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.

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.

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.

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.

A rapid and cost-effective approach for the development of polymorphic microsatellites in non-model species using paired-end RAD sequencing

As one of the most informative and versatile DNA-based markers, microsatellites have been widely used in population and conservation genetic studies. However, the development of microsatellites has traditionally been laborious, time-consuming, and expensive. In the present study, a rapid and cost-effective "RAD-seq-Assembly-Microsatellite" approach was developed to identify abundant microsatellite markers in non-model species using the roughskin sculpin Trachidermus fasciatus as a representative. Overlapping paired-end Illumina reads generated by restriction-site-associated DNA sequencing (RAD-seq) were clustered based on the similarity of reads containing the restriction enzyme recognition site and then assembled into contigs, which were used for microsatellite discovery and primer design. A total of 121,750 RAD contigs were generated with a mean length of 522 bp, and 19,782 contigs contained microsatellite motifs. A total of 156,150 primer pairs were successfully designed based on 16,497 contigs containing priming sites. Experimental validation of 52 randomly selected microsatellite loci demonstrated that 45 (86.54%) loci were successfully amplified and polymorphic in two geographically isolated populations of T. fasciatus. Compared with traditional approaches based on DNA cloning and other approaches based on next-generation sequencing, our newly developed approach could yield thousands of microsatellite loci with much higher successful amplification rate and lower costs, especially for non-model species with shallow background of genomic information. The "RAD-seq-Assembly-Microsatellite" approach holds great promise for microsatellite development in future ecological and evolutionary studies of non-model species.

A fibrinogen-related protein (TfFREP2) gene involving in the immune response of Trachidermus fasciatus against Vibrio anguillarum

Fibrinogen-related proteins play important roles in the immune responses. We have obtained a cDNA encoding a novel fibrinogen-related protein from roughskin sculpin Trachidermus fasciatus (T. fasciatus) and named it as TfFREP2. The N and C terminus of TfFREP2 contain a putative 21-amino acid signal peptide and a typical 217-amino acid fibrinogen-like domain, which is conserved in all fibrinogen-related proteins. TfFREP2 has three glycosylation sites and two potential calcium-binding sites that are possibly involved in calcium coordination. The results of tissue specific checking showed that the mRNA and protein of TfFREP2 were particularly abundant in skin and gill among all the tested tissues. TfFREP2 mRNA and protein expression changed significantly after being challenged by Vibrio anguillarum pathogen in those immune-barrier tissues, such as skin and gill. Furthermore, recombinant TfFREP2 is able to agglutinate and bind V. anguillarum in the presence of calcium ion. The above results suggest that TfFREP2 might be involved in the host defense of fish against V. anguillarum infection.

A galectin from roughskin sculpin, Trachidermus fasciatus: molecular cloning and characterization

Galectins are a family of β-galactoside-binding lectins, which have been proved to be involved in host-pathogen interactions by recognizing pathogen associated molecular patterns (PAMPs) on the surface of virus, bacteria, fungi and protozoa. In this study, a galactoside-binding lectin homolog was identified from roughskin sculpin Trachidermus fasciatus, named TfGal. The full-length of TfGal cDNA was 1016 bp with a 5' untranslated region (UTR) of 134 bp and a 3' UTR of 474 bp, and the open reading frame (ORF) is 408 bp. The deduced protein was composed of 135 amino acids, including a carbohydrate-recognition domain and a galactoside-type carbohydrate-binding motif H-NPR/W--E-R. The deduced amino acid sequence shared 58.52%-87.4% similarities with the galectins of the other fishes. Quantitative real-time PCR (qRT-PCR) analysis demonstrated that TfGal mRNA was abundantly expressed in the ovary, heart, stomach, skin, moderately expressed in the liver, brain, gills, spleen, and rarely expressed in the hemocytes, meat and intestine. The expression of TfGal mRNA in the hemocytes and the skin was dramatically up-regulated after challenged with LPS, reaching the highest level at 2 h post-challenge, and then dropped abruptly, while the expression of TfGal mRNA in the liver was up-regulated at 2-6 h post-challenge, and then returned to the normal level, with an increase at 96 h post-challenge again. However, no obvious change of the expression of TfGal mRNA was detected in the stomach. Recombinant TfGal purified from Escherichia coli (BL21) could agglutinate and/or bind microorganisms in Ca(2+)-independent manner. These results suggested that TfGal might be involved in the innate immune response of roughskin sculpin.