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

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.