Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes.

Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.

HSP90 and HSP70 Families in Lateolabrax maculatus: Genome-Wide Identification, Molecular Characterization, and Expression Profiles in Response to Various Environmental Stressors.

Heat shock proteins (HSPs) are a large class of highly conserved chaperons, which play important roles in response to elevated temperature and other environmental stressors. In the present study, 5 HSP90 genes and 17 HSP70 genes were systematically characterized in spotted seabass (Lateolabrax maculatus). The evolutionary footprint of HSP genes was revealed via the analysis of phylogeny, chromosome location, and gene copy numbers. In addition, the gene structure features and the putative distribution of heat shock elements (HSEs) and hypoxia response elements (HREs) in the promoter regions were analyzed. The protein-protein interaction (PPI) network analyses results indicated the potential transcriptional regulation between the heat shock factor 1 (HSF1) and HSPs and a wide range of interactions among HSPs. Furthermore, quantitative (q)PCR was performed to detect the expression profiles of HSP90 and HSP70 genes in gill, liver, and muscle tissues after heat stress, meanwhile, the expression patterns in gills under alkalinity and hypoxia stresses were determined by analyzing RNA-Seq datasets. Results showed that after heat stress, most of the examined HSP genes were significantly upregulated in a tissue-specific and time-dependent manners, and hsp90aa1.1, hsp90aa1.2, hsp70.1, and hsp70.2 were the most intense responsive genes in all three tissues. In response to alkalinity stress, 11 out of 13 significantly regulated HSP genes exhibited suppressed expression patterns. Alternatively, among the 12 hypoxia-responsive-expressed HSP genes, 7 genes showed induced expressions, while hsp90aa1.2, hsp70.1, and hsp70.2 had more significant upregulated changes after hypoxic challenge. Our findings provide the essential basis for further functional studies of HSP genes in response to abiotic stresses in spotted seabass.

Effects of Vibrio harveyi infection on serum biochemical parameters and expression profiles of interleukin-17 (IL-17) / interleukin-17 receptor (IL-17R) genes in spotted sea bass.

Vibrio harveyi is regarded as serious pathogen for marine fishes. To evaluate the physiological responses of spotted sea bass (Lateolabrax maculatus) after V. harveyi infection, four biochemical biomarkers including alanine amino transferase (ALT), albumin (ALB), total protein (TP) and glucose (GLU) were measured in serum. Our results showed that V. harveyi infection significantly influenced the concentration of ALT, ALB and GLU. Additionally, five interleukin-17 (IL-17) and five IL-17 receptors (IL-17R) genes were identified in spotted sea bass and their gene structures were characterized. Furthermore, the expression patterns of IL-17 and IL-17R genes were determined by qPCR in liver, intestine, spleen and head kidney after V. harveyi infection. All IL-17 and IL-17R genes exhibited time- and tissue-dependent expressions. Several tested genes were dramatically induced by V. harveyi treatment, particularly IL-17A/F1 in liver and head kidney, IL-17A/F2 in head kidney, IL-17RC in spleen with more than 10-fold increases, which suggested their potential essential roles against bacterial infection.

FOXO1A promotes neuropeptide FF transcription subsequently regulating the expression of feeding-related genes in spotted sea bass (Lateolabrax maculatus).

FOXOs belong to the forkhead transcription factor superfamily, several of which are suggested to be involved in the control of food intake. Previously, we proved that the neuropeptide FF (NPFF) peptide was involved in feeding regulation in spotted sea bass. In the present study, seven members of the foxo family were identified in the whole genome of spotted sea bass. The distributions of these genes in different tissues were analyzed by qRT-PCR. Variations in the foxo1a and npff expression profiles during short-term starvation showed similar expression patterns. The colocalization of foxo1a and npff in the telencephalon, hypothalamus, stomach and intestine further provided evidence that foxo1a may act directly to promote the transcription of npff. Thirteen predicted FOXO1 binding sites were found in the 5' upstream region of npff. Luciferase assay results showed that FOXO1A was able to activate npff transcriptional responses by directly binding DNA response elements, and the key regulatory areas and sites of FOXO1A on the npff promoter were confirmed by deletion and site-directed mutagenesis analyses. These findings may help to elucidate the role of FOXO1 in the regulation of feeding processes in teleosts.

Analysis of apolipoprotein multigene family in spotted sea bass (Lateolabrax maculatus) and their expression profiles in response to Vibrio harveyi infection.

Apolipoproteins (Apos), which are the protein components of plasma lipoproteins, play important roles in lipid transport in vertebrates. It has been demonstrated that in teleosts, several Apos display antimicrobial activity and play crucial roles in innate immunity. Despite their importance, apo genes have not been systematically characterized in many aquaculture fish species. In our study, a complete set of 23 apo genes was identified and annotated from spotted sea bass (Lateolabrax maculatus). Phylogenetic and homology analyses provided evidence for their annotation and evolutionary relationships. To investigate their potential roles in the immune response, the expression patterns of 23 apo genes were determined in the liver and intestine by qRT-PCR after Vibrio harveyi infection. After infection, a total of 20 differentially expressed apo genes were observed, and their expression profiles varied among the genes and tissues. 5 apo genes (apoA1, apoA4a.1, apoC2, apoF and apoO) were dramatically induced or suppressed (log2 fold change >4, P < 0.05), suggesting their involvement in the immune response of spotted sea bass. Our study provides a valuable foundation for future studies aimed at uncovering the specific roles of each apo gene during bacterial infection in spotted sea bass and other teleost species.