Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

Comprehensive genome-wide identification and functional characterization of mapk gene family in northern snakeheads (Channa argus)

The mitogen-activated protein kinase (MAPK) signaling cascade, integral to cellular regulation, orchestrates cell growth, differentiation, stress response, and inflammatory reactions to adapt to challenging environments. The northern snakeheads (Channa argus), a valuable freshwater species known for its hypoxia tolerance, rapid growth, and high nutritional value, lacks comprehensive research on its mapk gene family. In this study, we identified 16 mapk genes in northern snakeheads, among which mapk8, mapk12 and mapk14 have duplicate copies. Phylogenetic analysis confirmed the evolutionary conservation of this gene family. Structural and motif analyses further underscored the conserved nature of these genes. Expression pattern analysis under abiotic and biotic stress conditions showed significant differences expression of mapks in the gills and suprabranchial organ (SBO) after air exposure, as well as in the brain following cold stress, highlighting the extensive role of mapks in stress regulation. It was worth noting that the significant expression differences of mapks were also observed in the spleen after N. seriolae infection, implicating that these genes may be involved in the regulation of innate immune responses. Additionally, analysis of protein-protein interaction (PPI) networks suggested that the co-activation of multiple MAPK signaling pathways may play a key role in regulating an organism's response to biotic and abiotic stresses. This study provides a detailed description of the mapk gene family in the northern snakeheads and elucidates its biological functions under various stress conditions, offering valuable insights into the regulatory mechanisms of the mapk gene family.

Chromosome-level genome assembly of the northern snakehead (Channa argus) using PacBio and Hi-C technologies

The evolutionary origins of specialized organs pose significant challenges for empirical studies, as most such organs evolved millions of years ago. The Northern snakehead (Channa argus), an air-breathing fish, possesses a suprabranchial organ, a common feature of the Anabantoidei, offering a unique opportunity to investigate the function and evolutionary origins of specialized organs. In this study, a high-quality chromosome-level reference genome of C. argus was constructed using PacBio HiFi sequencing and Hi-C technology. The final genome assembly size is 712.14 Mb, with a scaffold N50 of 28.08 Mb. The assembled sequences were anchored to 24 pseudo-chromosomes and predicted 21,643 protein-coding genes. The genome comprises 27.70% repetitive elements and includes 3,588 (98.6%) complete BUSCOs, demonstrating superior contiguity and functional completeness compared to other published C. argus assemblies. This genome provides valuable genetic resources for exploring the evolution of the aquatic-aerial bimodal breathing system, including clarifying the evolutionary histories and adaptive strategies.

Genome sequencing and transcriptome analysis provide an insight into the hypoxia resistance of Channa asiatica

Channa asiatica is an economically valuable fish species and excellent model for studying hypoxic tolerance. However, the underlying genetic and molecular mechanisms are poorly understood. In this study, we assembled a high-quality C. asiatica genome (23 chromosomes, totaling 722 Mb) using a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing. Repetitive elements accounted for 28.39%of the C. asiatica genome, and 23,949 protein-coding genes were predicted, with 96.63 % of these functionally annotated. Moreover, a comparative genomic analysis of 12 fish genomes showed that gene families associated with oxygen binding and transport were expanded in C. asiatica. In addition, transcriptome analysis revealed that multiple oxidative stress pathways were activated when C. asiatica was exposed to air. In conclusion, this study provided high-quality genome assembly and transcriptome data, both serving as critical resources for researching the genetic basis of hypoxic tolerance in C. asiatica.

Effects of cold stress on the blood-brain barrier in Plectropomus leopardus

BACKGROUND

The leopard coral grouper (Plectropomus leopardus) is a commercially valuable tropical marine fish species known to be sensitive to low temperatures. A comprehensive understanding of the molecular mechanisms governing its response to acute cold stress is of great importance. However, there is a relative scarcity of fundamental research on low-temperature tolerance in the leopard coral grouper.

METHODS

In this study, a cooling and rewarming experiment was conducted on 6-month-old leopard coral groupers. Within 24 h, we decreased the ambient temperature from 25 °C to 13 °C and subsequently allowed it to naturally return to 25 °C. During this process, a comprehensive investigation of serum hormone levels, enzyme activity, and brain transcriptome analysis was performed.

RESULTS

P. leopardus displayed a noticeable adaptive response to the initial temperature decrease by temporarily reducing its life activities. Our transcriptome analysis revealed that the differentially expressed genes (DEGs) were primarily concentrated in crucial pathways including the blood-brain barrier (BBB), inflammatory response, and coagulation cascade. In situ hybridization of claudin 15a (cldn15a), a key gene for BBB maintaining, further confirmed that exposure to low temperatures led to the disruption of the blood-brain barrier and stimulated a pronounced inflammatory reaction within the brain. Upon rewarming, there was a recovery of BBB integrity accompanied by the persistence of inflammation within the brain tissue.

CONCLUSIONS

Our study reveals the complex interactions between blood-brain barrier function, inflammation, and recovery in P. leopardus during short-term temperature drops and rewarming. These findings provide valuable insights into the physiological responses of this species under cold stress conditions.

Genome-Wide Association Studies (GWAS) and Transcriptome Analysis Reveal Male Heterogametic Sex-Determining Regions and Candidate Genes in Northern Snakeheads (Channa argus)

The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to identify sex determination genomic regions and develop sex-specific markers. A total of 270 single-nucleotide polymorphisms (SNPs) and 31 insertion-deletions (InDels) were identified as being sexually dimorphic through GWAS and fixation index (Fst) scanning. Based on GWAS results, two sex-specific InDel markers were developed, effectively distinguishing genetic sex for XX females, XY males, and YY super-males via (polymerase chain reaction) PCR amplification. A major genomic segment of approximately 115 kb on chromosome 3 (Chr 03) was identified as the sex-determination region. A comparative transcriptome analysis of gonads for three sexes identified 158 overlapping differentially expressed genes (DEGs). Additionally, three sex-related candidate genes were identified near the sex determination region, including id2, sox11, and rnf144a. Further studies are required to elucidate the functions of these genes. Overall, two sex-specific InDel markers support a male heterogametic XX/XY sex-determination system in Northern snakeheads and three candidate genes offer new insights into sex determination and the evolution of sex chromosomes in teleost fish.

Histological observations and transcriptome analyses reveal the dynamic changes in the gonads of the blotched snakehead (Channa maculata) during sex differentiation and gametogenesis

BACKGROUND

Blotched snakehead (Channa maculata) displays significant sexual dimorphism, with males exhibiting faster growth rates and larger body sizes compared to females. The cultivation of the all-male population of snakeheads holds substantial economic and ecological value. Nonetheless, the intricate processes governing the development of bipotential gonads into either testis or ovary in C. maculata remain inadequately elucidated. Therefore, it is necessary to determine the critical time window of sex differentiation in C. maculata, providing a theoretical basis for sex control in production practices.

METHODS

The body length and weight of male and female C. maculata were measured at different developmental stages to reveal when sexual dimorphism in growth initially appears. Histological observations and spatiotemporal comparative transcriptome analyses were performed on ovaries and testes across various developmental stages to determine the crucial time windows for sex differentiation in each sex and the sex-related genes. Additionally, qPCR and MG2C were utilized to validate and locate sex-related genes, and levels of E2 and T were quantified to understand sex steroid synthesis.

RESULTS

Sexual dimorphism in growth became evident starting from 90 dpf. Histological observations revealed that morphological sex differentiation in females and males occurred between 20 and 25 dpf or earlier and 30-35 dpf or earlier, respectively, corresponding to the appearance of the ovarian cavity or efferent duct anlage. Transcriptome analyses revealed divergent gene expression patterns in testes and ovaries after 30 dpf. The periods of 40-60 dpf and 60-90 dpf marked the initiation of molecular sex differentiation in females and males, respectively. Male-biased genes (Sox11a, Dmrt1, Amh, Amhr2, Gsdf, Ar, Cyp17a2) likely play crucial roles in male sex differentiation and spermatogenesis, while female-biased genes (Foxl2, Cyp19a1a, Bmp15, Figla, Er) could be pivotal in ovarian differentiation and development. Numerous biological pathways linked to sex differentiation and gametogenesis were also identified. Additionally, E2 and T exhibited sexual dimorphism during sex differentiation and gonadal development. Based on these results, it is hypothesized that in C. maculata, the potential male sex differentiation pathway, Sox11a-Dmrt1-Sox9b, activates downstream sex-related genes (Amh, Amhr2, Gsdf, Ar, Cyp17a2) for testicular development, while the antagonistic pathway, Foxl2/Cyp19a1a, activates downstream sex-related genes (Bmp15, Figla, Er) for ovarian development.

CONCLUSIONS

This study provides a comprehensive overview of gonadal dynamic changes during sex differentiation and gametogenesis in C. maculata, establishing a scientific foundation for sex control in this species.

Chromosome level genome assembly and transcriptome analysis of E11 cells infected by tilapia lake virus

The E11 cell line, derived from striped snakehead fish (Channa striata), possesses a distinctive feature: it is persistently infected with a C-type retrovirus. Notably, it exhibits high permissiveness to piscine nodavirus and the emerging tilapia lake virus (TiLV). Despite its popularity in TiLV research, the absence of genome assembly for the E11 cell line and Channa striata has constrained research on host-virus interactions. This study aimed to fill this gap by sequencing, assembling, and annotating the E11 cell line genome. Our efforts yielded a 600.5 Mb genome including 24 chromosomes with a BUSCO score of 98.8%. In addition, the complete proviral DNA sequence of snakehead retrovirus (SnRV) was identified in the E11 cell genome. Comparative genomic analysis between the E11 cell line and another snakehead species Channa argus revealed the loss of many immune-related gene families in the E11 cell genome, indicating a compromised immune response. We also conducted transcriptome analysis of mock- and TiLV-infected E11 cells, unveiling new perspectives on virus-virus and host-virus interactions. The TiLV infection suppressed the high expression of SnRV in E11 cells, and activated some other endogenous retroviruses. The protein-coding gene comparison revealed a pronounced up-regulation of genes involved in immune response, alongside a down-regulation of genes associated with specific metabolic processes. In summary, the genome assembly and annotation of the E11 cell line provide valuable resources to understand the SnRV and facilitate further studies on nodavirus and TiLV. The RNA-seq profiles shed light on the cellular mechanisms employed by fish cells in response to viral challenges, potentially guiding the development of therapeutic strategies against TiLV in aquaculture. This study also provides the first insights into the viral transcriptome profiles of endogenous SnRV and evading TiLV, enhancing our understanding of host-virus interactions in fish.

Targeting autophagy with natural products as a potential therapeutic approach for diabetic microangiopathy

As the quality of life improves, the incidence of diabetes mellitus and its microvascular complications (DMC) continues to increase, posing a threat to people's health and wellbeing. Given the limitations of existing treatment, there is an urgent need for novel approaches to prevent and treat DMC. Autophagy, a pivotal mechanism governing metabolic regulation in organisms, facilitates the removal of dysfunctional proteins and organelles, thereby sustaining cellular homeostasis and energy generation. Anomalous states in pancreatic β-cells, podocytes, Müller cells, cardiomyocytes, and Schwann cells in DMC are closely linked to autophagic dysregulation. Natural products have the property of being multi-targeted and can affect autophagy and hence DMC progression in terms of nutrient perception, oxidative stress, endoplasmic reticulum stress, inflammation, and apoptosis. This review consolidates recent advancements in understanding DMC pathogenesis via autophagy and proposes novel perspectives on treating DMC by either stimulating or inhibiting autophagy using natural products.

Effects of leucism on organ development and molecular mechanisms in Northern snakehead (Channa argus) beyond pigmentation alterations

Leucism, a widespread occurrence observed in Northern snakehead (Channa argus), bestows a striking white jade-like body coloration upon affected individuals and has gained substantial popularity in commercial breeding. While the visible manifestation of leucism in snakeheads is primarily limited to body coloration, it is crucial to explore the potential influence of leucism on organ development and elucidate the underlying molecular mechanisms. Through a comparative analysis of growth differences, our study revealed that at 150 days post-fertilization, the white variety exhibited an 8.5% higher liver index and intestinal index, but experienced a 20% and 38% decreased in spleen index and renal interstitial index, respectively, suggesting an enlarged digestive area but relatively smaller immune tissues. Nonetheless, no significant differences were observed in the intestinal flora between the two varieties, suggesting the exclusion of any exogenous impacts from symbiotic flora on the growth and development of the white variety. Importantly, transcriptome analysis demonstrated that the white variety exhibited higher expression levels of innate immune genes. Furthermore, annotation of the gene sets expressed in the liver and spleen revealed 76 and 35 genes respectively, with the white variety displaying lower expression in genes associated with "Viral protein interaction with cytokine and cytokine receptor", "Protein processing in endoplasmic reticulum", and "TNF signaling pathway", while exhibiting higher expression in "Estrogen signaling pathway". Notably, three genes, namely pcdhf 4, nlrc3 card 15-like, and a pol-like were identified in both the liver and spleen, indicating their potential involvement in altering the development and innate immunity of the white variety. This study reveals the systemic impact of leucism that extends beyond mere pigmentation alterations, highlighting the prominent characteristics of this phenotype and providing a foundation for future molecular breeding programs aimed at enhancing this variety.

Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

BACKGROUND

Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different.

RESULTS

In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P < 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P < 0.01).

CONCLUSIONS

C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.