Abstract:Bay scallop (Argopecten irradians) is an economically important bivalve species in China due to its fast growth rates and suitability for artificial breeding. There are five bay scallop subspecies distributed along the Atlantic coast of North America and the Gulf of Mexico that exhibit distinct growth and thermal stress tolerance characteristics, making them valuable resources for adaptive evolutionary studies. In this study, we used whole-genome resequencing analysis to uncover the genetic diversity and selective signatures of the bay scallop southern subspecies A. i. concentricus via comparison with the northern subspecies A. i. irradians. We identified a total of 15059961 high-quality single nucleotide polymorphisms (SNPs), of which 1616072 were unique to A. i. concentricus and 3319537 were unique to A. i. irradians. Following annotation analysis, a total of 23364701 effects were identified from the 15 million SNP sites. Only 2.819% of the loci were located in the exon regions; the majority of these SNPs were instead located in the intergenic (36.0%) and intron (32.3%) regions. Among the SNPs located within exons, silent mutations accounted for 55.1% (358166), missense mutations accounted for 43.7% (284415), and nonsense mutations accounted for 1.2% (7777). The total numbers of transitions and transversions across all SNPs were 97243196 and 82018037, respectively, resulting in a transitions/transversions ratio of 1.1856. Population structure, principal component analysis (PCA), and phylogenetic analysis based on genome-wide SNPs indicated significant genetic differentiation between A. i. concentricus and A. i. irradians. Linkage disequilibrium (LD) analysis showed that A. i. concentricus retained a higher level of LD compared to that of A. i. irradians, which may have been potentially influenced by domestication selection and inbreeding. Runs of homozygosity (ROH) analysis across the whole genome revealed that A. i. concentricus retained more ROH, indicating a higher level of inbreeding. Population genetic diversity analysis revealed a decrease in genetic diversity in certain regions of the A. i. concentricus genome compared to those of the northern subspecies population; this may be the result of continuous artificial selection for heat tolerance and inbreeding. Selective sweep analysis of A. i. irradians revealed 349 genes under positive selection, including GHSR, HSF1, HABP2, and DnaJ, which may be related to its corresponding rapid growth rate, strong heat tolerance, high immunity, and other environmental adaptation characteristics. Functional enrichment analysis revealed that the genes located in the selective sweep regions were primarily associated with cell signal transduction, maintenance of cell morphology, and regulation of metabolic processes. Overall, this study sheds light on the genetic differentiation and signatures of selection in bay scallop subspecies, thereby providing a valuable resource for scallop genomic research and molecular breeding.

Abstract:To understand the heat tolerance of Esox lucius across different stages of early development and to elucidate appropriate molecular markers for the improvement of heat tolerance traits, this study used upper thermal tolerance (UTT) as an evaluation index, conducted variance analysis of UTT, compared and analyzed the thermal tolerance of Esox Lucius at different developmental stages, and used genotyping-by-sequencing (GBS) to obtain heat tolerance traits that were related to simplified genome sequencing data sets of two extreme groups. We then evaluated heat resistance using a genome wide association study to explore the SNP markers that are associated with heat tolerance traits in Esox lucius. The corresponding results showed that there were significant differences in heat tolerance at different developmental stages during the early development of Esox lucius (P＜0.01). Heat tolerance was highest at the young stage, followed by the juvenile stage, with the lowest heat tolerance being observed at the larval stage. GWAS analysis, combined with FarmCPU and Blink models, showed that the correlations between the five SNPs and the heat tolerance traits of Esox lucius were highly significant (FDR P-value ＜0.01); these SNPs were located in the introns of clstn2, MAPK14, and VAPA genes, and the untranslated region at the 5ʹ end of the ANKS1B gene. These genes are directly or indirectly associated with stimulus and stress responses. In this study, candidate SNPs and genes associated with high temperature tolerance traits were preliminarily screened in Esox Lucius. These results provide a reference for future studies regarding the physiological and molecular mechanisms of high temperature stress tolerance in Esox Lucius, and therefore provide a scientific basis for the improvement of high temperature tolerance in Esox lucius.

Abstract:Schizothoracinae is an endemic fish of the Tibetan Plateau and its surrounding areas. The phylogenetic and adaptive evolutionary mechanisms of this subfamily are unclear, and the taxonomic status of Gymnocypris chilianensis remains controversial. This study evaluated the complete mitochondrial genome sequences of 65 species of Schizothoracinae in 11 specified genera, with the aim of providing a genomic basis for elucidating the above issues. The corresponding results are as follows: (1) Phylogeny. The results showed that the Schizothoracinae subfamily is not monophyletic but belongs to two different clades, with each taxon containing several generic species. The primitive taxa of the Schizothoracinae fishes were grouped into one clade; the specialized taxa and highly specialized taxa were grouped into another clade; (2) Adaptive evolution. The results showed that no positive selection sites were detected at any of the 13 protein-coding genes with ω ratios ＜1. Positive selection sites were also found in Atp6, ND2, ND3, ND4, and ND5. Nonetheless, positive selection primarily occurred in respiratory chain complex I (NADH1-6); the mitochondrial respiratory chain is the most important source of biologically reactive oxygen species (ROS), which may explain the adaptive evolutionary mechanism of the subfamily Schizothoracinae fishes in high-altitude hypoxic environments. For the divergence time study, the divergence time of the primitive taxon Schizothoracinae fishes was estimated to be before 3.200 Ma; the specialized taxon Schizothoracinae fishes began to differentiate between 5.972 Ma and 5.320 Ma in the late Miocene period; (3) Taxonomic status of G. chilianensis. Based on the Kimura two-parameter model, the genetic distance between G. chilianensis and Schizopygopsis kessleri was 0.0015. Nonetheless, the genetic distance between G. chilianensis and Gymnocypris eckloni was 0.0673 (＞0.0600), indicating species differentiation. Overall, it is clear that, at the molecular level, G. chilianensis is a distinct species of the genus Gymnocypris and not a subspecies of G. chilianensis. Therefore, this study provided evidence to resolve the long-standing disagreement over the taxonomic status of G. chilianensis.

Abstract:The aims of this study were to analyze the structure and diversity of intestinal microorganisms in wild Anguilla japonica eel larvae from the Yangtze River Estuary and to explore the function of these intestinal microorganisms. MiSeq 16S rRNA high-throughput sequencing technology was used to sequence the 16S rRNA of microorganisms in wild eel larvae at different pigment development stages from January to April. We then counted the number of operational taxonomic units (OTU) of intestinal microorganisms in the samples, analyzed species composition, abundance, and alpha diversity, and predicted the function of these intestinal microorganisms. A total of 1467 OTUs were identified from the Japanese eel larvae samples, with an average of 396 per sample; these microorganisms were determined to belong to 51 phyla, 140 classes, 286 orders, 414 families, 643 genera, and 959 species. Each sample had an average of 26 phyla and 229 genera; however, a significant decrease in this diversity was observed with increasing months. At the phylum level, the dominant microflora were Proteobacteria (81.33%) and Bacteroidota (10.61%). At the genus level, the dominant bacterial groups were Psychrobacter (35.10%), Pseudomonas (16.75%), Flavobacterium (7.99%), Achromobacter (4.82%), and Shewanella (4.21%), which differed from the intestinal microbial communities observed in other fishes. The abundance and diversity of intestinal microflora in eel larvae from the January group were significantly higher than those in other months (P＜0.05). Nonetheless, there was no significant difference in the structure and diversity of the intestinal microbial community among the other three groups or between the VA and VB stages of eel larvae at different pigment development stages (P＞0.05). According to KEGG path annotation, it was predicted that most of the genes encoded by the intestinal microflora of Japanese eel larvae were related to metabolism; further, the relative abundance of amino acid transport and metabolic functional groups was high. The composition of microorganisms in the intestinal tract of Japanese eel larvae is complex; therefore, the analysis of these intestinal microorganisms and their corresponding functions helps develop our understanding of the influence of intestinal microflora on Anguilla japonica feeding, thereby providing a theoretical basis for further studies on fish diet.

Abstract:In the present study, we evaluated the effects of dietary single strain or multistrain Lactococcus lactis on the intestinal health, innate immunity, and antioxidant activity of common carp. Common carp (44.79±0.13 g) were fed a control diet or one of the seven diets with supplementary Lactococcus lactis [Lactococcus lactis Q-8 (G1); L. lactis Q-9 (G2); L. lactis Z-2 (G3); L. lactis Q-8 and L. lactis Q-9 (G4); L. lactis Q-8 and L. lactis Z-2 (G5); L. lactis Q-9 and L. lactis Z-2 (G6); L. lactis Q-8, L. lactis Q-9 and L. lactis Z-2 (G7)] for 60 days. The corresponding results showed that the activities of intestinal digestive enzymes (protease, amylase, and lipase) and the expression of tight junction protein [Claudin, ZO-1] genes were significantly increased by treatment with dietary Lactococcus lactis; further, the effects of the multi-strain treatment groups were significantly higher. In addition, all treatment groups exhibited significantly higher microvilli length in the midgut and enhanced levels of tumor necrosis factor-alpha (TNF-α, except G6), interleukin-6 (IL-6), IL-12, IL-1β, IL-10 (except G7), transforming growth factor-beta (TGF-β), and nitric oxide (NO) production in the serum, compared to those of the control group. Multistrain treatment significantly increased the muscle thickness of the entire intestine; however, the effect on alkaline phosphatase (AKP) activity in the serum was not significant. Nonetheless, the regulatory effects of dietary Lactococcus lactis on the antioxidant capacity of the hepatopancreas were significantly higher than those of the control group, and the G7 group had a more prominent effect on glutathione peroxidase (GSH-Px), glutathione (GSH) and malondialdehyde (MDA) production. In conclusion, the three Lactococcus lactis strains evaluated in this study were effective in improving intestinal health, immune response, and antioxidant capacity in common carp and exhibited a synergistic effect when used as a combined dietary treatment. Overall, this study can provide an additional reference point for the application of probiotics in aquaculture.

Abstract:The Chinese mitten crab, Eriocheir sinensis, is one of the most important aquaculture species in China, with an annual aquaculture production of 808300 metric tons in 2021. The Chinese mitten crab exhibits six larval stages: Zoeae I-V and Megalopa. These larvae are primarily bred in outdoor earthen ponds; recent studies indicated that the water quality and species composition of the plankton community in these ponds can directly affect the production of breeding. However, little is known about the physical and chemical factors of the E. sinensis larvae-rearing process in breeding earthen ponds; additionally, the characteristics of plankton community succession and its relationship to environmental factors remain unknown. It limits our ability to improve E. sinensis larvae-rearing technology via the control of water quality parameters and plankton communities. Therefore, it is necessary to investigate the water quality paramebers and plankton community succession in E. sinensis breeding earthen ponds.

Abstract:Stock assessment involves providing scientific and quantitative evaluations to objectively inform fisheries management. However, data limitations are a common challenge for global stock assessments. Many exploited fish stocks in China lack quantitative assessments due to the limitations imposed by the data requirements of conventional stock assessment methods; ultimately, this hinders the advancement of total allowable catch (TAC) systems in China. The catch-based maximum sustainable yield (CMSY) and Bayesian Schaefer production model (BSM) are recently developed methods that are most suited for calculating the intrinsic population growth rate (r), carrying capacity or unexploited stock size (k), maximum sustainable yield (MSY), and other reference points of data for fishery management. Reference points for 19 commercial groups exploited by Chinese fisheries were calculated over time using CMSY and BSM methods by evaluating catch and abundance levels. The results showed that one stock collapsed, three stocks were severely declined, five stocks were overfished, five stocks were slightly overfished, and five stocks were healthy. The long-term assessment of stock status demonstrated that the proportion of stocks at biologically sustainable levels declined from 95% in 1980 to 26% in 2019. We also compared the CMSY and BSM methods. The BSM method, which integrated CPUE data, resulted in wider confidence intervals and moderated the trend of biomass trajectories, with a final exploited biomass relative to the biomass at maximum sustainable yield (B₂₀₁₉/B_msy) for three stocks that exceeded the overfished threshold. This suggested that CMSY may overestimate or underestimate B/B_msy depending on the trend of stock abundance. Overall, independent fishery surveys should be conducted to obtain CPUE and biological data to improve assessment accuracy.