species was Pseudorasbora parva(26.3%), and the subdominant spaecies was Carassius auratus(16.0%).&lt;/br&gt;Background: In Korea, from 1989 National Ecosystem Survey (NES) was conducted by ministry of environment for every 10 years to cover whole south Korea in 1/25,000 scale. The scope of NES including 8 taxa – vegetation, plant, fish, macro invertebrate, insect, birds, amphibian &amp; reptile, mammal and geomorphology. With the results of ecosystem survey we build up species and ecosystem database based on GIS environment. Ecosystem database is becoming very necessary to understand origins and relationship between human and nature and also to reduce ecosystem disturbance.&lt;/br&gt;New information: An ecological information platform can play important roles as a computing system to collect knowledge, distributed research findings and separated data from researchers. We designed and developed ecological information portal service (EcoBank 1.0) for collecting and providing ecological information for various stake-holders. Then, we developed basic functions to analyze ecosystem for each stake-holders (researchers, general public and policy makers). We successfully designed a computing system named EcoBank supporting the functions of Digital Object Identifier (DOI) publish and data quality management.

Japanese catadromous fourspine sculpin, Rheopresbe kazika (Jordan &amp; Starks) (Pisces: Cottidae), transferred from the genus Cottus

The scientific name Cottus kazika has been used for over a century as valid for the catadromous fourspine sculpin endemic to Japan. However, recent DNA sequence analyses have indicated a sister relationship between two catadromous species, so-called C. kazika and Trachidermus fasciatus with a great phylogenetic divergence, separated from a monophyletic freshwater spawning clade including the other Cottus species and Baikalian sculpins. Morphological, life-historical, ecological, and karyological characteristics have also suggested that the fourspine sculpin so-called C. kazika is neither a member of Cottus nor Trachidermus. Therefore, the fourspine sculpin is transferred to the genus Rheopresbe. The genus and R. kazika are re-described. The genus Rheopresbe is discriminated from related genus Trachidermus by not having bony ridges on both nape and cheeks and also by presence of entopterygoid, and from the genus Cottus by having teeth on palatines and four spines on preopercle ridges.

Effects of osmotic stress on Na+/K+-ATPase, caspase 3/7 activity, and the expression profiling of sirt1, hsf1, and hsp70 in the roughskin sculpin (Trachidermus fasciatus).

Osmoregulation mechanism underlying acclimation of migratory fish to different salinities has been a classical research topic for decades. In this study, the roughskin sculpin (Trachidermus fasciatus) were subjected to two different acute osmotic treatments (one extreme acute and one acute treatment, i.e., E-acute and acute group). Comparisons of branchial enzyme activity, as well as the time-course expression profiling of sirt1, hsf1, and hsp70 were performed to reveal changes at the physiological and molecular levels. As a result, the branchial Na+/K+-ATPase activity was significantly inhibited and the caspase 3/7 relating to apoptosis was significantly induced in the E-acute group; no significant difference of branchial enzyme activity was detected in the acute group. These results suggested that T. fasciatus could keep stable physiological levels when experiencing the acute salinity change but not under extreme osmotic stress. Significant variations of sirt1, hsf1, and hsp70 expression were determined in the four target tissues (gill, intestine, kidney, and liver). Similar profiling was detected between the time-course expression of sirt1 and hsf1, suggesting their association in the osmoregulation process. Tissue-specific gene expression patterns in all the three target genes showed that each tissue possesses its own gene expression pattern in response to salinity changes. The overall different expression profiling of sirt1, hsf1, and hsp70 under the extreme acute and acute osmotic treatments might respectively represent the molecular regulation of stress response and acclimation. The findings make it possible to provide more reliable data to decipher the mechanism of osmoregulation in migratory fish.

Molecular characterization and complement activating functional analysis of a new collectin(TfCol-11) from Trachidermus fasciatus

The complement system is a crucial component of the innate immune system that links innate and adaptive immunity. CL-11, a protein similar to Mannose-binding lectin (MBL), plays significant role in the innate immune system in mammals and fish, serving as an initiator of the lectin pathway of complement activation. In this study, a CL-11 homolog (TfCol-11) was identified in roughskin sculpin (Trachidermus fasciatus), and its expression and role in immune responses were characterized. The open reading frame of TfCol-11 is 795 bp long, encoding a 264 amino acid polypeptide. The deduced amino acid sequence of this protein is highly homologous to sequences in other teleosts, and is similar to vertebrate CL-11, containing a canonical collagen-like region, a carbohydrate recognition domain, and a neck region. Recombinant TfCol-11 purified from Escherichia coli(E.coli) was able to bind to different microbes in a Ca2+-independent manner. Meanwhile, a 993 bp-long of partial MASP cDNA with a 96 bp 5′ untranslated region (UTR) was also cloned from roughskin sculpin, containing 299 amino acids and consisting of three domains (CUB-EGF-CUB). qRT-PCR indicated that TfCol-11 and MASP mRNAs were predominately co-expressed in the liver. The temporal expression of TfCol-11 and MASP were both drastically up-regulated in the liver, skin, and blood by LPS challenge. Recombinant TfCol-11 purified from E.coli BL21(DE3) was able to agglutinate some bacteria in a Ca2+-dependent manner. In addition, an in vitro pull-down experiment demonstrated that TfCol-11 was able to bind to MASP, and in vivo experiments showed that TfCol-11 was associated with increased membrane attack complex (MAC) levels. It is therefore possible that TfCol-11 may plays a role in activating the complement system and in the defense against invading microorganisms in roughskin sculpin.

Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus.

Understanding the patterns of genetic diversity and adaptation across species’ range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.

Effect of a LECT2 on the immune response of peritoneal lecukocytes against Vibrio anguillarum in roughskin sculpin

Leukocyte cell-derived chemotaxin 2 (LECT2) is a multi-functional protein that is mainly synthesized by the liver. However, its role in roughskin scalping is less known. Here, we cloned a leukocyte cell-derived chemotaxin 2 (TfLECT2) genes in the liver of roughskin scalping, Trachidermus fasciatus, and studied its possible role involved in the immune response against Vibrio anguillarum (V. anguillarum) of peritoneal lecukocytes under in vivo conditions. The cDNA sequence of TfLECT2 is 566 bp in size. Its deduced amino acid (aa) sequence comprises 151 residues, of which the first 16 residues form a putative signal peptide and 101 residues compose a typical peptidase M23 domain in the C-terminal region. The domain structure is conserved in all LECT2 proteins, which suggests a close phylogenetic relationship between TfLECT2 and LECT2 in other fish species. Real-time quantitative PCR analysis revealed that TfLECT2 gene expression was dramatically increased in liver after V. anguillarum stimulation. Subsequently, TfLECT2 was prokaryotic expressed and purified to prepare anti-TfLECT2 antibody. After V. anguillarum challenge, leukocytes recruitment and LECT2 levels in peritoneal exudates were increased, and positively correlated with each other. Moreover, recombinant TfLECT2 administration significantly improved immune responses after infection, principally in stimulating the recruitment, phagocytosis and respiratory burst of leukocytes at the site of infection; however, anti-TfLECT2 treatment neutralized these abilities. Therefore, TfLECT2 may trigger the early immune events of peritoneal leukocytes and it will be useful to induce innate immune response of fish.

The complete mitochondrial genome of Trachidermus fasciatus (Scorpaeniformes: Cottidae) and phylogenetic studies of Cottidae

Trachidermus fasciatus is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China due to the declines in its abundance. We describe the complete mitogenome of T. fasciatus in this study. The mitogenome is 16,536 nucleotides long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two main non-coding regions. The overall base composition includes C (30%), A (26.3%), T (25.5%), and G (18.2%). Moreover, the 13 PCGs encode 3800 amino acids in total, all the PCGs use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 and Cytb use an incomplete stop codon T. The phylogenetic tree based on the neighbour joining method was constructed to provide relationship within Cottidae, which could be a useful basis for management of this species.