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Four species support recreational and commercial fisheries along the U.S. Atlantic Ocean and the Gulf of Mexico, with the Gulf of Mexico stock being overfished for over three decades. The study presented here is part of a fisheries-independent project initiated to determine an absolute abundance of , to expand biological knowledge of the species and to develop novel tools for fisheries management. Environmental DNA (eDNA) tools aimed at the detection and quantification of target species are starting to emerge in support of marine fisheries surveys. Key to progressing the field is Droplet Digital™ PCR (ddPCR™), a highly sensitive technique with advanced multiplexing and direct quantification capabilities that can provide fisheries scientists with improved interpretation of eDNA data. We developed and validated a novel tetraplex ddPCR™ assay able to detect and distinguish between , , , and from seawater eDNA samples. In order to groundtruth ddPCR™ data, and explore its capacity to provide abundance estimates, we compared ddPCR™ detections and quantifications to abundance data inferred from multiple camera (ROV, S-BRUV, chevron trap) and acoustic (VPS array) gears deployed during a fisheries research gear-calibration cruise. We demonstrated that with eDNA contamination controls and best practice protocols, it is viable to conduct eDNA research as part of a fisheries survey cruise. eDNA sampling was completed in less time than camera gears (15 min 2 h). Both eDNA and camera gears detected the presence of and at both sites and all sampling days, but not and . eDNA concentration data was higher for than at both sites for all sampling days, in line with abundance patterns obtained from camera gears. The highest correlation (r = 0.97) was obtained between the measures of eDNA between gear deployments and ROV. Incorporating eDNA in fisheries surveys would not require additional days at sea and could improve precision in fish detection and abundance. eDNA can be a valuable complement to camera gears deployed in geographic areas or seasons with poor visibility conditions, where fish may be present but cannot be confidently identified to the species level. The high correlation obtained between ROV and eDNA data collected between gear deployments adds to a growing number of studies demonstrating the potential of eDNA as an indicator of abundance for fisheries stock assessments. Time-series data from a carefully designed eDNA survey, that estimates relative abundance, could be used as an index of relative abundance for the stock assessment. To achieve this, investment into follow-up studies with increased sample sizes and spatial and temporal replication would be necessary to allow for year-to-year comparisons and validate the robustness of the correlation observed.

California yellowtail (CYT; Seriola dorsalis) is a promising candidate for marine aquaculture in the United States because there is an existing market and cultured Seriola spp. command prices as high as $27.70 per kg for head‐on gutted product. Methods for commercial‐scale Seriola spp. fingerling production and growout have been refined globally in recent years. Spawning can be accomplished without hormone therapy and adults spawn viable eggs when ambient water temperatures are between 15 and 22°C. Larval culture of CYT includes rotifers and Artemia, with the addition of greenwater. Larval survival to 1 g juveniles (45 days post hatch) is typically high at 30–60%. However, poor swim bladder inflation and skeletal malformations require culling and can reduce this yield substantially. Growout of CYT to market size at Hubbs‐SeaWorld Research Institute (HSWRI) has been completed on a very limited basis in flow through tanks where it takes 18–24 months to achieve a market weight of 3.5–4.0 kg. While culture of this species is commercially ready from a technical and business perspective, research is still needed to improve swim bladder inflation, reduce deformities, optimize nutrition across all life stages, and assist with disease diagnosis and control. Most notable among bottlenecks to commercialization in the United States is the need for growout capacity both for net pen and land‐based culture.

Immunoglobulins (Igs), also termed antibodies, orchestrate host-acquired immune responses against foreign antigens, including invasive pathogens. In fish, IgM, which is present predominantly circulating in the blood, is particularly important for humoral systemic immunity and protecting the host from pathogens. The efficacy of inactivated vaccines, a major type of vaccine commonly used worldwide in fish, is directly linked to the serum antibody level; however, the timing of the appearance of systemic IgM circulating in the blood has not been determined in fish. In the present study, we examined the dynamics of serum IgM levels in juvenile Japanese amberjack Seriola quinqueradiata, using a highly sensitive sandwich enzyme-linked immunosorbent assay (ELISA) that we developed for IgM. We found that serum IgM concentration in young fish up to 72 days post-hatching (d.p.h.) (mean ± standard error of the mean [SEM]; body weight: 5.73 ± 0.38 g, standard length [S.L.]: 72.2 ± 1.94 mm) was sustained at a low level, but that the level significantly increased from 79 d.p.h. onward, reaching a mean of 84.76 ± 9.23 μg/mL at 85 d.p.h. (body weight: 14.05 ± 0.92 g, S.L.: 101.1 ± 2.07 mm). These results suggest that systemic immunity mediated by IgM is only partially matured in the early growth stage of juveniles. The present findings could help establish effective vaccination programs for infectious diseases in young fish.

Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.

We report here the first case of natural hybridization between two yellowtails, Seriola quinqueradiata and Seriola lalandi, based on AFLP and mtDNA sequence data. Analysis of AFLP data using Bayesian model-based clustering methods revealed that 25 of 28 suspected hybrids are F1 hybrids and the remaining three are backcrosses to S. lalandi. Analysis of the mtDNA sequence indicated that hybridization is highly directional, as the majority of the F1 hybrids were offspring of S. quinqueradiata males and S. lalandi females. Considering the recent rapid distributional shift of S. quinqueradiata, our data indicate the need for further investigation of ongoing hybridization.

The Seriola genus includes species of worldwide commercial importance due to its rapid growth and easy adaptability to confinement conditions. However, like other fish species, large mortalities occur during their early life stages, where the main problems are caused by opportunistic bacteria. Disease control strategies are thus urgently needed. The present study aimed to evaluate the efficacy of phage vB_Pd_PDCC-1 during the early development of longfin yellowtail (Seriola rivoliana), as well as its effect on microbial communities. This broad-host-range phage was added to the culture every 3 days starting from the egg-stage until 12 days after hatching (DAH) at a concentration of 1.41×1010 plaque-forming units (PFU) per mL and at a multiplicity of infection (MOI) of 1. The results showed positive effects (p<0.05) on egg hatching, survival, growth, and pigmentation area in treated larvae. Moreover, high-throughput sequencing analysis of 16S rRNA genes showed that phage administration did not produce significant changes (p>0.05) in the composition and structure of the associated microbiota. However, sequences affiliated to the Gammaproteobacteria class were displaced by those belonging to the Alphaproteobacteria class over time regardless of the treatment received. At the family level, there was a decrease in Rhodobacteraceae, Pseudoalteromonadaceae, and Flavobacteriaceae in both groups over time. To our best knowledge, this study represents the first attempt to evaluate the effect of a phage as a biological control agent during ontogenetic development of longfin yellowtail larvae.Key points• Phages can be used against proliferation of Vibrio in fish cultures.• Seriola includes several important commercial fish species due to its rapid growth.• Phages do not cause significant changes in the associated microbiota.

Leptins and other related genes have been proven to play vital roles in food intake, weight control, and other life activities. While the function of leptins in yellowtail kingfish (Seriola lalandi) has not yet been explored, in the present study, we investigated the structure and preliminary function of four leptin-related genes in S. lalandi. In detail, the sequence of two leptin genes (lepa and lepb), one leptin receptor gene (lepr), and one leptin receptor overlapping transcript (leprot) gene were obtained by homology cloning and RACE methods, in which lepa and lepb have similar structure. Moreover, homologous sequence alignment and evolutionary analysis of all four genes were clustered with Seriola dumerili. The tissue distribution of these four genes in thirteen tissues of yellowtail kingfish was detected by RT-qPCR. Both lepa and leprot were highly expressed in the brain and ovary, while lepb was highly expressed in the pituitary, gill, muscle, and ovary; lepr was highly expressed in the gill, kidney, and ovary. Additionally, these four genes also played roles in embryo development and early growth and development of larvae and juveniles of yellowtail kingfish. Finally, the function of leptin and leptin-related genes was investigated during fasting and re-feeding adaption of yellowtail kingfish. The results showed that these four genes have different regulation functions in five tissues; for example, the mRNA levels of lepa, lepr, and leprot in the brain decreased during fasting and immediately increased after re-feeding, while the mRNA level of lepb did not show significant fluctuation during starvation but significantly lowered after re-feeding. However, lepa and lepb mRNA levels were significantly elevated during fasting and returned to control levels after re-feeding, and there were no significant changes in the expression of lepr and leprot in the liver during fasting and after re-feeding. Moreover, the body mass of fish in the experimental group was measured, and compensatory growth was found after the resumption of feeding. These results suggested that leptin and receptor genes play different functions in different tissues to regulate the physiological state of fish in food deficiency and gain processes.

Yellowtails Seriola quinqueradiata are an important fishery resource around Japan. Here we investigated the movement ecology and habitat utilization of this migratory fish. Archival tags were implanted in 26 adult yellowtails (61−90 cm in fork length) to examine their seasonal movement patterns and vertical distribution. Yellowtails were captured and released around Noto Peninsula in the Japan Sea on 27 May 2004. Eight individuals were recaptured more than 2 mo later, and we analyzed their daily position and vertical movement with ambient water temperature recorded in 60 or 120 s intervals. Most yellowtail individuals moved from the central coast of Japan to the north (from the west of Tsugaru Strait to the west of Hokkaido) in June. Individuals resided in the northern part of the Japan Sea from summer to mid-fall (late July to late October). Seasonal thermoclines developed during this northward movement and subsequent period of residency, with individuals primarily occupying the surface mixed layer during the daytime and at night; however, individuals made frequent short dives through the thermocline, especially during the daytime. These phenomena may be related to foraging based on the distribution of their prey. In late October, yellowtails started a rapid southward movement, primarily remaining in vertical thermal mixing coastal areas, and not entering the coldwater masses that formed offshore. This southward movement pattern might indicate that yellowtails avoid cold offshore water temperatures.

Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia’s putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.

Accurate identification of Seriola dumerili (SD) offers crucial technical support for aquaculture practices and behavioral research of this species. However, the task of discerning S. dumerili from complex underwater settings, fluctuating light conditions, and schools of fish presents a challenge. This paper proposes an intelligent recognition model based on the YOLOv8 network called SD-YOLOv8. By adding a small object detection layer and head, our model has a positive impact on the recognition capabilities for both close and distant instances of S. dumerili, significantly improving them. We construct a convenient S. dumerili dataset and introduce the deformable convolution network v2 (DCNv2) to enhance the information extraction process. Additionally, we employ the bottleneck attention module (BAM) and redesign the spatial pyramid pooling fusion (SPPF) for multidimensional feature extraction and fusion. The Inner-MPDIoU bounding box regression function adjusts the scale factor and evaluates geometric ratios to improve box positioning accuracy. The experimental results show that our SD-YOLOv8 model achieves higher accuracy and average precision, increasing from 89.2% to 93.2% and from 92.2% to 95.7%, respectively. Overall, our model enhances detection accuracy, providing a reliable foundation for the accurate detection of fishes.