Aquaculture

As global reptile populations continue to decline, improving reproductive success in managed populations of listed species, such as Phrynosoma cornutum (the Texas horned lizard) has become increasingly critical for species survival. One understudied area of reproductive research in reptile species is gamete collection and storage, a crucial component for maintaining genetic diversity. In Texas, semen was collected from wild P. cornutum (n = 20) in June 2025. Semen collection was performed via electroejaculation (EEJ) under alfaxalone anesthesia. Prior to semen collection, snout-vent-lengths (SVL) and weights were recorded and testes measurements were taken using a portable ultrasound. Average sperm motility and concentration across all lizards was 83.7% and 85.7 x 106 sperm/mL, respectively. While lizards with longer SVLs had higher sperm motility, weight and testis size did not affect sperm parameters. Samples were extended in INRA96 and divided for use in cold-storage longevity or cryopreservation trials. Samples under cold-storage conditions were assessed for motility daily for 10 days. Motility was not significantly reduced until 48 hours post-collection and maintained 19% motility at day 10. For cryopreservation, samples were diluted 1:1 in INRAFreeze cryopreservation media and frozen in liquid nitrogen, then immediately thawed. Average post-thaw sperm motility was 13.9%, with the highest post-thaw motility recorded at 38.2%. This is the first report of semen storage and cryopreservation in Phrynosoma and provides valuable insight into semen storage potential in reptile species.

Pacific cod is a key species in North Pacific fisheries, and its stock assessment and management units are separated according to biological, geographical, and administrative information. Understanding the fine-scale genetic population structure of this species is crucial for effective management, particularly in regions such as Japan, where complex coastal geography and localised fisheries management prevail. Therefore, in this study, we analysed genome-wide single nucleotide polymorphisms (SNPs; 6,035 loci) in 496 individuals of Pacific cod sampled from 33 sites around the Japanese archipelago via genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. Our analyses revealed three major genetic groups: Japanese Broad Range, Northernmost Honshu-Hokkaido (NHH), and Western Sea of Japan groups. These groups exhibited significant genetic differentiation (global FST = 0.056), distinct levels of nucleotide diversity, and group-specific genome-wide patterns of Tajimas D. Moreover, demographic history reconstruction based on whole-genome sequencing of three representative individuals revealed that each genetic group followed distinct demographic trajectories since the last glacial period. Importantly, the NHH group, related to the Mutsu Bay spawning aggregation and previously shown to exhibit strong natal homing in tagging surveys, was genetically identified for the first time in this study. Isolation-by-distance was observed across Japanese waters and within the Japanese Broad Range group, but not within the NHH group, suggesting that gene flow is generally restricted by geographic distance, except within the NHH group. To evaluate the potential for genetic stock identification, we extended a resampling-based cross-validation framework by incorporating outlier detection to assess marker selection strategies. Over 500 background SNPs were required to achieve >90% assignment accuracy for genetic stock identification, whereas only eight or more outlier SNPs showed comparable performance. These findings suggest that carefully selected SNP panels, particularly those including outlier loci, substantially improve stock discrimination. Overall, our study demonstrates the fine-scale genetic structure and demographic history of Pacific cod in Japanese waters and highlights the utility of practical marker strategies for enhancing the biological realism of fisheries assessment and supporting sustainable fisheries management.

Pseudomonas aeruginosa is a clinically significant bacterial pathogen that poses a serious threat to aquaculture. However, there are limited information on Massilia isolates against pathogenic P. aeruginosa in aquaculture. In the present study, a facultative predator, M. varians isolate P2-4, was isolated from aquaculture sediment using Chinese mitten crab Eriocheir sinensis-pathogenic P. aeruginosa as the prey bacterium, and its genomic feature, bacteriolysis-related genes, safety, bacteriolytic spectrum, and in vitro and in vivo antibacterial effects against pathogenic P. aeruginosa in E. sinensis were further characterized. Isolate P2-4 consisted of one chromosome and one plasmid (with a total of 75 tRNAs, 7 5S rRNAs, 7 16S rRNAs, 7 23S rRNAs, 34 sRNAs, 5,238 coding genes, 20 genomic islands, 1 prophage, 23 insertion sequences, and 102 repeat sequences), and harbored 19 bacteriolysis-related genes (pilA, pilB, pilC, pilD, pilF, pilG, pilH, pilM, pilO, pilP, pilQ, pilS, pilR, pilT, mltA, mltB, mltC, mltD, and dacB) associated with cellular motility and cell wall lysis. In addition, the isolate carried no virulence genes, was unable to produce haemolysin, hydrogen sulfide, nitrite and ammonia, and avirulent in E. sinensis with a 7-day acute intraperitoneal LD50 value of above 5.0 x 108 CFU/mL. Furthermore, the isolate possessed a wide bacteriolytic spectrum against pathogenic Shewanella algae, Aeromonas caviae, A. hydrophila, and Photobacterium damselae besides P. aeruginosa, exhibited bacteriolysis rates of 99.35% to 99.99% towards the pathogenic P. aeruginosa at 1.0x103 to 1.0x10{square} CFU/mL, and displayed relative percentage survivals of 42.31% to 73.08% against P. aeruginosa infection in E. sinensis at doses of 6.0 x 103 to 6.0 x 105 CFU/g diet. To our knowledge, this study for the first time demonstrates a M. varians strain as a potential biocontrol agent against pathogenic P. aeruginosa in aquaculture.

Transcriptomic analyses are widely used to elucidate the molecular mechanisms driving gametogenesis and reproduction in fish, yet their accuracy depends heavily on appropriate normalization of gene expression data. Conventional approaches that rely on single or multiple reference genes are problematic during teleost oogenesis, as profound structural and physiological remodeling of the ovary challenges the assumption that commonly used reference transcripts remain stable. In this study, we assessed by qPCR the transcriptional variability of four widely used reference genes (actb, ef-1, gapdh, and 18S rRNA) throughout the oogenic cycle of the thicklip grey mullet (Chelon labrosus), using geNorm and NormFinder analyses, and we additionally evaluated total cDNA concentration as an alternative normalization factor. To examine the performance and interpretive consequences of each normalization strategy, we compared expression patterns of key steroidogenic genes (star, cyp19a1a, and cyp11b) normalized by individual reference genes, combinations of reference genes, or total cDNA concentration. All evaluated reference genes displayed notable transcriptional variability across oogenesis, confirming their limited suitability as sole internal controls. In contrast, normalization approaches integrating multiple reference genes and/or total cDNA concentration consistently provided greater stability and more reliable biological interpretation. These results support a refined and more robust normalization framework for transcriptional analyses in fish ovaries, particularly during stages of extensive tissue remodeling. Our findings demonstrate cDNA-based normalization is straightforward, rapid, and easy to implement across laboratories, providing a practical alternative for achieving accurate, reproducible transcript quantification in fish ovary studies.

Global climate change has increased the frequency and severity of stressful temperatures that freshwater fishes experience, necessitating rapid and sensitive methods to monitor wild populations. Tissues used to measure transcriptional responses traditionally involved invasive or lethal sampling, which may be undesirable for imperilled species. Epidermal mucus offers a non-lethal and minimally invasive alternative, but whether thermal thresholds can be detected in mucus to identify fish experiencing thermal stress is unclear. Bull trout (Salvelinus confluentus) are a legally protected salmonid and cold-water specialist, generally occupying waters 12 {degrees}C and below, with higher temperatures resulting in cellular stress. Therefore, we measured a suite of 56 genes using high-throughput qPCR to compare machine learning classifiers developed with transcriptional profiles of epidermal mucus, gill, liver, and muscle to classify laboratory reared juvenile bull trout as below (9 {degrees}C, 12 {degrees}C) or above (15 {degrees}C, 18 {degrees}C) cellular thermal thresholds. Mucus profiles most resembled gills but represented an intermediate transcriptional response to all tissues. A reduced biomarker panel of 10 genes in mucus assigned fish to stress categories with 94.1% (95% CI = 71.3-99.9%) accuracy, which was comparable to gill (100.0%, CI = 82.4- 100%), liver (95.0%, CI = 75.1-99.9%), and muscle (100.0%, CI = 80.5-100.0%). Sex-specific temperature effects were evident in all tissues, but less pronounced in mucus and gill than in liver and muscle. Our findings demonstrate that transcriptional profiling of mucus can reliably identify individuals experiencing thermal stress, highlighting the promise of this non-lethal approach for monitoring at-risk species.

Red Mark Syndrome (RMS) is a widespread skin disease affecting rainbow trout (Onchorhynchus mykiss). It provokes substantial economic losses in aquaculture, and is putatively caused by a Rickettsiales bacterium named Midichloria-like organism (RMS-MLO), which is strongly associated with RMS lesions. However, RMS-MLO ecology and epidemiology in aquaculture systems remain poorly understood. In this study, we analysed environmental DNA to monitor the presence of RMS-MLO and its putative vector Ichthyophthirius multifiliis in a trout farm in Northern Italy over one year. Water and sediment samples were monthly collected from multiple water tanks. RMS-MLO was consistently detected by PCR throughout the study in all trout-containing tanks, both in water and sediment samples, but never in the trout-free inflow tank. We did not observe an increase in RMS-MLO abundance during the single RMS outbreak recorded nor in relation with the co-occurrence of I. multifiliis. Our findings indicate a long-term persistence of RMS-MLO in the aquaculture, possibly as a consequence of infections with low prevalence or abundance, rather than its entry from the external environment at the time of RMS outbreaks. Additionally, hints were recorded for a potential role of free-living aquatic microeukaryotes as additional occasional reservoirs. In contrast, I. multifiliis was negatively related with RMS-MLO, while it significantly increased in abundance during the RMS outbreak, particularly in the inflow tank. This supports that, rather than a stable reservoir, I. multifiliis may act as a facilitator of RMS outbreaks, which might indeed be triggered by the entry of this parasite in trout farms.

Natural extracts could improve sperm storage and artificial insemination (AI). This study, for the first time, evaluates the suitability of a blueberry extract (Vaccinium corymbosum) obtained from pomace using a sustainable methodology as a supplement for bull semen extenders. Cryopreserved semen doses from eight bulls were combined in 9 pools (3 bulls/pool), supplemented with 0%, 1%, 5%, or 10% extract, and incubated up to 5 h at 38 {degrees}C. Motility was assessed hourly using OpenCASA, and the effects of treatment and time were evaluated using linear mixed-effects models. Motility was significantly better preserved with 1% extract (total and progressive motility, improved linear velocity and linearities, and decreased BCF and fractal dimension, related to hyperactivation). The effect of 5% was overall positive, but it was below 1%, whereas 10% mostly showed a negative effect. These results show that this natural extract could safely supplement bull semen extenders at least between 1% to 5%, and even help improve sperm motility. Therefore, this extract offers an opportunity to enhance cattle semen extenders using a sustainable approach, potentially improving reproductive outcomes.

Telomere length (TL) is increasingly used in ecology as a biomarker of individual quality and environmental stress, yet research on non-model species with complex life histories remains limited. Because TL varies among tissues and across ages in a species-specific manner, identifying non-lethal tissues that reliably reflect whole-organism telomere dynamics is essential for longitudinal telomere studies in the field. This study aimed to evaluate tissue-specific TL in Japanese eel (Anguilla japonica), an endangered catadromous fish. We first mapped the chromosomal distribution of telomeric sequences using fluorescent in situ hybridization (FISH), the first application of this method in this species. We then tested whether muscle and caudal fin, which can be sampled easily and non-lethally, can serve as suitable proxy tissues for TL measurements in wild individuals. Relative telomere length (RTL) was quantified by qPCR in blood, brain, caudal fin, gonads, heart, liver, and muscle. FISH analysis confirmed telomeric repeats at all chromosomal ends, with only weak interstitial signals on three chromosomal pairs unlikely to affect qPCR-based estimates. A generalized additive mixed model and Wilcoxons signed-rank tests revealed significant inter-tissue differences: RTL was shortest in the brain and muscle and longest in liver, blood and caudal fin. Muscle and caudal fin RTL were significantly correlated with RTL in many other tissues, supporting their use as proxy tissues for longitudinal TL monitoring, including responses to environmental variation. Both total length and age were tested as explanatory variables for RTL, and the model including total length showed a better fit than the age-based model. Non-linear relationships between RTL and total length observed in several tissues suggest physiological shifts associated with growth and sexual differentiation. Overall, these findings advance understanding of telomere dynamics in eels and establish muscle and caudal fin as suitable tissues for repeated, non-lethal TL assessment in ecological and conservation contexts.

The Leray-XT primer pair has been widely used to amplify the mitochondrial cytochrome c oxidase subunit I (COI) gene from animals. In some marine metabarcoding studies, protists have also been amplified and sequenced using these primers. Here, we ask if the Leray-XT COI primer pair is suitable for observing ciliates and radiolarians, which are numerically and ecologically important components of marine protistan communities. We show that while there are sufficient COI reference sequences for ciliates in NCBI for taxonomic assignments, there are currently only two COI reference sequences for radiolarians. Using in-silico analyses, we additionally show that while the reverse primer Leray-XT primer can bind and potentially amplify both ciliates and radiolarians, the forward primer cannot bind to either taxon. These results show that the Leray-XT primer pair is not suitable for observing ciliates and radiolarians, although it may be useful for observing other marine protistan taxa.

Understanding population structure is critical for effective fisheries management in species with complex life histories and variable recruitment. Southern flounder (Paralichthys lethostigma) is a valuable flatfish species with declining populations in the Southeast United States. Improved management may depend on a better understanding of fine-scale and temporal population genetic structure in this region; however, such structure remains poorly characterized. To address our lack of understanding of the spatial and temporal population structure of this important species, we used double digest reduced-representation genome sequencing (ddRADSeq) on juveniles from estuaries in North Carolina and Texas between 2014 and 2023. We found significant genetic differentiation between the Gulf of Mexico and Atlantic populations, supporting the management of these regions as distinct stocks. By contrast, we detected significant variance in genetic structure within Texas and North Carolina populations that was not consistent across sampling years between estuaries in close proximity. The population genetic structure of southern flounder suggests significant, temporally variable genetic differences within estuarine locations that may result from variation in larval dispersal and recruitment patterns. Our findings highlight the value of integrating fine-scale, multi-year genetic data to capture temporal dynamics and avoid misleading conclusions based on single-year or broad-scale sampling.

Development and use of assisted reproductive technologies (ARTs) in non-domestic species provides novel tools for species conservation. As a first step towards in vitro embryo production, we developed an OPU technique for two antelope species, scimitar horned oryx (Oryx dammah) and roan antelope (Hippotragus equinus) utilizing a custom-made needle guide and existing OPU equipment utilized by livestock and human practitioners. Females were anesthetized and placed in sternal recumbency for transvaginal OPUs. Prior to OPUs (36 - 45 hours), SHO and roan were either hormonally stimulated with follicle stimulating hormone (FSH, 140 or 250IU) as a single injection or not. A total of 32 and 26 OPUs were completed in SHO (n=10) and roan (n=7), respectively, representing one to four OPUs per animal at monthly intervals. A total of 141 oocytes were recovered from 215 follicles in SHO and 31 oocytes from 58 follicles in roan. FSH dose (250IU) increased (P<0.05) the number of follicles aspirated and the number of oocytes recovered in SHO. No effects of FSH were observed in roan (P>0.05). Good quality oocytes were recovered from all females and procedures were conducted in four consecutive months with no evidence of scar tissue buildup or reduced capacity to recover quality oocytes. These ARTs can be used to develop in vitro embryo production tools for population management and the preservation of female genetics; bolstering genetic diversity and guarding against extinction.

Conventional semen cryopreservation involves equilibration at 4{degrees}C and optimum freezing rates. We hypothesized that a cholesterol-based semen extender obviates the need for equilibration, minimizing total processing time for semen cryopreservation. Experiments were conducted to determine the effects of semen extender (egg yolk- or cholesterol-based) and freezing method (routine or fast) on post-thaw sperm characteristics and fertility of beef and bison semen. In Experiment 1, beef semen diluted in tris-egg yolk-glycerol (TEYG) or cholesterol-cyclodextrin tris-glycerol (CCTG) extender underwent routine or fast freezing method. Cholesterol from animal and plant origins were compared. The routine method included 90-min equilibration at 4{degrees}C and routine freezing (RE-RF, total time 97 min) whereas the fast method included no equilibration and fast freezing (NE-FF, total time 14 min). Post-thaw sperm quality was assessed by CASA, and in vitro fertilization. Post-thaw sperm motility was not affected by the origin of cholesterol (animal or plant), but was lowest in the TEYG NE-FF group (24% vs 43-51%, P < 0.05). In vitro cleavage and blastocyst development rates did not differ between RE-RF and NE-FF groups. In Experiment 2, bison semen was diluted in TEYG or plant-CCTG extender and frozen as in Experiment 1. Post-thaw sperm motility was lowest in the TEYG NE-FF group (10% vs 39-51%, P < 0.05). In Experiment 3, beef semen diluted in TEYG or plant-CCTG extender underwent either a routine (RE-RF) or modified freezing (NE-RF, total time 25 min) method. Post-thaw sperm characteristics did not differ between extenders but were greater using routine freezing (RE-RF) compared to the modified method of freezing (NE-RF). Pregnancy rates were similar between extenders (TEYG vs plant-CCTG) using the modified freezing method without equilibration and insemination at 72 h after progesterone device removal. In conclusion, beef and bison semen diluted in cholesterol-based extender may be cryopreserved without equilibration.

The sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and North-East Pacific but genetic improvement has been hindered by limited understanding of the genetic basis of economically important traits. We conducted the first genome-wide association study (GWAS) for this species using 202 self-fertilised pseudo-F1 individuals derived from 12 populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD-seq-derived SNP markers and phenotyped in a common garden experiment for four morphological traits (blade length, blade width, blade area, stipe length) and six metabolic traits related to nitrogen metabolism. We identified 26 significant marker-trait associations, with phenotypic variance explained (PVE) ranging from 0.65% to 52.44%. Major-effect loci were detected for blade width (52.44% PVE) and blade area (45.22% PVE) and a locus on chromosome 17 influenced both blade length and blade area. Marker-based heritability estimates ranged from 0.75 to 0.99 for morphological traits and from 0.00 to 0.99 for metabolic traits, though with large standard errors. Cross-validation of genomic selection models yielded predictive abilities of 0.21-0.59 across traits. Our findings reveal a mixed genetic architecture with major-effect loci suitable for marker-assisted selection and polygenic traits amenable to genomic selection, providing a foundation for genomics-assisted breeding programs in kelp aquaculture.

Boar semen contains spermatozoa and seminal plasma (SP) that carries extracellular vesicles (EVs) among other components. However, artificial insemination (AI) doses produced by AI companies are highly diluted based solely on sperm concentration. The aim of this study was to evaluate the integrity of EVs isolated from AI doses, characterize the protein and miRNA content from high-fertility (HF) and reduced-fertility (RF) boars, and evaluate their functional impact on spermatozoa after dilution by a coincubation up to 24 hours at 38 {degrees}C. Proteomics identified 108 differentially expressed proteins between HF and RF EVs (97 upregulated in HF, 11 in RF), and transcriptomics revealed 80 differentially expressed miRNAs (DEMs) in EVs, 52 in SP, and 3 in spermatozoa, showing inverse expression in various shared DEMs between fertility rates, suggesting compartment-specific regulation. Functional coincubation demonstrated that EVs remain biologically active after dilution. HF EVs improved sperm quality parameters and reduced oxidative stress, while RF EVs increased total and progressive motility. Overall, our findings show that EVs from AI doses retain structural integrity, carry fertility-associated protein and miRNA signatures, and functionally modulate sperm quality in vitro. These features highlight porcine EVs as promising biomarkers and potential tools to optimize reproductive performance in swine production.

Primarily inhabiting the harsh, high-altitude environment of the Qiangtang National Nature Reserve exceeding 5,000 meters above the sea (m.a.s.l.), the golden wild yak is critically endangered, with fewer than 300 individuals remaining in the world, a situation exacerbated by the significant challenges of conducting research and conservation of their genetic resources. Somatic cell nuclear transfer (SCNT) can be an effective method for their preservation, but facing several obstacles in this context, including the hypoxic stress at high altitude that impairs embryonic development due to in vitro manipulation, and constraints of long-distance embryo transport. In the present study, the ear tissue was collected from a childhood male golden wild yak at Xizang Geye Wildlife Rescue Station (4800 m.a.s.l.) and send to Institute of Animal Science at Beijing to derive fibroblast cells. Using fibroblast cells of the golden wild yak as nuclear donors, and bovine oocytes from a local slaughterhouse at Beijing as recipients, the interspecific SCNT (iSCNT) embryos were generated and in vitro developed to blastocysts. To maintain the embryonic viability after long-distance transportation from Beijing to Xizang, iSCNT blastocysts were subjected to cryopreservation by vitrification method. Thawing of vitrified iSCNT blastocysts were completed at Xizang Dangxiong Yak Breeding Innovation Base (4200 m.a.s.l.), and transferred into the uterine horn of domestic yaks. 257 days after blastocyst transfer, a cloned golden wild yak was successfully harvested on January 10, 2026. This work demonstrates, for the first time, that interspecies somatic cell nuclear transfer can successfully produce a cloned offspring under extreme conditions, spanning 4800 m.a.s.l. donor origin, long-distance vitrified embryo transportation, and high-altitude blastocyst transfer at 4200 m.a.s.l., establishing a viable strategy for conserving critically endangered high-altitude species.

The genus Trichiurus is the most economically valuable fish in the family Trichiuridae, currently recognized to include 10 valid species. However, historically numerous morphologically similar congeners have been erroneously assigned as synonyms or subspecies of T. lepturus. In this study, we examined 16 hairtail specimens collected from the southern waters of Java Island, Indonesia. Integrated morphological and mitochondrial phylogenetic analyses (COX1 and 16S rRNA), compared against global Trichiurus sequences, revealed that these specimens form an independent lineage that diverged early from other congeners. Consequently, we describe this lineage as a previously undescribed cryptic species. Diagnostic characters include: first anal-fin spine below 36th-37th dorsal-fin rays; anus below 35th-36th dorsal-fin rays; anteriormost tip of supraoccipital well posterior to posterior distal margin of eye; anterior margin of the pectoral-fin spine non-serrated; fangs on both jaws with barb-like processes; upper jaw long, mean 16.6% (15.5-17.6%) of preanal length; snout short, 12.0% (10.9-13.1%) of preanal length; eye small, diameter 5.3% (4.3-5.7%) of preanal length; and absence of hyperostosis on dorsal cranium. We herein propose the name Trichiurus javaensis sp. nov., and provide a formal morphological description and diagnostic characterization of this species.

AO_SCPLOWBSTRACTC_SCPLOWImproving feed efficiency in pigs is essential for reducing production costs and environmental impacts. This study examines the influence of circadian feeding rhythms and genetic polymorphisms on feed efficiency variability using two pig lines divergently selected for Residual Feed Intake (RFI) over ten generations. Feeding behavior was monitored using automatic concentrate dispensers, recording 6,494,097 visits from 3,824 pigs to analyze meal frequency, duration, and diurnal patterns. LRFI pigs ate less frequently, with larger meals and longer durations, they exhibited two distinct feeding peaks: one around 8:00 AM and a higher one at 5:00 PM and they consumed more feed during the diurnal period and less at night. HRFI pigs showed a smoother, less rhythmic feeding behavior with increased nocturnal intake. The differences between the two RFI lines became more pronounced as the number of generations of selection increased, suggesting a genetic basis. Feeding behaviors, including intake during the two main diurnal peaks, were found to be heritable (heritability estimates: 0.30-0.40) and genetic correlations were observed between feed intake and RFI, especially for intake between the two peaks. Then, we investigated the evolution of allele frequencies of single nucleotide polymorphisms (SNPs) in DNA sequences surrounding 10 core clock genes (ARNTL, CLOCK, CRY1, CRY2, NPAS2, NR1D1, PER1, PER2, PER3, RORA) along generations of selection. SNPs with significant frequency changes were mapped to regulatory regions and transposable elements, especially in HRFI line, suggesting potential functional impacts on circadian regulation. These results underscore the role of feeding behavior and genetic variation in feed efficiency, offering insights for breeding programs aimed at improving metabolic efficiency and sustainability in pig production.

Scyphozoan jellyfish have a complex life cycle that includes a characteristic transition known as strobilation. Retinoid signaling has been suggested to be involved in jellyfish metamorphosis and development. However, the genomic basis of signaling pathways associated with metamorphosis has not been sufficiently compared at the class level. Experimental studies have reported that indole compounds can induce metamorphosis in some jellyfish species. Indole- and tryptophan-derived metabolites are known to function as ligands for the aryl hydrocarbon receptor (AhR) in other organisms. However, the potential role of AhR signaling in jellyfish metamorphosis has not been previously explored. We compared the distribution of retinoid- and AhR-associated gene families across multiple scyphozoan genomes. This analysis aimed to characterize their distribution patterns in relation to signaling pathways associated with development and environmental responses. A standard gene prediction and annotation pipeline was applied to 20 species from 21 publicly available scyphozoan reference genome assemblies retrieved from the NCBI database. The distribution and copy number of these gene families were compared across species. Retinoid-associated gene families were detected across almost all Scyphozoa genomes, and core components of AhR signaling (AhR, ARNT) were identified in most species. These results suggest that scyphozoan genomes contain genetic components of retinoid- and AhR-related signals. This study presents the distribution of gene families related to developmental signaling across Scyphozoa using a comparative genomic approach. It does not imply direct functional involvement of retinoid or AhR signaling, but instead focuses on potential signaling pathways at the genome level. It also provides an overview of currently available scyphozoan genomic data. These findings provide a basis for future hypothesis generation and functional validation in jellyfish metamorphosis research.

Intraspecific morphological variability presents a complex challenge for biological systematics and biomonitoring, particularly for organisms with high phenotypic plasticity, such as zooplankton. Morphological differences between individuals of the water flea species Bosmina longirostris (Crustacea: Cladocera) are difficult to distinguish visually, parthenogenetic females look morphologically uniform within the species; nevertheless, they demonstrate differences attributable to their geographic origin and developmental stage. A reference dataset of microscopic images was created for the study, including populations from two geographically separated regions (seven ones from European Russia and seven ones from Sakhalin Island in the Pacific Ocean (Far East of Russia) and two age groups, demonstrating the ability of a neural network classify to successfully the intraspecific morphological variation. This study demonstrates that deep learning methods are prospective for the detection and understanding of fine morphological intraspecific differences in the cladocerans.

ABSTRACT Objective: This study aimed to systematically analyze the correlation between body weight and body measurement traits and the growth pattern of female Jiangyue donkeys. Methods: A total of 484 female Jiangyue donkeys were selected to determine their body weight (Y) and 11 body measurement traits, including withers height (X1), body length (X2), chest circumference (X3), cannon circumference (X4), head length (X5), neck length (X6), chest width (X7), chest depth (X8), rump height (X9), rump length (X10) and rump width (X11). SPSS 27.0 statistical software was used to conduct descriptive statistics, correlation and regression analysis on body weight and body measurement traits, and the optimal regression equation between them was established by the stepwise method and validated. Furthermore, four growth curve models (Logistic, Gompertz, Brody and Von Bertalanffy) were used to fit the body weight of 241 female Jiangyue donkeys at different months of age. Results: The body weight of female Jiangyue donkeys was significantly positively correlated with all body measurement traits (p<0.01), with the highest correlation coefficient observed for chest circumference. The optimal regression equations for body weight established by stepwise regression yielded R2 values of 0.918 and 0.844 for growing and adult donkeys, respectively (p<0.01). Among the four growth curve models, the Von Bertalanffy model exhibited the best fitting effect (R2=0.99992), with an estimated asymptotic body weight of 184.41 kg, which was close to the measured values of growing female donkeys. Conclusion: The regression models for body weight estimation and the Von Bertalanffy growth curve model for growth pattern evaluation established in this study can serve as effective tools and production management of female Jiangyue donkeys.