Abstract:The morphological variations among different populations of Coilia nasus, collected from the south branch (NZ) and north branch (BZ) of the Yangtze Estuary, Neihe of Chongming (NH) and Shengsi (SS) in Zhejiang Province, were assessed to determine the population compositions using traditional morphology and the truss network model. All morphological variable data were analyzed using multivariate statistical approaches, such as one-way analysis of variance (ANOVA), principal component analysis (PCA), discriminate function analysis (DFA), and cluster analysis (CA). ANOVA revealed significant differences in all morphological variables among the groups, except head length behind the eyes, tail length, the dorsal origin of the caudal fin-origin of the pelvic fin, termination of the anal fin-origin of the anal fin, the origin of the anal fin-origin of the pelvic fin, and end of operculum-end of operculum (P＜0.05). Based on the coefficient of variation (CV), the morphological variation among different C. nasus populations in the Yangtze Estuary was very small. The differences among the groups were mainly due to differences in the lateral trunk and head length. The lateral trunk was the primary variation axis, while the head length was the secondary variation axis. The stepwise discriminant comprehensive rate was 80.60%, and the cross-validated comprehensive discriminant rate was 76.30%. The BZ group had the best discrimination accuracy rate (95%), indicating the best discriminant effect, while the NH group had the lowest discrimination accuracy. According to the CA results, the four populations can be divided into three groups: Group I, the NZ and NH populations; group II, the SS population; and group III, the BZ population. The results of CA were similar to those of DFA, indicating the homogeneity and heterogeneity of the population differences. The lateral trunk and head length were identified as the main differences among the different populations of C. nasus in the Yangtze Estuary, which may be caused by differences in diet and habitat use.

Abstract:Perca fluviatilis (Perca), which belongs to the Perciformes order and Percidae family, and commonly known as Eurasian perch, is a precious species of freshwater fish favored for its delicious meat, high nutritional value, short growth period, and strong disease resistance. Perca fluviatilis is widely distributed in Europe and North Asia. To determine the genetic status of Perca fluviatilis in Xinjiang, the genetic diversity of four Perca fluviatilis populations in the Wulungu River and Kalaeerqisi River in Xinjiang was analyzed using mitochondrial CO I, Cyt b, and D-loop sequences, and then compared with that of the European populations. The CO I, Cyt b, and D-loop sequences of the four populations in Xinjiang had 3, 10, and 10 variable sites, respectively (accounting for 0.49%, 0.90%, and 1.92%, respectively, of the total sequence length), which defined 4, 11, and 11 haplotypes, respectively. Further, the haplotype diversity was 0.065±0.022, 0.276±0.049, and 0.186±0.046, respectively, and the nucleotide diversity was 0.00011±0.00004, 0.00033±0.00007, and 0.00084±0.00013, respectively, indicating low genetic diversity. No shared haplotype was found between the Chinese Xinjiang and European Perca fluviatilis populations. Further, the haplotype cluster tree and network diagram revealed obvious separation, thereby indicating different genetic pedigrees. Based on the Cyt b and D-loop sequences, the estimated variation among the populations of Wulungu Lake (WL), Jili Lake (JH), and Wulungu River (WR) in the Wulungu River basin in Xinjiang, China, was ?0.005% and 0.44%, respectively, and the coefficient of genetic differentiation (F_st) was ?0.00045 and 0.00436, indicating a low degree of differentiation (F_st＜0.05). Of note, the F_st between any population was low (F_st: ?0.01158?0.01803), indicating frequent genetic communication and the same genetic pedigree. In particular, shared haplotypes were identified between the two lakes, with a negative F_st and frequent gene exchanges with no genetic differentiation. Based on the CO I gene, the four populations of Kalaeerqisi (ER) and WR, WL, and JH were estimated to vary by 1.57% among the populations, with an F_st of 0.01568. However, the ER population and WL population had a moderate genetic differentiation (F_st=0.06614＞0.05), while the ER and WR populations had a high genetic differentiation (F_st=0.24627＞0.15). The replenishing of genetic resources may not occur due to the blockage of the dam. Further, the Kalaeerqisi River formed an independent genetic pedigree. Overall, these findings serve as a reference for the diversity of Xinjiang Perca fluviatilis populations and the development and utilization of germplasm resources.

Abstract:The sea raven, Hemitripterus villosus, is a common species in the northwestern Pacific Ocean. Owing to the significant role of the sea raven in the flesh and caviar industries, it has become one of the economically important species in China, Korea, and Russia. Owing to the decrease in resources for sturgeons in the caviar industry, sea raven is one of the best alternative candidates. However, due to anthropogenic activities, such as overfishing and pollution, the fishery resources for sea raven have been overexploited and have declined in recent years. Further, due to limited biological and genetic information on this species in Chinese coastal waters, the development of resource management and conservation, as well as fisheries and related processing industries, have been markedly restricted. To obtain useful genetic information to implement sound management and conservation plan, whole-genome analysis based on high-throughput sequencing data was performed to estimate basic genomic information and develop genome-wide genetic markers of this species at low cost. Genomic information was estimated based on the k-mer distribution pattern (k=17) using GCE v1.0.0 software. The genome sequence was then assembled to contig and scaffold levels using SOAPdenovo v2.01 software, with k=41. Subsequently, genome-wide microsatellite motifs were identified using MISA software. Primers were designed using Primer3 software. A total of 52.04 Gb of clean sequencing data was generated. K-mer analysis revealed that the genome size of H. villosus was approximately 713.18 Mb, with a heterozygosity rate of 0.26% and repeat sequence rate of 38.61%. Based on preliminary genome assembly results, the Contig N50 and Scaffold N50 were 7433 bp and 19 388 bp, respectively, with a final sequence size of approximately 577 Mb and GC content of 43.49%. The levels of continuity and completeness of this assembly were low; hence, further studies are needed for improved high-quality genome assembly. Based on the assembled genome sequence, 583 498 microsatellite motifs were detected throughout the genome, with a relative abundance of 1010 microsatellite motifs per Mb. Among them, the ratio of dinucleotides was the highest (55.61%), followed by that of mononucleotides (33.39%). AC/GT and AGG/CCT were dominant in the dinucleotides and trinucleotide repeats, respectively, and the repeated copy number of microsatellites mainly ranged from 5 to 17 times. To preliminarily validate the effectiveness of identifying microsatellites, ten motifs were randomly selected for primer design. After PCR amplification and electrophoresis detection, nine microsatellite motifs were successfully amplified. However, further confirmation is still needed to validate the effectiveness of identifying microsatellites and their polymorphisms at the population level. The genome survey results revealed a simple genome of H. villosus, which could be assembled using the sequencing strategy of “Illumina+PacBio+Hi-C” to generate a high-quality chromosomal level genome assembly. The screened microsatellite loci could also be used as effective molecular markers for subsequent genetic studies. Owing to the limitations of our study, further analyses are needed to improve the quality of genome assembly, confirm the effectiveness of the identified microsatellite loci in population genetic studies, and conduct comparative analyses between samples from different geographic localities. The findings of this study provide not only basic information for evolutionary biology and genetic assessments of the sea raven, H. villosus, but also scientific references for fishery and germplasm resource management and conservation from a genetic perspective.

Abstract:As primary producers, phytoplankton play an important role in the material cycle and energy flow of marine ecosystems. Changes in the phytoplankton community can effectively reflect changes in climate and marine ecological environment and affect the bait availability of fishery organisms. During extreme climate events, such as El Ni?o, the phytoplankton community displayed an obvious interannual variation trend, which affected the fishery yield by affecting the food chain. Based on the phytoplankton and water environment survey results of 12 voyages on the Miaodao Archipelago waters in May (dry season) and August (wet season) from 2015 to 2020, the interannual variation of phytoplankton community and its relationship to environmental factors according to climate change were evaluated based on precipitation data and three El Ni?o events during the survey period. A total of 109 species belonging to 45 genera and four phyla were identified. Bacillariophyta accounted for 85.32% of the total number of algae, followed by Dinoflagellates (11.93%). During the dry season, the abundance of diatom was always higher than 90%, and Paralia sulcata was identified as the dominant species. In the wet season, the abundance proportion of dinoflagellates gradually increased from 0.5% to 58.7%, and Chaetoceros nipponicus and Tripos muelleri were the dominant species. The main environmental factors affecting the phytoplankton community were water temperature, precipitation, and SiO₃ ^2–Si levels. The dominant diatom species were mainly regulated by the levels of NO₃ ^– -N, SiO₃ ^2–Si, and DIN related to precipitation, while the main influencing factor of dinoflagellate abundance was the water temperature. A significant negative correlation was found between the abundance of Paralia sulcata and SiO₃ ^2–-Si concentration (P＜0.05). Further, the abundance of Chaetoceros nipponicus showed a significant positive correlation with precipitation levels in the first two months (P＜0.05). The similarity of the phytoplankton community structure under extreme drought was significantly lower than that during other voyages. During the El Ni?o influence period of 2018/2019 and 2019/2020, the phytoplankton abundance in the dry and wet periods of 2019–2020 decreased by 93.2% compared with that of 2015–2018. The changes in the number and abundance of the phytoplankton species occurred in the next year of El Nino, which may be related to the climate changes in the coastal waters north of the Yangtze River in China, such as the reduced rainfall in the subsequent year owing to the El Ni?o effect. Extreme climate events became one of the important driving factors for the interannual variation of phytoplankton communities. Due to climate change, the interannual increase in water temperature, decrease in precipitation, and decrease in nutrient level led to noticeable changes in the phytoplankton community, such as a decrease in phytoplankton abundance and the succession of the phytoplankton community. These results serve as a reference for the rational exploitation and utilization of fishery resources and planning of fishery resource expansion and conservation.

Abstract:Evaluations of the age structure, growth pattern, and reproductive characteristics of Triplophysa stewarti are required for collecting basic biological data on Triplophysa and providing a theoretical basis for the protection of the ecological environment and fishery resources in the endorheic lake area in southern Tibet. In this study, we analyzed the age, growth, and reproductive characteristics of 1616 Triplophysa stewarti samples collected from Lake Chugutso, Tibet, using otolith identification for age data and biological measurement data. The growth equation was obtained using a functional fit, and dissected the gonads to observed their development. The age distribution of the collected Triplophysa stewarti ranged from 1 to 6 years, with fewer fishes having greater age and showing a tendency for lower age instead. The age of the female population mainly ranged from 1 to 2 years, while that of the male population mainly ranged from 3 to 4 years. The body length of all Triplophysa stewarti samples ranged from 3.47–14.30 cm, while their body weight ranged from 0.40–28.70 g. The relationship between body length and body weight was described by the linear equation, W=0.0102L^3.0115. Its growth characteristics are in accordance with the von Bertalanffy growth equation: L_t=13.891[1?e^{?0.168(t+2.895)}](R² =0.940); W_t=28.179[1? e^{?0.168(t+2.895)}] ^3.0115 (R² =0.991). The inflection age of the growth curve occurred at 3.65 years at a body length of 9.26 cm and body weight of 8.31 g. The male to female population ratio of Triplophysa stewarti was 1 : 3.01, with highly significant differences revealed by the χ² test (P＜0.01). The Fulton fertility and Clark fertility for male fishes were 1.07 and 0.88, respectively, and 1.03 and 0.76, respectively, for female fishes. The sexual maturity of Triplophysa stewarti was identified at the age of 1. Further, the maturity coefficient was 1.57% for the male population and 2.37% for the female population. Absolute fecundity ranged from 1040 to 10176 grains/tail, with an average of 4397 grains/tail. Triplophysa stewarti exhibited slow growth and less fullness, with a low gonadal maturation coefficient in females, which may be affected by the special geographical location and ecological environment of Lake Chugutso, Tibet. The age distribution of Triplophysa stewarti followed a simple pattern due to a large proportion of young individuals, which is intrinsically linked to the predatory behavior of numerous migratory and transit birds. Both the age distribution and growth characteristics of Triplophysa stewarti indicate that the population exists in a limited state. Therefore, the management of the domestic sewage and waste of the residents of Zhegu Town should be strengthened to reduce the impact of human activities on the fish habitat. Further, water flowing into the lake must be managed, the amount of water entering the lake must be monitored, and the swampiness of the lake must be reduced. A scientific guide should also be provided to the residents, and the importance of protecting local ecosystems should be emphasized.

Abstract:To comparatively investigate and analyze the muscle quality and edible value of three Seriola fishes, the texture characteristics and basic nutritional composition of the muscle of S. lalandi, S. dumerili, and S. quinqueradiata in the East China Sea were evaluated. Texture analysis (TPA) was performed to assess the muscle texture characteristics of the three Seriola species, and conventional biochemical methods were employed to detect the components of water, protein, ash, fatty acid, and amino acid in the muscles. The muscle hardness, adhesion, mastication, and resilience of S. lalandi were significantly higher than those of S. dumerili and S. quinqueradiata. Further, S. lalandi had the highest muscle protein content, S. dumerili had the highest muscle water content, and S. quinqueradiata had the highest muscle fat content. The three Seriola fishes had higher essential amino acid content than the recommended standards of the Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO). According to the scores of amino acid score (AAS) and chemical score (CS), methionine was the first limiting amino acid in the muscle of the three Seriola species, and valine was the second limiting amino acid. Furthermore, the content of fresh amino acids in the muscle and their proportion to the total amino acids were found to be relatively high, which may be the primary reason for the delicious taste of the muscles of the three Seriola species. A total of 20 types of fatty acids were detected in the muscles of the three Seriola species; however, methyl linolenate (c18 : 3n6) was only detected in S. quinqueradiata, and methyl docosadienoic acid (c22 : 2) was only detected in S. dumerili. The content of unsaturated fatty acids in the muscles of Seriola was relatively high, and their EPA+DHA content was associated with evident advantages, ultimately indicating that these three Seriola species have high nutritional value based on their high levels of unsaturated fatty acids. S. dumerili muscle had the highest content of major elements, while S. quinqueradiata muscle had the highest content of trace elements. Overall, the muscles of the three Seriola species were found to be rich in amino acids, fatty acids, and other nutritional elements, which support their industrial development and commercial prospect as promising candidates for open ocean aquaculture. Our study findings highlight the culture and commercial potential of Seriola fishes.

Abstract:Sinilabeo decorus tungting is a category of endangered fish that urgently requires resource protection. A histological study of the digestive system of larvae must be required to improve the survival rate of the artificial larvae of S. decorus tungting. In this study, the digestive system of S. decorus tungting from 2 to 80 days post-hatch (DPH) was studied using tissue sectioning technique, HE (hematoxylin-eosin) staining, and histochemical staining. The initial digestive system appeared to have a differentiated buccopharyngeal cavity and intestine at 2 DPH; However, the buccopharyngeal cavity was not opened outward. Further, hepatocytes closely surrounded the foregut and formed the hepatic cord. At 4 DPH, the gastrointestinal epithelial cells began to differentiate functionally, and the hepatocyte mass increased accordingly, filling between the yolk sac and digestive tract with light cytoplasmic staining and hepatic sinusoids initially. The digestive tract was connected, and the larvae were found to have entered the endo-exotrophic period. At 6 DPH, the cleft of the mouth deepened, assuming the shape of “＞,” and the snout was gradually shaped with mucus cells. The callose pad of the throat was keratinized, and the mucosal epithelium of the branchial arch was thickened. Mucus cells and taste buds were initially observed. The muscular layer of the esophagus was found to become thicker, with circular muscles as the major type. Several vacuoles were formed between hepatocytes, which became smaller. There were folds and striated margins on the intestinal epidermis. Further, the folds from the foregut to the hindgut became shorter as the goblet cells increased. At 9 DPH, the muscular layer of the posterior pharyngeal callose pad was identified, and the mucosal layer on the opposite side of the callose pad began to sag and form folds. The esophageal circular muscle developed; however, the longitudinal muscle did not manifest. Goblet cells were distributed in the intestine and the posterior segment to a greater extent. At 10 DPH, the lip cells displayed a keratinization trend, and the comb processes were formed on the surface of the callose pad. At 13 DPH, the yolk sac was completely absorbed, and the endo-exotrophic period transitioned to the exogenous nutrition period. At 43 DPH, the structures of the oropharyngeal cavity, gill, and intestine aligned with those of adult fish and gradually developed and improved as the fish grew. Herein, the development process for the digestive system of larvae and juveniles was further divided into three stages: endogenous nutrition period, endo-exotrophic period, and exogenous nutrition period. The change in feeding habits was found to be relative, and the digestive function was found to improve accordingly.

Abstract:Water pollution in aquaculture occurs mainly due to fish feces and uneaten feed. Supplying excess food to fish does not accelerate their growth; instead, this excess can cause issues, such as reduced digestion efficiency and increased water pollution. Therefore, an appropriate feeding frequency must be selected to optimize fish growth and minimize negative impacts. Matching the feeding frequency with peak appetite may enhance growth, improve feed conversion efficiency, and minimize water pollution. The return of fish appetite is associated with the gastric evacuation rate. The gastric evacuation of fish is affected by several factors, including fish size. To date, only a few studies have been conducted on the effects of the size of the Atlantic salmon (Salmo salar), an ecologically and culturally important salmonid fish, on the gastric evacuation rates in this species. Therefore, we aimed to determine the gastric evacuation rates and associated mathematical models of Atlantic salmon of different sizes and provide theoretical information for the feeding frequency in the context of aquaculture practice. The gastric evacuation experiment using two sizes of Atlantic salmon (176.15±27.52 g and 323.33±43.91 g) was carried out by analyzing the gastric contents. After adapting to the experimental environment for 27 days and fasting for 48 h, the wet and dry masses of the stomach contents of Atlantic salmon were assessed at predetermined postprandial times (0, 3, 6, 9, 12, 18, and 24 h) via serial slaughtering. Thereafter, the relative wet and dry masses at different time points were fitted using four mathematical models (linear, exponential, square root, and logistic models). The gastric evacuation time for 80% dry mass was calculated as the optimal feeding frequency after selecting the optimal model for each size. The water content in Atlantic salmon increased significantly from 0 to 3 h after feeding and then tended to be stable. Due to the moisture in the stomach, gastric evacuation of the wet mass displayed a different trend from that of the dry mass in both sizes of salmon. The dry-mass fitting model could reflect the gastric evacuation more accurately than the wet-mass fitting model. The optimal dry mass gastric evacuation model of small- and large-size Atlantic salmon aligned with the exponential model (reflecting a trend of fast and then slow) and square root model (reflecting a trend of slow and then fast), respectively. The gastric evacuation times of 80% dry mass in small- and large-size Atlantic salmon were 12.23 and 18.06 h, respectively, which indicated that the small-size Atlantic salmon had faster gastric evacuation time than the large-size salmon. In this study, a “lag phase” was observed within 3 h postprandial. Further, the “lag phase” of the small-sized salmon was found to be shorter than that of the large-sized salmon, which caused differences between the gastric evacuation models for the two salmon sizes. The small-sized salmon may have a faster gastric evacuation rate as softening of the dry feed occurs faster with water during the early digestion of the smallsized Atlantic salmon. These results could provide biological parameters and theoretical references for an innovative feeding strategy applicable to the production of Atlantic salmon.

Abstract:Out-season crab at lunar June (Eriocheir sinensis) refers to a juvenile male crab that has not completed reproductive molting, which occurs in June as per the lunar calendar. In recent years, the breeding scale and supply of the outseason crab at lunar June from the main river crab production area in China have increased rapidly. However, the edible yield and nutritional composition of the outseason crab from different areas are unknown. In this study, the edible yield, color parameters, proximate composition, and fatty acid composition of the outseason crabs at lunar June from six major crab producing areas in China (Huzhou in Zhejiang Province, Yangcheng Lake in Jiangsu Province, Chongming in Shanghai, Changdang Lake in Jiangsu Province, Hongze Lake in Jiangsu Province, and Weishan Lake in Shandong Province) were compared. The meat yield, hepatopancreas index, and total edibility of the outseason crab at lunar June ranged from 10.17%–11.87%, 27.83%–29.23%, and 39.44%– 40.37%, respectively, with no significant differences found among the groups (P＞0.05). The L* (brightness) and b* (yellowness) values of the outseason crab at lunar June from Weishan Lake were significantly higher than those of crabs from other regions (P＜0.05). Further, the outseason crab at lunar June from Yangcheng Lake had the highest a* (redness) values; crab hepatopancreas from Huzhou had the lowest L* and b* values; and outseason crabs from Weishan Lake had the highest L*, a*, and b* values. The hepatopancreas of the outseason crab at lunar June from Chongming had the highest moisture and ash. In addition, the crude protein and crude fat contents of the outseason crab at lunar June from Hongze Lake were significantly higher than those of the crabs from Huzhou (P＜0.05). The moisture, crude fat, and ash contents of the muscles of the six groups were not found to differ (P＞0.05) significantly. Moreover, only the crude protein contents of the outseason crab at lunar June from Hongze Lake and Weishan Lake were significantly higher than those of the crabs from Huzhou and Changdang Lake (P＜0.05). The total polyunsaturated fatty acid (∑PUFA) content in the hepatopancreas of the outseason crab at lunar June from Hongze Lake was significantly higher than that of the crabs from Yangcheng Lake and Weishan Lake. Further, these crabs had the highest DHA, EPA, and total long-chain polyunsaturated fatty acid (∑LC-PUFA) content (P＜0.05). The muscle of outseason crab at lunar June from Huzhou had the highest ∑PUFA content, while the muscle of the outseason crab at lunar June from Hongze Lake had the highest DHA content. The n-3/n-6 ratio of the crab from Hongze Lake was also significantly higher than that of the crab from Huzhou (P＜0.05). In summary, the edible yield and proximate composition of the outseason crab at lunar June from the six major production areas were similar; however, large differences in color and fatty acid composition were found among these crabs. The a* and b* values of the outseason crab at lunar June from Yangcheng Lake and Weishan Lake were relatively high. Further, the edible tissues of the outseason crab at lunar June from Yangcheng Lake, Changdang Lake, and Hongze Lake had high DHA content, which may be related to their breeding environment and feeding bait.

Abstract:One of the most economically-important fish cultivated in China, the Chinese perch (Siniperca chuatsi), refuses any dead prey fish or artificial diets as they begin to consume the feed. This special food habit markedly increases the production costs and reduces the economic benefits of Chinese perch aquaculture. However, some of these fish can be trained to change their inborn feeding habits to consuming artificial diets after food habit domestication. The roles of phosphoenolpyruvate carboxykinase-1 (pck1) and taste 1 receptor 1 (t1r1) and the possible regulatory mechanism mediated by DNA methylation in food habits transformation were explored. Two groups of mandarin fish were used in the study after domestication: Group W, which consumed live prey fish, and Group C, which consumed artificial diets. The expression levels and DNA methylation status in the upstream region of the transcriptional initiation site of pck1 and t1r1 were detected in the caudal fin, liver, and brain of the fishes from the two groups. The mRNA level of pck1 was significantly higher in the liver than that in the brain and caudal fin (P＜0.05). Methylation of pck1 was generally less frequent in the liver compared with that in the brain and caudal fin; however, the expression levels of pck1 were not necessarily related to the DNA methylation extent in different tissues. For example, compared with caudal fin, the pck1 mRNA levels were relatively higher in the brain; however, some CpG sites were highly methylated. Compared with the caudal fin and liver, a higher expression level of t1r1 was found in the brain (P＜0.05). However, no differences were found in the methylation levels at the CpG sites in these tissues (P＞0.05). Compared with Group W, the expression levels of pck1 were significantly lower in the liver, aligning with a greater extent of methylation at –2169 nt in Group C (P＜0.05). The transcription levels of t1r1 were lower in the brain of Group C (P＜0.05), and the DNA methylation extent did not significantly differ between the two groups at any of the CpG sites in the brain (P＞0.05). Herein, no evidence supported the hypothesis that the DNA methylation status of pck1 and t1r1 in the brain and liver (tissues that can be sampled repeatedly) could be deduced from that in the caudal fin (a tissue that cannot be sampled repeatedly) despite the strong correlations found between the absolute methylation levels in red blood cells (cells that can be sampled repeatedly) and those in the liver, kidney, and brain (tissues that cannot be sampled repeatedly) in previous studies using small songbird. These studies also revealed that the DNA methylation status in the blood cells is a potential biomarker for the DNA methylation status in other tissues. Nonetheless, our results indicate that pck1 and t1r1 might be responsible for the food habit transformation of Chinese perch from consuming live prey fish to artificial diets. Further, the DNA methylation levels in the CpG island of pck1 might be pivotal for fish as their food habits could be successfully transformed into consuming artificial diets via the regulation of pck1 expression. Of note, the DNA methylation of t1r1 may not be the major regulatory factor in food habit transformation. Collectively, our findings enable a better understanding of the role of pck1 and t1r1 in the food habit transformation of Chinese perch and serve as a reference for future research on the genetic regulatory mechanism of food habit transformation in Chinese perch, especially based on DNA methylation.

Abstract:The validity of the mitochondrial cytochrome C oxidase subunit I (CO I) sequences from Schizothoracids in GenBank as a molecular marker was determined in this study. Multiple sequence alignment, divergence from reference sequence assessment, and phylogenetic reconstruction were employed to evaluate the sequence homology, species diagnosis, and phylogenetic resolution of CO I sequences from Schizothoracids in GenBank. The primary alignment result for 1431 downloaded sequences revealed three sequences with significantly large indels; however, their homologous status was questionable. BLAST search and sequence information in GenBank confirmed that these sequences were Schizothoracid CO I sequences that were submitted as complements. Accordingly, prior to alignment, complement transition of these sequences should be carried out. Complete multiple sequence alignment revealed that all Schizothoracid CO I fragments in the GenBank nucleotide database were from near the 5? end to the middle of this coding gene. To retain more variation information, 35 short sequences were eliminated from the dataset. As a result, 1,396 sequences with 527 bp were analyzed, and 228 CO I haplotypes were defined. Intra-specific sharing haplotypes were common in species with multiple available sequences. However, 41 inter-specific sharing haplotypes were shared by more than one species. The average pairwise p-distance within the Schizothoracid CO I haplotypes was 9.5%, which is comparable with the cogeneric species level in fish. The average pairwise p-distances within the primitive, specialized, and highly specialized Schizothoracids were even shorter, a character of recent radiation that may reflect a short speciation history mainly driven by the elevation of the Qinghai-Tibet Plateau. Specimen misidentification was found in some Schizothoracid CO I sequences in GenBank, suggesting confirmation steps before use, such as comparison with reference sequences or inference from the phylogenetic reconstruction. Generally, the CO I sequence is a good molecular marker for Schizothoracids identification and primary evolutionary analysis, and the phylogenetic relationships among the three evolutionary grades of Schizothoracids are well resolved using this marker. Integrative analyses, including morphology, ecology, mitochondrial and nuclear DNA diversity, and phylogeny, would aid in taxonomic resolution and further investigation of hybridization and speciation in Schizothoracids.

Abstract:Fish growth and development, reproduction regulation, immune regulation, and many other life activities are regulated by long non-coding RNA (lncRNA). As a polypeptide hormone, calcitonin plays an important role in regulating calcium metabolism in vertebrates. Notably, salmon calcitonin (sCT) has the highest biological activity. To explore the effect of sCT on the expression level of lncRNAs in the skeletal tissue of teleosts, intraperitoneal injection of sCT was administered to young rainbow trout (Oncorhynchus mykiss), and their scales were collected 24 h after the injection. The lncRNA expression profile was analyzed using high-throughput sequencing technology and bioinformatics methods. A total of 847 differentially expressed lncRNAs, including 247 upregulated and 600 downregulated lncRNAs, were identified in the scales of rainbow trout administered with sCT. Six lncRNAs were randomly selected for quantitative real-time PCR (qRT-PCR) analysis; the results of which indicated that the expression pattern of these lncRNAs aligned with the RNA-Seq results. GO annotation revealed that the target genes of the aforementioned differentially expressed lncRNAs were mainly annotated in the functions of transcription regulation, transportation, signal transduction, membrane, cytoplasm, metal ion binding, and nucleotide binding. KEGG pathway enrichment analysis showed that target genes of the differentially expressed lncRNAs were significantly enriched in thiamine metabolism, inflammatory mediator regulation of TRP channels, platelet activation, glutamatergic synapse, neurotrophin signaling pathway, arrhythmogenic right ventricular cardiomyopathy (ARVC), and NF-kappa B signaling pathway. Accordingly, five lncRNAs (MSTRG.68909.2, MSTRG.39805.1, MSTRG.121429.1, MSTRG.9137.1, and MSTRG.43721.1) and their target genes might participate in the molecular regulation of O. mykiss calcium metabolism, and identification of these genes could provide a valuable dataset to elucidate the molecular regulation of bone metabolism in fish.

Abstract:Pharyngeal myxosporidiosis, caused by Myxobolus honghuensis, is one of the most severe parasitic diseases in the cultured allogenogynetic gibel carp, Carassius auratus gibelio (Bloch). The distribution of M. honghuensis in tissues and organs of covertly infected gibel carp was determined. Thirty 2-year-old fishes were collected from the pond, and the infection prevalence and intensity in gills, pseudobranch, spleen, liver, head kidney, middle kidney, ovary, blood, and muscle were detected via microscopic exam and quantitative PCR tests. Although the fishes did not display any obvious clinical signs, the real-time PCR tests revealed a 100% infection rate, and all fish used in this study had a covert infection of M. honghuensis. The infection prevalence of M. honghuensis in different tissues varied significantly (pseudobranch, 100%; ovary, 83.3%; gill, 73.3%; spleen, 70.0%; middle kidney, 36.7%; head kidney, 23.3%; liver, 10.0%; blood, 6.7%; and muscle, 0%). The infection intensity of M. honghuensis was inferred based on the relative expression of 18SrDNA normalized to the β-actin gene of fish host, and the real-time PCR data were analyzed using the 2^–ΔΔCt method. The infection intensity in different tissues also was signifantly different: pseudobranch, 14.4349±70.0529; ovary, 0.9556±1.5627; spleen, 0.3644±0.7854; gill, 0.3339±0.2682; head kidney, 0.2722±0.3761; middle kidney, 0.0379± 0.1055; liver, 0.0019±0.0022; and blood, 0.0012±0.0011. In conclusion, the pseudobranch of gibel carp is an important target organ in M. honghuensis infection, and should be considered as the first choice in futhre pathogen detection and disease surveillance.