Toll-like receptors (TLRs) are central to pathogen recognition in teleost innate immunity. In this study, we surveyed 41 genomes from four representative teleost orders (i.e., Cypriniformes, Siluriformes, Perciformes, and Pleuronectiformes) for 15 TLR genes (TLR1–9, 12, 13, 18, 20–22) revealed a conserved core (TLR2/3/7 in nearly all examined species) alongside lineage-specific losses (TLR4/9/18/20/21/22), indicating both strong conservation and dynamic diversification of the TLR repertoire. We further identified and characterized 12 TLR genes in economically important darkbarbel catfish (Pelteobagrus vachellii). Corresponding cDNAs span 2089–4456 bp and encode proteins of 789–1,087 aa, with canonical extracellular LRR arrays and C-terminal TIR domains but notable “non-classical” features (such as absence of signal peptides in TLR1/13; no transmembrane segment in TLR7; multiple transmembranes in TLR3/8/13/18/22), suggesting subcellular and functional heterogeneity of various TLR genes. Subsequent gene-structure comparisons uncovered gene-specific exon–intron organizations and variable UTR lengths, implicating differential post-transcriptional regulation. Predicted 3D structures retain the traditional hallmark LRR horseshoe fold with subtle variations potentially tuning ligand specificity. Genomic synteny with Pseudobagrus ussuriensi and Pangasianodon hypophthalmus reveals conserved chromosomal organization, and phylogeny construction resolves each TLR subtype into well-supported monophyletic clades, which underscore evolutionary stability. Functionally, exogenous Aeromonas hydrophila challenge triggered rapid, tissue-dependent TLR up-regulation in the kidney, liver, and especially gill (with some transcripts > 1000-fold), highlighting coordinated mucosal and systemic surveillance in darkbarbel catfish. Taken together, these valuable data provide a comprehensive framework for the structural, evolutionary, and inducible expression landscape of catfish TLRs and establish a foundation for in-depth studies on antibacterial immunity in diverse teleost species.

Sinibotia species, investigated for morphology and species divergence owing to comparable body patterns and frequent sympatric occurrences, show high morphological similarity and close phylogenetic relationships, which challenge their accurate distinguishing via conventional morphological methods. Hence, multivariate morphometric (MM) and geometric morphometric (GM) analyses were used to assess the morphological differences between Sinibotia species (S. superciliaris, S. reevesae, S. robusta, S. pulchra, and S. zebra) habiting the Tuo River (Zizhong County) and Li and Lipu Rivers (Pingle County) based on 40 morphological traits and 34 landmarks. The morphological traits of S. robusta contrasted with those of S. pulchra and S. zebra, whereas S. superciliaris and S. reevesae showed similar morphologies, consistent with the cluster results. MM analysis using discriminant function analysis along with GM methods such as canonical variate analysis and relative distortion analysis enabled the differentiation between the Sinibotia species. Morphological variations were primarily reflected in snout length, nasal snout distance, head depth, body depth, caudal fin length, and dorsal fin length. MM effectively quantified linear size differences, whereas GM better captured and visualized complex variations in overall shape. The combined morphological evidence presented in this study contributes significantly to the identification of species, phylogenetic relationships, and ecological adaptations of Sinibotia species, thereby strengthening the theoretical rationale for the conservation and sustainable utilization of this genus.

Gymnodiptychus integrigymnatus is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of G. integrigymnatus. The complete mitochondrial genome of one individual of G. integrigymnatus was sequenced using the Illumina HiSeq X Ten sequencing platform and comprehensively characterized. The mitochondrial genome was 16,714 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a typical control region. The genome composition showed a positive A + T skew (0.029) and a negative G + C skew (−0.198). All tRNAs were predicted to form typical cloverleaf secondary structures, except for tRNA-Ser (GCT), which lacked the DHU stem. Phylogenetic reconstruction based on 13 PCGs revealed that the subfamily Schizothoracinae was not a monophyletic group. Two major clades were identified within this subfamily: one comprising primitive taxa (Percocypris, Aspiorhynchus, and Schizothorax) and the other consisting of specialized and highly specialized groups. Gymnodiptychus integrigymnatus was distinct from both its congeners and the specialized clade and was instead recovered within a highly specialized group of the Schizothoracinae subfamily. This study offers novel perspectives on the taxonomy and phylogenetic relationships within the Schizothoracinae subfamily, with a specific focus on G. integrigymnatus, thereby enhancing the understanding of the systematics and phylogeny of the Schizothoracinae subfamily.

The Chinese sturgeon (Acipenser sinensis) is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp. Additionally, 20,887 transcripts were effectively identified and classified as known homologous genes. We also identified 787 HKGs, and the number of TSGs varied from 25 in the liver to 2073 in the brain. TSG functions were mainly enriched in certain signaling pathways involved in specific physiological processes, such as voltage-gated potassium channel activity, nervous system development, glial cell differentiation in the brain, and leukocyte transendothelial migration in the spleen and pronephros. Meanwhile, HKGs were highly enriched in some pathways involved in ribosome biogenesis, proteasome core complex, spliceosome activation, elongation factor activity, and translation initiation factor activity, which have been strongly implicated in fundamental biological tissue functions. We also predicted five modules, with eight hub genes in the brown module, most of which (such as rps3a, rps7, rps23, rpl11, rpl17, rpl27, and rpl28) were linked to ribosome biogenesis. Our results offer insights into ribosomal proteins that are indispensable in ribosome biogenesis and protein synthesis, which are crucial in various cell developmental processes and neural development of Chinese sturgeon. Overall, these findings will not only advance the understanding of fundamental biological functions in Chinese sturgeon but also supply a valuable genetic resource for characterizing this extremely important species.