Jiale Li

Pearl color is the primary determinant of its value, and the mantle donor tissue (saibo) used in pearl culture plays a critical role in color formation. To elucidate the molecular mechanisms underlying nacre color, we performed comparative transcriptomic analyses of saibo tissues from Sinohyriopsis cumingii displaying three representative phenotypes: white (W), purple (P), and golden (G). A total of 364 differentially expressed genes (DEGs) (102 upregulated and 162 downregulated genes) were identified in W vs. P. A total of 770 DEGs (467 upregulated and 303 downregulated genes) were identified in W vs. G. KEGG pathway analysis revealed significant differences in the expression of genes mainly involved in pigment-based and structural coloration, including amino sugar and nucleotide sugar metabolism (ko00520), cell adhesion molecules (ko04514), tyrosine metabolism (ko00350), ECM-receptor interaction (ko04512), and PI3K-Akt signaling pathway (ko04151). Subsequent integrative analyses across W vs. P and W vs. G groups identified 45 key regulatory genes, which were classified into four functional categories: extracellular matrix protein synthesis and biomineralization (e.g., chit, silkmaxin, bmp2/7, profilin, perlucin2), organic pigment metabolism (e.g., tyr, typ, dbh, bco2, gst5, ldlr, cpox, pks-like 1, pks15), metal ion metabolism and accumulation (e.g., hip-like, fcr1, ferritin 2), and epigenetic regulation (e.g., metK, mbd4/6, mettl24/27, alkbh6). Taken together, our findings reaffirm the complex nature of pearl coloration and reveal that structural coloration, pigment biosynthesis, and epigenetic modulation collectively shape nacre color formation, which paves the way for further functional elucidation of color-related genes and facilitates selective breeding practices in S. cumingii.

Sex determination in vertebrates exhibits remarkable evolutionary plasticity, with diverse mechanisms and master sex-determining (MSD) genes arising independently across lineages. Among these, dmrt1, a dosage-sensitive gene, has repeatedly been recruited as an MSD gene through gene duplication or allelic diversification. However, the biochemical basis of such evolutionary transitions, particularly those driven by allelic diversification, remains largely unexplored. Here, we generated haplotype-resolved genome assemblies for both XX and XY black carp (Mylopharyngodon piceus) and identified a ∼40-kb region on chromosome 4, containing only dmrt1, as the candidate sex-determining locus. We discovered two Y-specific insertions in the dmrt1 promoter: a 13.4-kb highly repetitive element and an 11-bp motif. Functional assays revealed that these insertions act as enhancer and a promoter element, respectively, driving early, allele-specific upregulation of dmrt1 prior to gonadal differentiation. Notably, the 13.4-kb insertion contains transposable elements functioning as cis-regulatory modules with transcription factor binding sites that mediate Y-specific activation. Our findings reveal a transposable element–mediated regulatory innovation that promoted dmrt1’s evolution as a male-determining gene via allelic diversification, providing new insights into how mobile genetic elements drive the origin and diversification of sex-determining systems in vertebrates.

To elucidate the molecular mechanisms by which grass carp respond to high-concentration NaHCO₃ stress, this study employed RNA-sequencing technology to perform transcriptome analysis on the gill and liver tissues of the treatment group with 30 mmol/L NaHCO₃ and the control group (0 mmol/L). Through sequencing of 12 libraries constructed from 6 gill samples and 6 liver samples, a total of 41.86 GB of high-quality data from gill tissues and 41.49 GB of high-quality data from liver tissues were obtained. The analysis revealed that there were 1223 and 439 significantly differentially expressed genes (DEGs) in the gill and liver tissues, respectively, under NaHCO₃ stress. Functional enrichment (GO) analysis indicated that grass carp respond to alkaline stress by regulating biological processes such as protein hydrolysis, ATP-binding activity, and lipid metabolism. Pathway (KEGG) analysis further revealed that immune-related signaling pathways were significantly activated to resist external stress, and the elevation of energy metabolism levels may provide necessary support for the stress-resistance process. This study systematically revealed the molecular adaptation strategies of grass carp in a high-alkali environment, providing an important theoretical basis for the molecular breeding of saline-alkali-tolerant grass carp varieties and the research on stress-resistance mechanisms.

Grass carp (Ctenopharyngodon idella), a globally important aquaculture species, exhibits protein-dependent growth plasticity, requiring genetic improvement for sustainable production. This study integrates genome-wide association analysis (GWAS) and genomic selection (GS) to unravel the genetic architecture of four growth traits, body weight, body length, body height, and body depth, in grass carp fed with diets of varying protein levels (20%, 25%, 30%, and 35%). Using a 21K liquid SNP array, we identified 62,736 high-quality SNPs across 24 chromosomes, with 90 SNPs significantly associated with growth traits. Notably, three SNPs (SLG14_24417024, SLG14_24417039, SLG24_30276273) exhibited pleiotropic effects on multiple traits. Functional annotation of 276 candidate genes near significant SNPs revealed enrichment in keratinocyte development, septin cytoskeleton organization, and heat acclimation pathways. Genomic prediction achieved accuracies up to 0.79 for body weight traits using 1533 optimal markers. This study provides the first comprehensive SNP resource for grass carp growth traits with different dietary treatments, bridging GWAS and genomic prediction to accelerate marker-assisted selection. Our findings not only advance genetic breeding strategies but also inform protein diet optimization, minimizing economic and environmental costs in aquaculture.

The grass carp (Ctenopharyngodon idella) is highly susceptible to infections caused by Aeromonas species, particularly A. hydrophila and A. veronii. However, the immunological mechanisms underlying co-infection by these pathogens remain largely uncharted. This study investigated the pathogenesis and host immune response in grass carp following concurrent infection with A. hydrophila and A. veronii. Mortality was observed as early as 24 h post-infection, with cumulative mortality reaching 68%. Quantitative analysis demonstrated significantly elevated bacterial loads in hepatic tissue at 3 days post-infection (dpi). Histopathological evaluation revealed severe hepatic lesions characterized by cellular necrosis, cytoplasmic vacuolization, and hemorrhagic manifestations. Comparative transcriptomic analysis of hepatic tissues between co-infected and control specimens identified 868 and 411 differentially expressed genes (DEGs) at 1 and 5 dpi, respectively. Gene ontology and KEGG pathway analyses revealed significant enrichment of immune-related genes primarily associated with Toll-like receptor signaling and TNF signaling cascades. Notably, metabolic pathways showed substantial suppression while immune responses were significantly activated after infected. These findings provide novel insights into the host–pathogen interactions during Aeromonas co-infection in grass carp, which may facilitate the development of effective prevention and control strategies.

Allometric growth is a typical characteristic of crustaceans, which mainly occurs among individuals, life stages, tissues, and between sexes. The red swamp crayfish Procambarus clarkii is an economically important crustacean species in the world. To date, the molecular regulatory mechanisms of neuroendocrine system in the allometric growth of P. clarkii remain unclear. In this study, P. clarkii exhibiting significant allometric growth among individuals were sampled from three full-sibling families. The brain, eyestalk, nerve cord, and Y-organ were dissected for transcriptome analysis. Key functional genes were identified by random forest and DESeq2 methods. The gene pathways were enriched utilizing Kyoto Encyclopedia Genes and Genomes (KEGG) analysis. Gene topological analysis was established through weighted gene co-expression network analysis (WGCNA), and hub genes were screened by protein–protein interaction (PPI) networks. Transcriptomic analysis results were validated via qRT-PCR. RNA-Seq identified 31 differentially expressed genes (DEGs) (7 up- and 24 downregulated); 301 DEGs (23 up- and 278 downregulated); 1308 DEGs (474 up- and 834 downregulated); and 64 DEGs (52 up- and 12 downregulated) in the brain, eyestalk, Y-organ, and nerve cord, respectively. Crucial functional genes such as CHIA in the brain and perlucin-like in the eyestalk were notably identified. WGCNA revealed two hub modules, while PPI networks identified neuroendocrine regulators module which hub genes mainly including CP1876-like and cuticle protein AM1199-like, and structural components module which hub genes mainly including CUB& CCP Domain-Containing Protein, ARRDC, and E3 Ubiquitin protein ligase MCYCBP2-like. Correspondingly, the significant gene pathways such as amino sugar and nucleotide sugar metabolism (pcla00520) and insect hormone biosynthesis (pcla00981) were enriched. The results revealed the complex interactions and regulatory relationships of hub genes within hub modules to coordinate molting and growth. The results of RNA-Seq analysis were validated by the consistency of gene expression in qRT-PCR. In present study, key functional genes in the neuroendocrine system regulating allometric growth among individuals were identified, and significant pathways mainly include hormone synthesis were screened, thus constructing a neuroendocrine molecular regulatory network for the allometric growth of P. clarkii. Building on these investigations, a comprehensive mechanism whereby neuroendocrine regulators interact with structural components to coordinate molting and growth was proposed. The result would provide valuable insights into the molecular regulatory mechanisms of allometric growth, highlighting the interplay between the neuroendocrine system and relevant tissues.