A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila

The immune defense response and immune-related genes expression in Odontobutis potamophila infected by Aeromonas salmonicida

Aeromonas salmonicida belongs to the Aeromonas family, which could widely infect economic fish, causing diseases and huge economic losses. Recently, A. salmonicida was also detected in diseased Odontobutis potamophila. Transcriptomic model of A. salmonicida-infected O. potamophila was analyzed to reveal immune response. A total of 113,282 unigenes were obtained and annotated in six databases. After 12 h of infection with A. salmonicides, a total of 614 differentially expressed genes (DEGs) (355 up-regulated genes and 259 down-regulated genes) were identified in the head kidney tissues. Following 24 h of infection, a total of 1689 DEGs were detected in the head kidney tissues, including 313 up-regulated genes and 1376 down-regulated genes. GO and KEGG pathway analyses were conducted to provide functional insights and a clearer understanding of the signal transduction pathways associated with the DEGs. Further analysis of the complement and coagulation cascades pathway and PPAR signaling pathway exhibited that the expression of immune genes was widely activated at the beginning of A. salmonicides infection. Additionally, six DEGs were randomly selected and validated using quantitative real-time PCR, showing expression patterns consistent with the high-throughput sequencing data. These results offer important insights that enhance the understanding of immune response in O. potamophila against A. salmonicida infection.

Validation of male-specific markers confirmed an XY/XX-type sex determination system in Chinese dark sleeper (Odontobutis sinensis)

Next generation sequencing (NGS) method has been successfully used to identify sex-specific markers in many fish species. The Chinese dark sleeper (Odontobutis sinensis) is a commercially important aquaculture species in China. Here, by conducting whole genome sequencing of three females, three males and one female mixed pool, we initially identified 658 male-specific sequences and 242 female-specific sequences of Chinese dark sleeper. Based on polymerase chain reaction (PCR) confirmation, three markers showed 100 % male-specific amplification in 16 female and 16 male individuals from the Wuhan population, and this result was further validated using an additional 16 females and 16 males from the Guangdong population, demonstrating the reliability of these markers across multiple populations. These findings suggest a male heterogametic sex determination system in Chinese dark sleeper. Moreover, male-specific genes including high mobility group box 3 (hmgxb3) and insulin-like growth factor 2b (igf2b) were identified through NR annotation, which might be candidate sex-determining genes in Chinese dark sleeper. Generally, these validated male-specific markers first demonstrated the existence of an XY-type sex determination system in Chinese dark sleeper and would make a significant contribution to the development of all-male breeding and understanding of sex determination mechanisms.

Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti)

Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques. According to the PacBio sequencing, C. guichenoti genome was successfully assembled to 1100.1 Mb size, with a Contig N50 size of 25.0 Mb, and containing 731.0 Mb of repeats. Hi-C sequencing data was utilized for chromosome assembly and 25 chromosome sequences were ultimately yielded, with a total length of 1076.8 Mb. Moreover, a total of 22,506 protein-coding genes were predicted with average intron length of 2293 bp. Evolutionary analysis and divergence time prediction revealed that C. guichenoti was closely related to C. heterodon and they phylogenetically diverged from common ancestor ~20.7 million years ago (Mya), following the separation of Cyprinidae at 28.3 Mya. In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources.

Effects of Quercetin on the Intestinal Microflora of Freshwater Dark Sleeper Odontobutis potamophila

Flavonoids have antimicrobial and anti-oxidation properties. The effects of the flavonoid quercetin on the intestinal microflora of freshwater dark sleeper Odontobutis potamophila were tested for the first time. Odontobutis potamophila juveniles were treated with quercetin for 21 days at one of three concentrations (2.5, 5.0, or 10.0 mg/L) and compared with a control group that was not treated with quercetin. Quercetin improved the stability of the intestinal flora in O. potamophila and the probiotic bacteria Bacillus spp. and Lactobacillus spp. increased in species abundance after the low concentration quercetin treatments. Furthermore, the abundance of pathogenic bacteria Plesiomonas spp., Aeromonas spp., and Shewanella spp. decreased after the fish had been exposed to quercetin. Activity of hepatic antioxidant enzymes (superoxide dismutase, SOD), (glutathione S-transferase, GST), (glutathione peroxidase, GSH-Px), and (total antioxidant capacity, T-AOC) increased in the livers of O. potamophila treated with quercetin, thereby increasing their hepatic antioxidant capacity and their ability to scavenge free radicals.

Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologies

The largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game or domesticated fish. Here a high-quality chromosome-level reference genome of M. salmoides was produced by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. Ultimately, the genome was assembled into 844.88 Mb with a contig N50 of 15.68 Mb and scaffold N50 length of 35.77 Mb. About 99.9% assembly genome sequences (844.00 Mb) could be anchored to 23 chromosomes, and 98.03% assembly genome sequences could be ordered and directed. The genome contained 38.19% repeat sequences and 2693 noncoding RNAs. A total of 26,370 protein-coding genes from 3415 gene families were predicted, of which 97.69% were functionally annotated. The high-quality genome assembly will be a fundamental resource to study and understand how M. salmoides adapt to novel and changing environments around the world, and also be expected to contribute to the genetic breeding and other research.

Effect of quercetin on muscle growth and antioxidant status of the dark sleeper Odontobutis potamophila

Quercetin is a flavanol beneficial in reducing fat, promoting muscle growth, and Anti-oxidation. To study its effects in freshwater fish, the full-length cDNA of the follistatin (FST) and myostatin (MSTN) genes of the dark sleeper Odontobutis potamophila were cloned for the first time. Juvenile individual O. potamophila was exposed to quercetin at one of four concentrations (0, 2.5, 5, and 10 mg/L) for 21 days. The expression level of MSTN which inhibits muscle growth in the quercetin solution was lower than in the unexposed control group. The genes that promote muscle growth are in TGF-β superfamily like FST, TGF-β1 (transforming growth factor-beta 1), and Myogenic regulatory factors (MRFs) like Myf5 (myogenic factor 5), MyoD (myogenic differentiation), MyoG (myogenin), were higher than in the control group. Apolipoprotein and growth hormone receptor transcription levels in the quercetin-treated fish were significantly lower than in the control group. The concentrations of triglyceride, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol in the muscle tissue decreased, and the lipid-lowering function of quercetin was also demonstrated at the biochemical level. In this study, we analyzed the mRNA levels of AKT, Keap1 (kelch-like ECH-associated protein 1), Nrf2 (NF-E2-related factor 2) oxidation-related genes in the Nrf2/ARE antioxidant pathway, and Malondialdehyde (MDA), catalase (CAT) activity and glutathione (GSH) content in the hepatopancreas of O. potamophila after quercetin treatment, the mRNA expression of AKT, Nrf2 and CAT activity and GSH content are higher than in the control group. Quercetin enhances antioxidant properties and positively affects muscle growth. The results showed that quercetin has no significant effects on the growth performance of O. potamophila, but is effective in increasing muscle growth rate and lowering muscle fat content.

Pathogenicity of Aeromonas veronii causing mass mortalities of Odontobutis potamophila and its induced host immune response

Aeromonas veronii is a freshwater bacterium associated with many diseases in aquatic animals. However, few cases of A. veronii infection were reported in Odontobutis potamophila, which has been becoming a promising fish species in China in recent years. In this study, the dominant bacteria were isolated from diseased O. potamophila showing signs of hemorrhage on fins, ulceration on the dorsal and abdomen. The representative isolate Stl3-1was identified as A. veronii based on analysis of its morphological, physiological, and biochemical features, as well as 16S rRNA and gyrB gene sequences. The median lethal dosage (LD₅₀) of the isolate Stl3-1 for O. potamophila was determined as 4.5 × 10⁵ CFU/mL. Histopathological analysis revealed that the isolate Stl3-1caused considerable histological lesions in the fish, including tissue cell degeneration, necrosis, and inflammatory cell infiltrating. Detection of virulence-related genes showed that A. veronii Stl3-1 was positive for exu, ompA, lip, flaH, hlyA, aer, flgM, tapA, act, flgA, gcaT and flgN. Additionally, quantitive real-time PCR (qRT-PCR) was also undertaken to analyses the host defensive response in O. potamophila infected by A. veronii. The immune-related gene expressions in O. potamophila during experimental infection were monitored at different point of time, and the results showed that the expression levels of MHC II, Myd88, TLR, and SOD were significantly up-regulated in liver, gill, spleen, and head kidney. The results revealed that A. veronii was a pathogen causing mass mortalities of O. potamophila and will contribute to better understanding the host defensive response against A. veronii infection.

Sexual dimorphism in Odontobutis sinensis brain-pituitary-gonad axis and liver highlighted by histological and transcriptomic approach

In this study, sexual dimorphism in Chinese dark sleeper (Odontobutis sinensis) brain-pituitary-gonad axis and liver was highlighted by histological and transcriptomic approach. The results showed that there were two significant differences between males and females. Firstly, males grew larger and faster than females. Transcriptomic analysis and qPCR validation indicated that two key growth genes, insulin-like growth factor (igf) and 25-hydroxyvitamin D-1 alpha hydroxylase (cyp27b), were more highly detected in male liver than that in female liver. Secondly, histological analysis displayed that the liver in males showed an obvious ivory fatty phenomenon with more fat vacuoles and lipid droplet aggregation compared to that in females. Transcriptomic analysis indicated that the transcript level of vitellogenin (vtg) in male liver were significantly lower than that in female liver. After 17β-estradiol (E2) treatment of primary cultured hepatocytes, the vtg mRNA expression was induced significantly, while dihydrotestosterone (DHT) treatment had little effect on it. Generally, this study will provide some ideas for further exploring the mechanism of sexual dimorphism in Odontobutis sinensis.