Population genetic structure and demographic history of the fat greenling Hexagrammos otakii

Molecular and functional characterization of peptidoglycan recognition protein-L2 from Hexagrammos otakii (Ho-PGRP-L2) involved in innate immune response

Peptidoglycan recognition proteins (PGRPs), a family of pattern recognition receptors, play diverse roles in antimicrobial defense. This study investigated the role of a long-type peptidoglycan recognition protein designated as Ho-PGRP-L2 in the antibacterial immune response of the economically important fish species Hexagrammos otakii. Ho-PGRP-L2 was successfully cloned and characterized, which possesses a signal peptide, a typical PGRP domain, and a Zn2+ binding domain including four specific amino acid residues which were required for amidase activity. The qRT-PCR analysis revealed that Ho-PGRP-L2 was predominantly expressed in the liver, with very low levels in the other tissues. The recombinant Ho-PGRP-L2 protein (rHo-PGRP-L2) exhibited polysaccharide-binding, bacteria-binding, bacteria agglutinating, amidase, and antibacterial activities, indicating its function as a recognizer and effector within the antibacterial immune response. Additionally, rHo-PGRP-L2 enhanced phagocyte chemotaxis, indicating its role as an 'immune activator'. These findings indicated that Ho-PGRP-L2 of H. otakii was involved in host defense against bacterial infections, laying a foundation for developments in H. otakii aquaculture disease management.

Whole-Genome Sequencing of Hexagrammos otakii Provides Insights into Its Genomic Characteristics and Population Dynamics

Hexagrammos otakii, also commonly called "Fat Greenling", is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70-15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics.

A Chromosomal-level genome assembly and annotation of fat greenling (Hexagrammos otakii)

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.

Does the Colonizing Population Exhibit a Reduced Genetic Diversity and Allele Surfing? A Case Study of the Midday Gerbil (Meriones meridianus Pallas) Expanding Its Range

Colonizing populations at the leading edge of range expansion are expected to have a reduced genetic diversity and strong genetic structure caused by genetic drift and allele surfing. Until now, few studies have found the genetic signatures of allele surfing in expanding wild populations. Using mtDNA markers, we studied the genetic structure of the population of midday gerbils (Meriones meridianus) expanding their range to the west in Kalmykia (southern Russia) following the new cycle of desertification, re-colonizing areas abandoned in the mid-2010s. In the colonizing population, we found a reduced genetic diversity, the redistribution of haplotype frequencies-in particular, in favor of variants rare in the core population-and strong genetic structure combined with strong differentiation from the core population-patterns suggestive of allele surfing on the wave of expansion. In terms of genetic diversity and spatial structuration, the western edge population sampled in 2008 before its collapse in 2017 occupies the intermediate position between the current colonizing and core population. This suggests that reduced genetic diversity and increased genetic differentiation are general features of marginal populations, enhanced by the founder and allele-surfing effects at the leading edges of expanding ranges.

Recombinant expression and immune function analysis of C-reactive protein (CRP) from Hexagrammos otakii

C-reactive protein (CRP) belongs to the short-chain pentraxin family and functions as a soluble pattern recognition molecule (PRM) aiding in host defense against pathogens. In the present study, a CRP gene, designated HoCRP, was cloned from Hexagrammos otakii for the first time. The full length of the HoCRP cDNA sequence is 821 bp, which contains an open reading frame (ORF) of 675 bp encoding a 224 amino acid protein. The deduced protein is predicted to have a theoretical isoelectric point (pI) of 5.30 and a molecular weight of 25.4 kDa. The recombinant HoCRP protein (rHoCRP) was expressed in E. coli to further characterize the functions of HoCRP. Saccharide binding experiments demonstrated that rHoCRP exhibited a high affinity for various pathogen-associated molecular patterns (PAMPs). Furthermore, bacterial binding and agglutination assays indicated that rHoCRP had the capability to recognize a wide spectrum of microorganisms. These findings suggest that HoCRP functions not only as a PRM for binding PAMPs but also as an immune effector molecule. Considering the role CRP plays in the classical complement pathway, the interaction between rHoCRP and rHoC1q was assessed and proven by a Pull-down and Elisa assay, which implied that rHoCRP may be able to activate complement. In addition, phagocytosis enhancement by rHoCRP in the presence or absence of complement components was analysed by flow cytometry. The results showed that rHoCRP could synergistically enhance the phagocytosis of RAW264.7 cells with complement, providing further evidence of complement activation by rHoCRP through the opsonization of specific complement components. In summary, our findings suggest that rHoCRP may play a crucial role in host antibacterial defense by recognizing pathogens, activating the complement system, and enhancing macrophage function.

Mucous cell histopathology and label-free quantitative proteomic analysis of skin mucus in fat greenling (Hexagrammos otakii) infected with Vibrio harveyi

Hexagrammos otakii is favored by consumers and aquaculture practitioners because of its strong adaptability and fast growth. However, recently, frequent outbreaks of diseases in the breeding of H. otakii have led to significant economic losses, especially due to bacterial diseases, which limit the healthy breeding of H. otakii. As a luminescent Gram-negative bacterium, Vibrio harveyi is the main pathogenic bacteria of H. otakii. In this study, the histopathology and label-free quantitative proteomics analysis were performed to reveal the changes of skin mucus proteins in H. otakii after infection with V. harveyi. The histopathological changes in the skin of H. otakii showed that when the bacteria were injected into the epithelial cells, it caused an increase in the number of mucous cells and a certain degree of damage and deformation in skin. Moreover, the quantitative proteomics analysis revealed a total of 364 differentially expressed proteins (DEPs), and these DEPs were found to be involved in environmental information processing, metabolism, infectious diseases: bacteria, replication and repair. More importantly, the enrichment analysis of the DEPs revealed that these different proteins were mainly targeted immune-related pathways. After infection of bacteria, the host's immune ability will be weakened, causing V. harveyi to enter the organism more easily, resulting in increased mucus in H. otakii, which will eventually lead to a decline in its physical function. These results provided an insight into a series of physiological changes after the bacterial infection of fish at the proteomic level and basic data for further exploration of the potential mechanism of skin mucus. Taken together, the results indicated more opportunities for the future designs and discoveries of effective antibacterial vaccines and antibacterial drugs for H. otakii.

Full-length transcriptome sequencing combined with RNA-seq analysis revealed the immune response of fat greenling (Hexagrammos otakii) to Vibrio harveyi in early infection

Fat greenling (Hexagrammos otakii) is an important commercial marine fish species cultured in northeast Asia, but its available gene sequences are limited. Vibrio harveyi is a causative agent of vibriosis in fat greenling and also causes severe losses to the aquaculture industry in China. In order to obtain more high-quality transcript information and investigate the early immune response of fat greenling against V. harveyi, the fish were artificially infected with V. harveyi, and five sampling points were set within 48 h. Iso-Seq combined with RNA-Seq were applied in the comprehensive transcriptome analysis of V. harveyi-infected fat greenling. Total 42,225 consensus isoforms were successfully extracted from the result of Iso-Seq, and more than 19,000 ORFs were predicted. In addition, total three modules were identified by WGCNA which significantly positive correlated to the infection time, and the KEGG analysis showed that the immune-related genes in these modules mainly enriched in TLR signaling pathway, NF-κB signaling pathway and Endocytosis. The activation of inflammation and endocytosis was the most significant characteristics of fat greenling immune response during the early infection. Based on the WGCNA, a series of high-degree nodes in the networks were identified as hub genes. The protein structures of cold-inducible RNA-binding protein (CIRBP), poly [ADP-ribose] polymerase 1 (PARP1) and protein arginine N-methyl transferase 1 (PRMT1) were subsequently found to be highly conserved in vertebrate, and the gene expression pattern of CIRBP, PARP1, PRMT1 and a part of TLR/NF-κB pathway-related genes indicated that these proteins might have similar biological functions in regulation of inflammatory response in teleost fish. The results of this study provided the first systematical full-length transcriptome profile of fat greenling and characterized its immune responses in early infection of V. harvey, which will serve as the foundation for further exploring the molecular mechanism of immune defense against bacterial infection in fat greenling.

Transcriptome analysis of immune response in fat greenling (Hexagrammos otakii) against Vibrio harveyi infection

Fat greenling (Hexagrammos otakii) is an important aquaculture fish species in northern China. Unfortunately, Vibrio infections have caused considerable losses to the fat greenling aquaculture industry. However, the study on immune response of fat greenling against Vibrio species has not been reported yet. In this paper, the immune response of fat greenling against V. harveyi at gene expression level was studied by transcriptome analysis. A total of 189753 high-quality unigenes with a N50 length of 672bp were obtained by transcriptome profiling, which provided abundant data for the future study of fat greenling. Comparative analysis showed that 5425 differentially expressed genes (DEGs) were identified on day 3 post-infection (3dpi), containing 1837 up-regulated and 3588 down-regulated genes. Further annotation and analysis revealed that the DEGs were enriched in complement and coagulation cascades, ribosome, oxidative phosphorylation, glycine, serine and threonine metabolism and peroxisome proliferator-activated receptor (PPAR) signaling pathway. These pathways were mainly associated with phagocytosis and pathogen clearance, rarely involved in bacteria adhesion and pathogen identification, which suggested that the host might begin to clear and kill the invading bacteria on 3dpi. The research might provide a valuable resource to further study immune response and suggest strategies against V. harveyi infection in fat greenling.

Radiological dose rates to marine fish from the Fukushima Daiichi accident: the first three years across the North Pacific

A more complete record is emerging of radionuclide measurements in fish tissue, sediment, and seawater samples from near the Fukushima Daiichi Nuclear Power Plant (FDNPP) and across the Pacific Ocean. Our analysis of publicly available data indicates the dose rates to the most impacted fish species near the FDNPP (median 1.1 mGy d(-1), 2012-2014 data) have remained above benchmark levels for potential dose effects at least three years longer than was indicated by previous, data-limited evaluations. Dose rates from (134,137)Cs were highest in demersal species with sediment-associated food chains and feeding behaviors. In addition to (134,137)Cs, the radionuclide (90)Sr was estimated to contribute up to approximately one-half of the total 2013 dose rate to fish near the FDNPP. Mesopelagic fish 100-200 km east of the FDNPP, coastal fish in the Aleutian Islands (3300 km), and trans-Pacific migratory species all had increased dose rates as a consequence of the FDNPP accident, but their total dose rates remained dominated by background radionuclides. A hypothetical human consumer of 50 kg of fish, gathered 3 km from the FDNPP in 2013, would have received a total committed effective dose of approximately 0.95 mSv a(-1) from combined FDNPP and ambient radionuclides, of which 0.13 mSv a(-1) (14%) was solely from the FDNPP radionuclides and below the 1 mSv a(-1) benchmark for public exposure.