Vertebrates have undergone two rounds of whole‐genome duplication (WGD), termed 1R and 2R, with a third, teleost‐specific duplication (TSGD or 3R) occurring in ray‐finned fishes. In the order Cypriniformes, additional lineage‐specific WGDs have further contributed to species diversification. While polyploidy is well characterized in species like common carp and goldfish, other polyploid taxa—particularly loaches—remain understudied. Here, high‐quality, chromosome‐level genome assemblies are presented for two loach species: Sinibotia superciliaris (Golden Chinese Loach) and Parabotia fasciatus (Yichang Sand Loach). By integrating these genomes into a comparative framework with 20 other cypriniform species, key phylogenetic relationships are reconstructed, and introduce a novel subgenome partitioning method (M3). Unlike previous approaches, M3 uses differential sequence divergence to accurately and rapidly assign subgenomes, completing partitioning within minutes and outperforming existing tools. Applying M3, a markedly reduced subgenome is uncovered in the Golden Chinese Loach, with lineage‐specific molecular changes in several candidate genes, suggesting potential adaptive significance. This study offers a comprehensive view of polyploidy and subgenome evolution in loaches, highlighting the genomic complexity shaped by repeated WGDs in Cypriniformes and providing valuable resources for future research on vertebrate genome evolution and adaptation.

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.

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.

Sperm storage within the female reproductive tract is widespread among animal species with internal fertilization, such as the fish family Poeciliidae, wherein the females possess a sperm storage micropocket (SSP) that can store sperm for up to a year. However, the underlying mechanism and morphogenesis of SSP remain unclear. Here, using histological analysis, we found that the SSP of the western mosquitofish (Gambusia affinis) was associated with protrusions arising from the previtellogenic oocyte (PO). Similar protrusions occur in the PO of Poecilia reticulata, P. latipinna, Xiphophorus helleri, and X. maculatus, suggesting that such PO-derived protrusions might be a universal feature in Poeciliidae. These protrusions exhibit significant differences in structural composition compared to the cytoplasm. Furthermore, the area of these protrusions positively correlates with the total area of the oocytes. After maturing, the protrusions split from the oocytes, leaving behind sac-like structures composed of germinal epithelium, which later develop into the SSP for storing sperm. The bottom of the SSP is composed of a single layer of germinal epithelium. We describe and depict the protrusion formation process in the fish family Poeciliidae during the previtellogenic stage, elucidating the SSP morphogenesis.