Shufang Liu

The commercial designation “cod” (鳕) is applied to multiple fish species, raising concerns regarding seafood authenticity and nutritional consistency. This study combined DNA barcoding with comparative nutritional profiling to authenticate frozen products marketed as “cod” (鳕) from major Chinese e-commerce platforms and to evaluate nutritional differences among the identified species. Among the 36 products analyzed, eight fish species were identified: three Gadiformes species (55.6%) and five non-Gadiformes species (44.4%). Interspecific differences were observed in proximate composition, amino acid composition, free amino acid profiles, and fatty acid composition. True cod species exhibited higher protein contents (>19.0%), lower lipid contents (0.51–1.02%), and higher proportions of EPA + DHA (35.61–37.10% of total fatty acids) than non-Gadiformes species. In contrast, non-Gadiformes species generally contained higher lipid levels (15.02–23.09%), lower proportions of long-chain ω-3 PUFA, and distinct flavor-related amino acid profiles. Lepidocybium flavobrunneum showed the lowest EPA + DHA proportion (5.81%) and the highest concentration of bitter-tasting free amino acids (0.661 g/100 g). These findings reveal substantial nutritional heterogeneity among the authenticated species marketed as “cod” (鳕), demonstrating that DNA barcoding provides an essential foundation for linking species identity to nutritional quality assessment.

Otolith morphology has long been recognized as an effective tool for fish species discrimination; however, the extent to which it reflects phylogenetic relationships remains debated, particularly among closely related taxa. In this study, we investigated otolith and sulcus morphology in the critically endangered Chinese bahaba (Bahaba taipingensis) and four closely related sciaenid species to evaluate their taxonomic utility as well as phylogenetic and evolutionary significance. Otolith and sulcus outlines were quantified using wavelet coefficients, species discrimination was performed with a random forest classifier, and associations between morphological variation and genetic divergence were assessed through phylogenetic reconstruction based on the 13 mitochondrial protein-coding genes and Mantel tests. Otolith outlines exhibited significant interspecific variation and achieved a high classification accuracy of 90.32%, whereas sulcus morphology achieved 78.06%, demonstrating that both morphological traits are effective for species identification, with otolith outlines providing greater discriminatory power. Wavelet coefficient analyses further revealed that low-level coefficients, representing overall outline features, contributed most to species discrimination, whereas high-level coefficients, representing fine-scale marginal features, were more closely associated with genetic divergence. A significant correlation was detected between fine-scale otolith shape variation and mitochondrial genetic distance, indicating that otolith morphology retains a detectable phylogenetic signal among closely related sciaenid species. In contrast, sulcus morphology showed only a comparatively weak association with phylogeny, suggesting that otolith and sulcus morphology have followed partially independent evolutionary trajectories. Overall, our findings demonstrate that otolith outline and sulcus morphology provide complementary characters for species identification, and that detailed otolith morphology better reflects evolutionary history than sulcus morphology. This study establishes a practical identification framework for B. taipingensis and its closely related species and provides a morphological foundation for future investigations of archeological otoliths, historical population dynamics, and evolutionary diversification within Sciaenidae.

N. chui is an economically important marine fish species distributed along the coastal waters of China, renowned for its delicate flesh texture and high-quality dried swim bladder. However, its scientific name and taxonomic relationship with N. coibor have long remained controversial, hindering accurate resource assessment and germplasm management. To address this issue, we sequenced and annotated the first complete mitochondrial genome of N. chui (GenBank accession: PZ024444). The circular mitogenome is 16,504 bp in length and contains 37 typical genes, with gene arrangement, nucleotide composition (A + T content: 52.07%), and codon usage patterns consistent with general teleost characteristics. Phylogenetic analyses based on 13 concatenated protein-coding genes revealed that N. chui and N. coibor form a maximally supported monophyletic clade (bootstrap support = 100%), with a pairwise genetic distance of 0. These mitochondrial results strongly suggest that the two nominal taxa are very closely related and may represent the same species. However, formal taxonomic synonymy cannot be established on mitochondrial evidence alone and requires further evaluation through examination of type material and comparative morphological study. Gene-specific selection pressure analyses showed that most mitochondrial protein-coding genes were subject to purifying selection, with ATP8 exhibiting the highest mean ω among genes with ω < 1, whereas ND5 and ND6 showed elevated ω values that warrant cautious interpretation. This study provides essential mitochondrial genomic resources for future research on species delimitation, phylogeny, and conservation of this important sciaenid fish.

The snailfish family (Liparidae) represents one of the most rapidly speciating and ecologically diverse lineages of marine fishes, with species distributed across a broad bathymetric range from intertidal zones to the hadal depths. Despite their ecological and evolutionary significance, phylogenetic relationships and adaptive mechanisms within Liparidae remain poorly resolved due to morphological conservatism, phenotypic plasticity, and limited genomic resources due to challenges such as sampling difficulties and a reliance on partial mtDNA markers. In this study, we sequenced, assembled, and annotated the complete mitochondrial genomes of two snailfish species, Liparis chefuensis and Liparis tanakae, collected from the Yellow Sea. The mitogenome of L. chefuensis is 18,870 bp in length, encoding 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, while that of L. tanakae spans 17,485 bp and contains 13 PCGs, 2 rRNAs, and 23 tRNAs. Phylogenetic reconstruction based on the concatenated sequences of 13 mitochondrial PCGs from 15 liparid species revealed that L. chefuensis clusters within the subgenus Lyoliparis, contradicting its previous classification under Careliparis and suggesting a need for taxonomic reassessment. Notably, we identified distinct patterns of tRNA gene rearrangement in the cluster between ND2 and COI, which suggest a link to both phylogeny and habitat depth. Shallow-water species (100 m) display the derived tRNA^Trp-tRNA^Asn-tRNA^Cys-tRNA^Tyr-tRNA^Ala-tRNA^Cys/tRNA^Ala (WNCYAC/A) configurations. These rearrangements are hypothesized to originate from tandem duplication events followed by random gene loss, potentially reflecting adaptive evolution to deep-sea environments. Additionally, L. tanakae exhibits a markedly higher number of non-canonical G–U and A–C base pairs in its tRNA secondary structures, indicating substantial structural divergence. Our findings not only provide essential mitogenomic resources for snailfish systematics and species identification but also propose that tRNA rearrangements in mitochondrial genomes may serve as genomic innovations facilitating deep-sea colonization. This study enhances our understanding of mitochondrial genome evolution and environmental adaptation in marine fishes.

Suruga fundicola, one of the few known deep-dwelling gobies, is found in Japan, South Korea, and China. Owing to the limited availability of specimens, little is known about its mitogenome characterization, phylogenetic relationship, and adaptive evolution. In this study, we sequenced four complete mitogenomes using the DNBSEQ platform and Sanger sequencing. The mitogenomes in length ranged from 17,138 to 17,352 bp, primarily due to the variation in the number of long tandem repeat (LTR) sequences within variable region 3 (VR3). Although the gene composition and arrangement of the S. fundicola mitogenome are largely consistent with those of other gobies, we identified an expansion of the ND2 gene (78 bp), and an unexpected noncoding region (NC, 35 bp) located between the ND2 and tRNA^trp genes. To further investigate the variation in VR3, we sequenced this region in all nineteen individuals with the Sanger sequencing method. We detected eight distinct LTR types, containing one–three mutation sites, which formed ten different VR3 patterns. Most VR3 patterns (14/19) consisted of a single type of pure LTR, while the remaining five exhibited heterogeneous patterns composed of two different LTRs. Notably, in LTR types T1 and T3, which co-occur in heterogeneous patterns P1 and P9, we found their respective pure patterns (P2–3 and P7). Recombination provides a better, more plausible mechanism for generating the heterogeneity patterns than slipped-strand mispairing, which better explains the homogeneous LTR expansions. These findings provide evidence of recombination in the control region of a vertebrate mitogenome. A phylogenetic analysis confirmed that S. fundicola has a close relationship with Am. hexanema and C. stigmatias. Compared to five shallow-water species of the AcanthogobiusGroup, the deep-dwelling goby S. fundicola was found to be under stronger purifying selection. Within its mitochondrial protein-coding genes (PCGs), ND2 and ND6 genes were subject to stronger purifying selection than the others. Additionally, four genes showed signs of selection sites with high credibility (one in ATP6, ND3, and ND4; eight in ND2). This study provides valuable genomic resources for S. fundicola and enhances our understanding of the phylogenetic relationship, mitogenome recombination, and adaptive evolution of the goby.