Insect antimicrobial peptides (iAMPs) form a central component of innate immunity and represent promising templates for developing next-generation antimicrobials. However, conventional AMP identification approaches rely heavily on sequence alignment and motif similarity, which may overlook divergent, short, or noncanonical peptides. Existing insect AMP databases remain taxonomically limited, and high-throughput transcriptomic pipelines frequently generate large numbers of speculative candidates. To overcome these constraints, we developed iAMP-Deep, an alignment-free, multilayered artificial intelligence framework that integrates physicochemical descriptors, motif/domain signatures, and protein-language model (PLM) embeddings and employs ensemble learning and anomaly-aware post-processing for insect-derived AMP discovery. We compiled a curated dataset of experimentally validated insect AMPs and length-matched non-AMPs, including source accession numbers and family labels. To reduce homology-driven leakage, sequence clustering at ≥80
Semen quality influences mating efficiency and is a key trait for evaluating reproductive performance. Sperm concentration and motility are important indicators of semen quality and are closely associated with the microenvironment and dynamic regulation of apoptosis during spermatogenesis. Cysteinyl aspartate-specific proteinase 9 (Caspase9) is a key component of the intrinsic mitochondrial apoptotic pathway and contributes to the balance between spermatogenesis and apoptosis. However, studies on Caspase9 gene polymorphisms, protein characteristics, and expression in male sheep reproduction remain limited. The cloned Caspase9 coding sequence encoded a protein of 426 amino acids. Bioinformatic analyses predicted Caspase9 to be an unstable protein, with an instability index of 50.11 and an average hydropathy score of − 0.350, and predicted the absence of a signal peptide and transmembrane regions. Two conserved domains, CARD and CASc, were identified. Nine SNPs were identified in the Caspase9 gene. The g.252 locus showed low polymorphism, whereas the other eight loci showed moderate polymorphism. Three SNPs, g.252 C > T, g.345 G > A, and g.397 T > C, were synonymous mutations. After correction for multiple comparisons, the ejaculate volume of rams with the CC genotype at the g.129 C > T locus was significantly greater than that of rams with the CT and TT genotypes (P < 0.01). Caspase9 mRNA expression in the testis was significantly upregulated after sexual maturity, accompanied by a significant increase in Caspase9 protein expression (P < 0.01). NFATc4 mRNA expression in the testis was significantly downregulated after sexual maturity, whereas its protein expression was significantly increased (P < 0.01). VEGF mRNA expression was significantly higher in the testis than in the other reproductive tissues (P < 0.05), whereas testicular VEGF protein expression did not differ significantly between reproductive stages. This study characterized the Caspase9 gene and protein in Qianhua Mutton Merino rams and identified nine SNPs. The g.129 C > T polymorphism was significantly associated with ejaculate volume after multiple-comparison correction. Caspase9 showed tissue- and reproductive-stage-dependent expression, with both its mRNA and protein expression in the testis significantly increased after sexual maturity. NFATc4 and VEGF also exhibited distinct expression patterns among reproductive tissues and developmental stages. These findings provide a basis for further investigation of Caspase9 as a candidate molecular marker associated with semen-quality traits and its potential role in male reproductive function in sheep.
Averrhoa carambola L., belonging to the family Oxalidaceae of the order Oxalidales, is a commercially valuable fruit tree extensively grown in tropical and subtropical regions. However, its mitochondrial genome remains uncharacterized. In this study, we report the first complete assembly and comprehensive characterization of the A. carambola mitochondrial genome, providing an essential genomic resource for evolutionary and functional studies. The assembled mitochondrial genome is represented as a 421,040 bp master-circle conformation, with a GC content of 44.56
Eucommia ulmoides is a valuable medicinal and economic tree species whose seedling establishment is often constrained by slow early growth and vulnerability to stress. Plant growth-promoting bacteria (PGPB) represent sustainable alternatives to chemical inputs; however, PGPB associated with E. ulmoides and the genetic basis underlying their plant growth-promoting activities remain underexplored. An N-acyl-homoserine lactone (AHL)-producing isolate, designated Pseudomonas sp. P77, was obtained from the root tissues of E. ulmoides. Functional assays showed that the strain displayed diverse plant growth-promoting characteristics, including phosphate and potassium solubilization, indole-3-acetic acid (IAA) production, and biofilm-forming capacity. UPLC–MS/MS analysis identified multiple AHLs in P77 culture samples, with C6-HSL, C8-HSL, and 3-oxo-C10-HSL among the major detected compounds. Inoculation with P77 significantly promoted the growth of E. ulmoides seedlings, as reflected by increased biomass, and was accompanied by enhanced antioxidant enzyme activities. Whole-genome sequencing generated a high-quality complete circular chromosome of 7.10 Mb with a GC content of 61.25
Dmrt1 is a conserved master male-sex-determining gene in vertebrates. In the tongue sole (Cynoglossus semilaevis), an economically important fish with a ZZ/ZW sex determination system and remarkable female growth superiority, loss of dmrt1 leads to a feminized phenotype in ZZ males. However, the underlying epigenetic regulatory mechanism remains unclear. To investigate this, we performed whole-genome bisulfite sequencing (WGBS) on the brain and gonads of wild-type and dmrt1⁻/⁻ males, integrated with RNA-seq data. Compared to wild-type males, we identified 2,993 and 15,173 differentially methylated regions (DMRs) in the brain, and 261,627 and 13,401 DMRs in the gonads of wild-type females and dmrt1⁻/⁻ males, respectively. This indicates that dmrt1 deficiency is associated with extensive alterations in DNA methylation. Further analysis revealed 49 genes whose promoter methylation levels were significantly negatively correlated with their expression. Functional enrichment analysis associated these genes with diverse biological processes including signal transduction and cellular communication, protein modification, metabolic processes, and cell adhesion. Crucially, several are potential key factors in sex regulation, influencing: sex determination and early gonadal development (wt1, nanos1, tmem88); gametogenesis and germ cell function (chd1l, pdia4, serpine2, ak1, hgsnat, mmp14, map7d2b, exoc3l4, slc6a15, slc27a4, stc2); and cellular architecture and hormonal signaling (dag1, adamts17, kalrn, pde8a, lats2, flna, tas1r3, krt13, hebp2, igfbp3, ugt3). Overall, these findings provide novel molecular evidence and a set of candidate pathways for understanding the epigenetic mechanisms of sex determination in teleost fish.
