The Wuzhishan miniature pig is regarded as a highly promising translational model for cardiac xenotransplantation due to its close physiological resemblance to humans. However, a comprehensive single-cell atlas systematically delineating the postnatal developmental dynamics of its heart has been lacking. In this study, we constructed the first high-resolution integrated single-cell and single-nucleus transcriptomic atlas of the Wuzhishan miniature pig heart, spanning five critical developmental stages from neonatal to adult. We systematically characterized the cellular panorama and dynamic landscape of postnatal cardiac maturation, and uncovered the remodeling of intercellular communication networks during heart development. Through cross-species comparative analysis, we identified a unique ventricular cardiomyocyte subpopulation with highly active lipid metabolism (VCM-LM-SR) specific to the Wuzhishan miniature pig. This subpopulation not only exhibits highly active lipid metabolism but also occupies a hub position in the adult cardiac cellular interactome. Further analysis revealed that the activity of multiple human cardiac disease-related pathways is significantly lower in cardiomyocytes of the Wuzhishan miniature pig compared to other species examined, indicating a distinct transcriptional baseline in this donor animal. In summary, this atlas not only elucidates the cellular and molecular dynamics of cardiac development in the Wuzhishan miniature pig but also, through cross-species analysis, reveals a species-specific metabolic adaptation phenotype in this breed. These findings provide a novel perspective and a foundational resource for studying human cardiac metabolism using large animal models.
The Cryptotympana genus represents a significant biological resource in health products and traditional medicine. C. mandarina and C. recta are commonly used as regional substitutes for the legal species of medicinal Cicadae Periostracum. To address the demand for supplementary molecular tools in resource identification and diversification, this study presents the first comparative analysis of mitochondrial genome architecture between C. mandarina and C. recta. Employing high-throughput sequencing technologies, we assembled complete circular mitogenomes of 15,574 bp (C. mandarina) and 15,802 bp (C. recta), each containing 37 canonical genes (13 protein-coding genes [PCGs], 22 tRNAs, 2 rRNAs). The two mitogenomes were highly similar in A + T bias, AT-skew, and GC-skew. Most PCGs exhibited ATN initiation codons, while all tRNAs demonstrated typical cloverleaf structures except for trnS1, which lacked the dihydrouridine arm. Notably, the sliding window, genetic distance, and Ka/Ks ratio analyses indicated that the ATP8 and ND2 genes are moderately conserved at the sequence level yet contain the highest proportions of variable sites among the 13 PCGs, suggesting they may serve as supplementary molecular markers for distinguishing between C. mandarina and C. recta. Phylogenetic reconstruction based on concatenated mitochondrial PCGs strongly supported a monophyletic relationship among 45 representative Cicada species (43 retrieved from NCBI plus the two newly sequenced), including C. atrata, the officially recognized source species of Cicadae Periostracum in the Chinese Pharmacopoeia. In conclusion, this study expands genomic resources for Cryptotympana taxonomy and provides a molecular basis for authentication, supporting the conservation and sustainable use of these medicinal insects.
The family Triozidae (Hemiptera: Psylloidea) comprises a diverse group of plant-feeding insects. Despite the ecological significance of this family, their mitochondrial genomic resources remain scarce and phylogenetic relationships remain incompletely resolved. Here, we present the first complete mitogenome of Bactericera gobica. By integrating this newly sequenced genome with nearly all available Triozidae mitogenomes, we establish the most comprehensive dataset to date for the family. This expanded resource enables robust comparative analyses to elucidate mitogenomic evolution, clarify generic phylogenetic status, and reconstruct the divergence history of Triozidae. The B. gobica mitogenome is 14,865 bp in length, containing the standard set of 37 genes with a typical insect gene arrangement and a strong AT bias (72.1
Diabetic foot ulcer (DFU) is a common complication of diabetes that substantially reduces patients’ quality of life. Polymethyl methacrylate (PMMA)-induced membrane therapy, in which PMMA implantation elicits the formation of a bioactive membrane initially recognized for its role in supporting bone regeneration, has gained increasing attention for its potential in wound healing. In this preliminary exploratory study, we investigated the transcriptomic alterations associated with PMMA-induced membrane therapy in DFU tissues. We conducted ribonucleic acid sequencing (RNA-seq), weighted gene co-expression network analysis (WGCNA), and machine learning techniques on human DFU tissue samples to identify differentially expressed genes (DEGs) associated with induced membrane formation and function, analyzing their potential roles in the healing process. Gene expression analysis enabled the construction of a gene co-expression network, revealing 18 distinct modules, of which the turquoise module exhibited the strongest correlation with induced membrane formation. Integration of induced membrane-associated genes with DEGs across different conditions, we identified 422 overlapping genes. Functional enrichment analysis revealed that these genes were primarily involved in the citric acid cycle, respiratory electron transport, and adenosine triphosphate (ATP) synthesis via chemiosmotic mechanisms. Given that effective wound healing requires coordinated regulation of these fundamental processes, we next sought to identify the most critical regulatory nodes within this gene set. To achieve this, we applied machine learning approaches, including Random Forest (RF), least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE). This integrated strategy identified four candidate biomarker genes: ATP synthase F1 subunit delta (ATP5F1D), small nuclear ribonucleoprotein D2 polypeptide (SNRPD2), ribosomal protein L26 (RPL26), and nucleolar complex associated 4 homolog (NOC4L). These genes are functionally enriched in mitochondrial energy metabolism and protein biosynthesis pathways, suggesting their potential roles in supporting the regenerative microenvironment of the induced membrane. Collectively, our findings underscore the critical role of the induced membrane in DFU healing and generate hypotheses regarding its potential molecular mechanisms.
Aegilops tauschii (DD, 2n = 2x = 14) is a well-studied wild species because it is the D-genome donor of bread wheat. Morphologically intermediate accessions are special types that are different from ssp. tauschii (cylindrical spikes) and ssp. strangulata (moniliform spikes). The understanding of the evolution of the intermediate type is very limited. The morphology and genetic mismatching of subspecies structure has long been a puzzle for this species. The present study addressed this puzzle using the spikelet index as an objective criterion to score spike morphology. Afterwards, fluorescence in situ hybridization (FISH) karyotyping was used to analyse the subspecies structure. Among the 399 studied accessions, 238, 56 and 105 accessions had cylindrical, moniliform and intermediate spikes with mildly moniliform spikelets, respectively. All the F1 plants from 25 reciprocal crosses between ssp. tauschii (cylindrical spikes) and ssp. strangulata (moniliform spikes) showed intermediate spikes. Based on spikelet index (SI), the 336 accessions with SI data were clearly divided into two clusters, SI-C1 (low SI) and SI-C2 (high SI), which corresponded to the previously assembled phylogenetic lineages L1 and L2, respectively. FISH karyotyping using the probes oligo-pTa-535 and (CTT)10 also divided the 399 accessions into two clusters, FISH-C1 and FISH-C2, which perfectly matched SI-C1 and SI-C2. The FISH markers 2D-CTT-4 and 2D-535 could be used to accurately distinguish the two clusters. Twelve accessions had obvious chromosomal rearrangements, most of which originated from Iran. Comparison of FISH patterns between Ae. tauschii and 219 common wheat cultivars showed that the wheat D genome matched the FISH-C2 pattern; in particular, the intermediate-spike accessions from the southwestern and southern Caspian region showed FISH patterns resembling those of common wheat. In this study, the intermediate accessions were placed into ssp. strangulata. The treatment reconciles the botanical and genetic categorizations: ssp. tauschii is taxonomically aligned with the cytogenetic and molecular lineage designated SI-C1/FISH-C1/L1, whereas ssp. strangulata corresponds to SI-C2/FISH-C2/L2. The intermediate-spike accessions of ssp. strangulata from the southwestern and southern Caspian region made an important contribution to the wheat D genome.
Asparagus cochinchinensis is a well-known medicinal herb native to East Asia, appreciated for its therapeutic effects, nutritional value, and cosmetic uses such as skin whitening. Despite its wide-ranging ecological adaptability and economic importance, in-depth genomic research, especially focusing on its organellar genomes, remains insufficient. In this research, we performed comprehensive sequencing, de novo assembly, and functional annotation of the mitochondrial genome (mitogenome) of A. cochinchinensis. The mitogenome consists of three independent circular chromosomes measuring 327,009 bp, 175,491 bp, and 83,175 bp, summing to 585,675 bp with a GC content of 45.83
Long-term continuous cropping, low fertilizer use efficiency, and fixation of phosphorus and potassium in nutrient-deficient soils severely constrain sustainable tobacco production. Multifunctional plant growth-promoting rhizobacteria (PGPR) with robust environmental adaptability offer a promising strategy to reduce chemical fertilizer inputs. A multifunctional bacterial strain EL9 was isolated from tobacco rhizosphere and identified as Priestia megaterium. It showed a colorimetric value equivalent to 55.47 mg·L⁻1 IAA, solubilized 427.60 mg·L⁻1 phosphate, and mobilized 172.29 mg·L⁻1 potassium. Whole-genome sequencing revealed a 5.10 Mb genome carrying genetic features potentially involved in IAA production, including the tryptophan biosynthesis gene cluster and the amiE gene. Additional genes related to phosphorus transport, sulfate assimilation, and core carbon/nitrogen metabolism were also identified. Pot experiments showed that EL9 significantly increased IAA, available phosphorus, and potassium in rhizosphere soils of tobacco, Chinese cabbage, and wheat, accompanied by enhanced plant growth and root development. Field trials confirmed improved tobacco agronomic traits and cured leaf quality. Genomic safety assessment revealed no complete or obvious pathogenicity determinants based on in silico analyses, and additionally, plate assays suggested preliminary antagonistic activity against Fusarium oxysporum. Priestia megaterium EL9 is a promising multifunctional PGPR with a well-characterized genetic repertoire and showed promising efficacy in pot experiments across three crop species (tobacco, Chinese cabbage, and wheat) and in field trials with tobacco, supporting its potential as a biofertilizer for sustainable agriculture.
The gut microbiome of infants and young children (0–24 months) represents a critical interface for investigating the drivers of early-life resistome establishment. Therefore, this study investigated the factors driving resistome acquisition and profiles in early life. Here, we analyzed fecal metagenomes from infants and young children across six countries, including the United States, Norway, Spain, the United Kingdom, Denmark, and Nicaragua. This study showed that, rather than inducing uniform ARG enrichment, early-life antibiotic exposure was associated with pronounced restructuring of the gut microbial community, characterized by a decreased microbial and resistome abundance. Multidrug resistance (MDR) genes (often via efflux pumps) predominated in the gut resistomes of infants and young children, followed by genes conferring resistance to peptide antibiotics and glycopeptides, with substantial contributions from tetracycline, macrolide, and fluoroquinolone resistance genes. Geographic context, feeding practices, and age emerged as significant determinants of resistome diversity and structure. Collectively, these findings indicate that the infants and young children’s gut resistome is developmentally sensitive to antibiotic perturbation, while a substantial fraction of resistance genes appears to be structured by early-life ecological and dietary factors. This highlights infancy as a critical window during which resistome composition is shaped by multiple non-exclusive forces, with implications for understanding the origins of antimicrobial resistance trajectories later in life.
The tomato leafminer, Tuta absoluta, is a highly invasive pest that exhibits strong adaptive capacity under nutrient stress. Competing endogenous RNA (ceRNA) networks regulate post-transcriptional gene expression through interactions among miRNAs, lncRNAs, circRNAs, and mRNAs, and may play important roles in nutrient stress adaptation. However, the involvement of ceRNA-mediated regulation in T. absoluta remains largely unknown. In this study, we employed whole-transcriptome sequencing to identify differentially expressed (DE) miRNAs, messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in T. absoluta under fresh tomato feeding compared with starvation. We identified 46 DEmiRNAs, 2143 DEmRNAs, 391 DElncRNAs, and 1635 DEcircRNAs, and constructed putative DElncRNA–DEmiRNA–DEmRNA and DEcircRNA–DEmiRNA–DEmRNA regulatory networks based on computational prediction and expression correlation analyses. Functional enrichment analysis revealed that DEmRNAs, miRNA target genes, and circRNA host genes were predominantly involved in chitin metabolism, lipid catabolism, fatty acid biosynthesis, and detoxification pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further demonstrated significant enrichment in pathways including AMPK signaling, insulin signaling, and biosynthesis of unsaturated fatty acids. Notably, miR‑6497a and miR‑6498‑5p were predicted to represent key regulatory hubs within the putative ceRNA network, interacting with multiple DElncRNAs, DEcircRNAs, and DEmRNAs. Collectively, this study reveals a competing endogenous RNA (ceRNA) network in T. absoluta under starvation stress, highlighting non-coding RNA (ncRNA) roles in metabolic adaptation and detoxification, and providing candidate targets for RNAi‑based control.
The yak (Bos grunniens) is a representative domestic animal of the Qinghai-Tibet Plateau and surrounding high-altitude regions, primarily distributed at elevations above 3,000 m across the plateau and its adjacent alpine and subalpine zones. Yaks provide humans with diverse resources including meat, milk, hides, wool, and labour, serving as a vital livelihood and economic pillar for pastoralists on the plateau. They constitute an indispensable component of the local livestock economy. The Sangsang yak is an indigenous breed endemic to the Sangsang region of Tibet. This study aims to elucidate its population genetic structure and evolutionary relationships, which holds important implications for the conservation of breed resources and the exploitation of favorable traits. The PCA results revealed that Sangsang yak was separated from other yak populations in the first and second principal components and exhibited a relatively independent genetic structure, which was further supported by the NJ phylogenetic tree. While population structure indicates genetic divergence, the genome-wide outlier analyses did not yield regions passing strict multiple testing corrections. Therefore, all detected genomic outliers are defined as purely suggestive candidate regions. These loci may be related to potential adaptive characteristics of Sangsang yak, including high-altitude tolerance and immune adaptation. The KIT gene was identified as a shared suggestive candidate locus across all comparison groups. This finding raises the hypothesis that Sangsang yak may have unique immune-related adaptive characteristics. This study utilized an integrated approach of whole-genome sequencing combined with population genetic analyses to systematically investigate and clarify the population structure and evolutionary characteristics of the Sangsang yak. Although no genomic regions reached statistical significance after strict multiple testing corrections, we obtained multiple suggestive outliers that may be associated with high-altitude tolerance and immune function. This research provides critical genomic insights for the scientific conservation and rational exploitation of Sangsang yak genetic resources.
Single-cell RNA sequencing annotation can achieve high label accuracy when suitable references are available, but assigned labels do not necessarily expose the regulatory features associated with cell identity or state. Existing regulator-activity methods address related biological questions, whereas graph-informed topic models face a separate reproducibility problem when regulatory vocabulary terms are generated stochastically. We developed RegPathTopic to construct deterministic graph-derived vocabulary terms and evaluate them under matched controls. RegPathTopic converts TF-target graphs into regulatory paths and TF-centered modules, scores and filters these terms, calibrates them against degree-matched controls, and learns topic representations from gene-only, regulatory-only, or combined matrices. Across seven benchmark settings, RegPathTopic achieved a macro-F1 of 0.975 in the filtered CellTypist internal benchmark, matching the best gene-only topic baseline. In CellTypist and scIB transfer, it achieved macro-F1 values of 0.970 and 0.830, respectively, with positive margins over the displayed predecessor-style and degree-matched graph-derived controls. These margins did not extend to all comparator families: gene-only transfer, several established annotation tools, and decoupler TRRUST activity baselines were stronger in relevant settings. Vocabulary audits showed that retained paths and modules remained explicit and traceable through topic-level outputs; these analyses establish feature traceability rather than validated TF activity or causal regulatory interpretation. The present evidence supports RegPathTopic as a reproducible framework for constructing and auditing graph-derived topic vocabularies and testing them against matched graph controls. It does not establish RegPathTopic as a superior annotation method or as a replacement for dedicated regulator-activity approaches. Perturbation-supported or orthogonal biological validation is required before the traced vocabulary terms can be interpreted as validated regulatory programs.
Junken meat sheep undergo a developmental coat color transition from black fleece at birth to white body fleece by approximately 179 days of age, but the associated epitranscriptomic features remain unclear. Here, integrated MeRIP-seq and RNA-seq analyses were performed using skin samples from three newborn black-fleeced lambs and three 179-day-old white-fleeced lambs. m6A peaks were mainly enriched in CDS regions and near stop codons, with the canonical GGACU motif detected in both groups. Across three paired comparisons, 1,273–1,716 differential m6A peaks and 400–1,657 differentially expressed genes were identified. Functional enrichment analysis highlighted processes related to hair follicle development, epidermal morphogenesis, extracellular matrix remodeling, focal adhesion, and Wnt, TGF-β, PI3K-Akt, Notch, and melanogenesis-related pathways. Integrative analysis revealed comparison-dependent m6A–expression coupling patterns, including hyper-down in C11 vs. C1 and predominant hypo-up patterns in C22 vs. C2 and C33 vs. C3. Candidate m6A-associated genes, including FZD7, GAS1, COL4A1, PXDN, LAMC3, ARID1A, FA2H and RAPGEFL1, were prioritized, and qRT-PCR supported the RNA-seq expression trends of selected genes. Given the confounding between age and coat-color stage, these findings represent candidate molecular features associated with developmental coat color transition and provide a basis for future m6A-site validation and functional studies.
The root of Isatis indigotica (Radix Isatidis) is a valuable traditional Chinese medicine rich in bioactive flavonoids, yet the regulatory mechanism by which leaf cutting affects root flavonoid metabolism remains unclear. In this two‑year (2024 and 2025) field experiment, we investigated the dynamic responses of root flavonoids in I. indigotica cultivar “Yulan No. 1” at five time points (0, 4, 8, 12, 16 days) after leaf cutting. Total flavonoid content was lowest at day 0 and highest at day 16 after leaf cutting and measured in both years and showed a consistent trend. Using UPLC‑MS/MS‑based widely-targeted metabolomics on the second‑year samples, 148 flavonoid metabolites were identified, among which 64 were differentially accumulated. K‑means clustering revealed six distinct temporal patterns. Eleven candidate differential metabolites showed strong positive correlations with total flavonoid content, with tenuifone exhibiting the highest correlation. Transcriptome sequencing identified 69 differentially expressed genes involved in flavonoid‑related pathways, including phenylpropanoid and flavonoid biosynthesis. Integrated correlation analysis constructed a metabolite‑gene network, highlighting multiple 4CL and CYP81E genes as candidate genes potentially involved in the flavonoid response. Notably, different isoforms of the same gene family showed opposite correlation directions with the same metabolites, indicating isoform‑specific regulatory complexity. Our findings demonstrate that leaf cutting induces a biphasic, quantitative reprogramming of root flavonoid metabolism with a largely conserved qualitative metabolite profile. This study provides a correlative metabolomic and transcriptomic landscape of leaf-cutting-induced flavonoid accumulation in I. indigotica roots, offering a theoretical basis for quality-oriented cultivation and identifying candidate metabolites and genes for further functional validation.
Tenocytes are the principal effector cells responsible for tendon homeostasis and repair, whose functions are governed by precise transcription programs. However, the epigenetic basis underlying the establishment and maintenance of their cellular identity, particularly the genome-wide landscape of chromatin accessibility, histone modifications and chromatin states remains largely unexplored. We performed a multi-omics analysis of primary tenocytes, including ATAC-seq, CUT Tag profiling of six key histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), and RNA-seq. By utilizing ChromHMM algorithm, we defined a comprehensive chromatin state map for tenocytes. We established a high-resolution epigenetic atlas, segmenting the tenocyte genome into 10 distinct states with well-defined biological functions. Integrative analysis revealed that active promoter states, marked by H3K4me3, H3K27ac, and open chromatin, were tightly linked to the high expression of genes essential for tendon function, including extracellular matrix components and key transcription factors. Motif analysis revealed a putative regulatory network of these genes, which was centered on ETS and Zinc-finger family transcription factors. In contrast, repressed promoter states, enriched for the Polycomb-associated mark H3K27me3, were found at genes mainly involved in alternative developmental pathways (e.g., neural, epidermal) and hormone secretion functions, suggesting an active silencing mechanism that safeguards tenocyte lineage fidelity. This study provides an integrated epigenomic landscape of tenocytes, establishing a chromatin-level blueprint for understanding their cellular identity. This resource identifies key regulatory elements controlling tendon signature gene expression and offers a valuable dataset for future investigations into the epigenetic regulation of tendon homeostasis and regeneration.
Runs of homozygosity (ROH) provide a genome-wide measure of autozygosity and are useful for evaluating the genomic consequences of selection and inbreeding in commercial pig populations. This study investigated ROH architecture and associations between ROH-based genomic inbreeding coefficients ( F_ROH ) and production-related traits in American Duroc (DD), American Landrace (LL), and American Yorkshire (YY) pigs. After quality control, 5,859 genotyped pigs were analysed. Using a 1 Mb ROH definition restricted to SSC1-18, we detected 416,225 ROH segments and observed the highest individual-level ROH in DD. Mixed models incorporating a genomic relationship matrix (GRM) identified 19 nominally significant F_ROH –trait associations (P < 0.05) among 51 population–trait tests, of which 13 remained significant after Benjamini–Hochberg FDR correction, with the broadest pattern in LL, fewer associations in DD, and nominal associations in YY restricted to BL and BH, with only BH surviving FDR correction. Sex-specific analyses detected F_ROH × Sex interactions that were nominally significant in DD, none of which remained significant after FDR correction across 45 estimable interaction tests. Segmented models further showed 25 nominally significant threshold responses (P < 0.05), none of which survived FDR correction (minimum q = 0.118); these exploratory patterns suggested that nominal candidate F_ROH breakpoints differed by population, trait, and ROH length class. These results indicate that the effects of genomic autozygosity on production traits vary across commercial pig populations with trait-dependent associations supported by FDR correction and sex- and ROH-length-class-related patterns remaining exploratory. The population-specific F_ROH associations and threshold responses observed in this study provide insight into how different sources of inbreeding may influence production performance. These findings provide a basis for population-specific evaluation of inbreeding load and for improving genomic management strategies in commercial pig breeding.
Cardiac regeneration has been characterized in individual species of fish and amphibians, vertebrates whose hearts are comparatively simple in structure, and function at low pressure. Here, we use quantitative proteomics to characterize the cellular response in the heart of the gecko (Eublepharis macularius) following injury. Gecko hearts are more complex, and function at higher pressure, than those of fish and amphibians. Hearts were damaged using a cryoprobe and wound sites were sampled at 3-, 14-, 30- and 100-days post injury (dpi). Samples were also taken from sham operated geckos. Overall, 579 proteins were differentially expressed across at least two time points. Importantly, we found increased expression of agrin at 14-dpi, a protein that facilitates cardiomyocyte dedifferentiation. This is the first time that an increase in agrin expression following cardiac injury, has been reported. Gene Ontology (GO) analysis indicates that by 14-dpi there is a decrease in oxidative and glycolytic capacity as well as in sarcomere organization and mitochondrial content. However, by 100-dpi these were all recovered. There were also no GO terms between sham and 100-dpi hearts, suggesting that the cardiac proteome is returning to the pre-injury state. This work indicates that heart regeneration in geckos involves reorganization of cellular pathways associated with mitosis, energy production and contractile function.
Hoxc13 is a critical transcription factor that regulates the expression of hair keratin genes. Our previous study showed that during mammalian evolution, the Hoxc13 protein acquired a characteristic polyglycine repeat (polyG) insertion. This insertion distinguishes Hoxc13 from its non-mammalian homologs and may contribute to hair production. To investigate the effect of the polyG fragment on the DNA-binding profile of Hoxc13, the normal Hoxc13-W protein and a polyG-deleted Hoxc13-S protein from cashmere goats were synthesized using an in vitro expression system. Their genomic binding profiles were compared using DNA affinity purification sequencing (DAP-seq), genome alignment, pathway enrichment, motif analysis, and molecular docking. Hoxc13-W and Hoxc13-S exhibited markedly different genome-wide DNA-binding capacities. Hoxc13-W identified 12,679 binding peaks, whereas Hoxc13-S identified only 3,634, with only 243 peaks shared between the two proteins. Functional enrichment analysis showed that Hoxc13-W specifically bound genes involved in key pathways regulating hair follicle morphogenesis and cycling. In contrast, Hoxc13-S targets were enriched primarily in the axon guidance pathway. Within the Wnt signaling pathway, Hoxc13-W bound 30 genes, whereas Hoxc13-S bound only 5. Motif analysis further demonstrated that the polyG fragment substantially influenced cis-regulatory motifs beyond the core Hoxc13-binding motif (5′-ATAAA-3′). Molecular docking analysis indicated that the polyG fragment altered the N-terminal structure of Hoxc13, thereby affecting its protein-protein interaction capacity. Collectively, these findings suggest that the polyG fragment enhances the Hoxc13-mediated gene regulatory network during the evolutionary transition from non-mammalian to mammalian vertebrates and may have contributed to the evolution of mammalian hair-related phenotypic traits.
Hu sheep are a well-known Chinese dual-purpose breed valued for meat production, early sexual maturity, high prolificacy, and adaptability to hot, humid environments. In this study, we combined whole-genome sequencing, GWAS, and eQTL analyses to investigate the genetic basis of growth and slaughter traits in 420 eight-month-old Hu sheep. Using a discovery cohort (N = 112) and a validation cohort (N = 308), we integrated high-throughput SNP genotyping and RNA sequencing, identifying 559,996 high-quality SNPs and multiple significant loci associated with traits such as live weight and carcass weight. Among the 2,368 cis-eQTLs detected, the most significant was linked to ZNF280B expression in the longissimus lumborum muscle. Functional validation showed that ZNF280B downregulation significantly inhibited skeletal muscle satellite cell proliferation and induced apoptosis, highlighting its critical role in muscle development and fat metabolism. The novelty of this study lies in its large sample size, comprehensive multi-trait analysis, and the integration of functional validation, providing reliable genetic markers for marker-assisted selection in Hu sheep. These findings deepen our understanding of the genetic mechanisms underlying growth and slaughter performance and offer valuable insights for improving production efficiency and promoting sustainable livestock development.
Long non-coding RNAs (lncRNAs) are important regulators of developmental gene expression, but their roles during key windows of embryonic hair follicle morphogenesis in cashmere goats remain unclear. This study aimed to identify temporally specific lncRNAs associated with early hair follicle development and to evaluate a candidate cytoplasmic lncRNA and its potential regulatory relationship in an in vitro dermal fibroblast model. Temporal screening identified 32 candidate lncRNAs with transient, stage-specific expression changes at embryonic day 55, suggesting that this stage may represent an important window of transcriptional regulation associated with embryonic hair follicle morphogenesis. Enrichment analysis showed positive enrichment of Wnt-related gene sets in the day 55 vs. day 45 and day 65 vs. day 55 comparisons; however, this finding does not constitute a direct measurement of Wnt pathway activity. Among the prioritized candidates, MSTRG.18075.2 showed relatively high expression at day 55 and was predominantly localized to the cytoplasm. In a heterologous 293T-cell reporter system, chi-miR-145-5p reduced the activity of wild-type reporters containing the predicted MSTRG.18075.2 or WNT16 3’ UTR site, whereas the corresponding mutant reporters did not show the same changes, supporting sequence-specific reporter responses mediated by these predicted sites. In cashmere goat dermal fibroblasts, MSTRG.18075.2 knockdown was associated with reduced apoptosis, slower cell-cycle progression, impaired proliferation and migration, and increased intracellular reactive oxygen species (ROS). Combined knockdown of chi-miR-145-5p partially reversed some phenotypes induced by MSTRG.18075.2 or WNT16 knockdown. These results are consistent with a candidate MSTRG.18075.2/chi-miR-145-5p/WNT16 regulatory model. This study provides supporting evidence for a relationship between MSTRG.18075.2 and the candidate chi-miR-145-5p/WNT16 regulatory axis at the levels of temporal expression, cytoplasmic localization, sequence-specific reporter responses, and in vitro cellular phenotypes. Because endogenous RNA complexes, downstream Wnt activity, and effects on hair follicle morphogenesis in vivo were not examined, the current findings do not directly establish an endogenous ceRNA mechanism or a causal relationship in vivo.
Rumen flukes, particularly the trematode Calicophoron daubneyi, are emerging parasites of livestock in Europe, yet transcriptomic insights into their environmental and intermediate host stages remain limited. Here, we present a comprehensive transcriptomic analysis of eggs at three distinct developmental stages (freshly excreted, early developmental and eye-spot stages), as well as rediae and cercariae, of C. daubneyi. High-quality RNA-sequencing (RNA-seq) datasets revealed both shared and stage-specific transcriptional profiles with each developmental stage exhibiting its own distinct expression pattern. Subsequent GO-Term enrichment analyses revealed that fully embryonated eggs in eye-spot-stage especially upregulated genes related to cilia assembly, movement and motility, reflecting preparation for miracidial hatching and host-seeking behavior. Rediae showed enhanced transcription of genes involved in diverse metabolic and biosynthetic processes, supporting rapid asexual proliferation within the snail intermediate host. Cercariae exhibited predominant upregulation of genes associated with signal transduction and energy metabolism, indicating the adaptation to its changing environmental conditions. These findings provide the first transcriptomic insights into the biology of C. daubneyi outside the definitive host, reveal molecular mechanisms underlying development, transmission and adaptation to a changing environment and identify stage-specific genes as potential targets for interventions aimed at disrupting the parasites life cycle and controlling rumen flukes in the future.
