Search Results (1,893)

Tea, a widely consumed beverage globally, is a vital agricultural product for many countries. Polyphenol oxidases (PPOs), copper-containing enzymes found in plants, fungi, and animals, are essential for physiological metabolism and enzymatic browning in tea plants (Camellia sinensis). Codon usage bias (CUB), a key evolutionary characteristic, offers valuable insights into species evolution and gene function. However, the codon usage patterns of Camellia sinensis polyphenol oxidase (CsPPO) genes remain undocumented. In this study, we conducted, for the first time, a comprehensive analysis of CUB in 24 CsPPO genes, comparing their CUB profiles with those of other Camellia species (Camellia lanceoleosa, Camellia nitidissima, Camellia ptilophylla) and non-Camellia species (Actinidia chinensis, Cornus florida, Rhododendron vialii) to elucidate potential evolutionary relationships and functional constraints influencing CUB. Nucleotide composition analysis revealed an AT-rich bias, with a preference for G/C-ending codons at the third position. Codon usage indices indicated low expression levels and weak CUB. RSCU and RFSC analyses revealed that the preferred and high-frequency codons were mostly G/C-ending. Codon usage frequency analysis suggested Zea mays as a suitable host for CsPPO gene expression. ENC-GC3s, PR2, and neutrality plots showed natural selection had a stronger impact than mutation on CUB. Additionally, measure independent of length and composition (MILC) values confirmed low PPO gene expression levels, and correlation analyses demonstrated that both nucleotide composition and gene expression affect CUB. Overall, codon usage in CsPPO genes is mainly shaped by natural selection, with weak bias and low expression potential, providing useful insights for future genetic engineering and heterologous expression. Full article

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding. Full article

Inducible CRISPR interference (CRISPRi) systems were established in Lactococcus lactis using both plasmid and chromosomal approaches. Expression of nuclease-deficient Cas9 (dCas9) from Streptococcus pyogenes was placed under the control of the nisin-inducible promoter P_nisA, while sgRNAs were transcribed from the constitutive P_usp45 promoter. To monitor expression, dCas9 was fused with superfolder GFP. Plasmid-based constructs successfully repressed a luciferase reporter gene and silenced the gene of the major autolysin, AcmA, leading to the expected morphological phenotype. However, plasmid systems showed leaky expression, producing mutant phenotypes even without induction. Chromosomal integration of dCas9 reduced its expression level by approximately 20-fold compared with plasmid-based expression, thereby preventing leaky activity and ensuring tight regulation. This chromosome-based (cbCRISPRi) platform enabled controlled repression of the essential gene ybeY, which resulted in severe growth defects. Restoration of wild-type phenotypes was achieved by introducing a synonymous codon substitution in the sgRNA target region. Transcriptome analysis of ybeY-silenced cells revealed downregulation of ribosomal protein genes and widespread effects on membrane-associated proteins, ATP synthase subunits, and various transporters. These inducible CRISPRi platforms provide robust and tunable tools for functional genomics in L. lactis, particularly for studying essential genes that cannot be deleted. Full article

Background: Pseudorabies virus (PRV), a critical porcine herpesvirus, induces severe diseases in both livestock and wildlife, imposing an incalculable burden and economic losses in livestock production. In this study, we investigated the evolutionary mechanisms and host adaptation strategies of the PRV gB gene through genomic alignment. The gB gene is highly conserved in PRV, and its encoded gB protein exhibits functional interchangeability across different herpesvirus species. Notably, the gB protein elicits the production of both complement-dependent and complement-independent neutralizing antibodies in animals, while also being closely associated with syncytium formation. Methods: Phylogenetic analysis and codon usage pattern analysis were performed in this study. A total of 110 gB gene sequences were analyzed, which were collected from [2011 to 2024] across the following regions: [Fujian, Shanxi, Guangxi, Guangdong, Chongqing, Henan, Shaanxi, Heilongjiang, Sichuan, Jiangsu, Jilin, Huzhou, Shandong, Hubei, Jiangxi, Beijing, Shanghai, Chengdu (China)], [Budapest, Szeged (Hungary)], [Tokyo (Japan)], [London (United Kingdom)], [Athens (Greece)], [Berlin (Germany)], and [New Jersey (United States)]. Results: The gB gene of PRV employs an evolutionary “selective optimization” strategy to maintain a dynamic balance between ensuring functional expression and evading host immune pressure, with this core trend strongly supported by its codon usage bias and mutation characteristics. First, the gene exhibits significant codon usage bias [Effective Number of Codons (ENC) = 27.94 ± 0.1528], driven primarily by natural selection rather than mere mutational pressure. Second, phylogenetic analysis shows that the second codon position of gB has the highest mutation rate (1.0586)—a feature closely linked to its antigenic variation and immune escape capabilities, further reflecting adaptive evolution against host immune pressure. Additionally, ENC-GC3 plot analysis reveals the complex regulatory mechanisms underlying codon bias formation, providing molecular evidence for the “selective optimization” strategy and clarifying PRV’s core evolutionary path to balance functional needs and immune pressure over time. Conclusions: Our study findings deepen our understanding of the evolutionary mechanisms of PRV and provide theoretical support for designing vaccines and assessing the risk of cross-species transmission. Full article

Soft-furred tree mice (genus Typhlomys), which are native to southern China and northern Vietnam, are unique rodents capable of echolocation. Little is known about their taxonomy, ecology, and natural history. In this study, we generated the complete mitochondrial genomes of seven species/putative species of Typhlomys. We conducted a comprehensive comparative analysis of these mitochondrial genomes focusing on sequence length, A+T content, A/T bias, A+T-rich regions, overlapping and intergenic spacer regions, nucleotide composition, relative synonymous codon usage, ancestral distributions, and the non-synonymous/synonymous substitution ratio (Ka/Ks). Additionally, we analyzed the phylogeny and adaptive evolution of these species/putative species. The mitogenomes of Typhlomys ranged from 16,487 to 17,380 bp in length, encoding the complete set of 37 genes typically found in mammalian mitogenomes. The base composition exhibited an A+T bias. The most frequently used codons were CUA (Leu), AGC (Ser), GGA (Gly) and UUA (Leu), UUG, CUG, CGU and GCG were the less frequently used codons. Ancestral distribution reconstruction suggests that Typhlomys originated in Central or Southwestern China. Notably, we found that the Ka/Ks ratio of the ND5 gene in T. huangshanensis was greater than 1, indicating that this gene has undergone positive selection for efficient respiration in higher elevations and colder climates. Full article

Excessive abdominal fat deposition accompanying rapid growth in broiler chickens seriously affects production efficiency. Using divergently selected broiler lines from Northeast Agricultural University, we integrated transcriptome sequencing, whole-genome resequencing, and three-dimensional genomic data to identify key SNPs affecting abdominal fat deposition. From 3,850,758 initial SNPs, 22,721 high-quality SNPs were selected (|ΔAF| ≥ 0.9) and validated to obtain 7341 reliable SNPs. GWAS identified 16 SNPs significantly associated with abdominal fat weight, while LD analysis revealed 22 highly linked SNPs, finally determining 2302 candidate SNPs. Transcriptome analysis identified 825 differentially expressed genes (p ≤ 0.05, |FC| ≥ 1.5). Functional annotation revealed 201 SNPs located in differentially expressed gene regions, including 8 coding SNPs and 193 non-coding SNPs, with an additional 15 SNPs potentially regulating through long-range chromatin interactions. Mechanistic analysis showed that coding SNPs regulate gene expression by altering codon translation rates or mRNA stability, while non-coding SNPs regulate transcription by affecting transcription factor binding. Phenotypic association analysis demonstrated that all 213 SNPs can cause ≥2-fold differences in abdominal fat weight, with 182 SNPs causing ≥3-fold differences. This study successfully identified 213 functional SNPs affecting abdominal fat deposition in broilers and revealed their molecular basis for regulating fat metabolism through multiple mechanisms, providing important genetic markers for low-fat breeding in broilers. Full article

Oocytes from women of advanced reproductive age exhibit diminished developmental potential, but the underlying mechanisms remain incompletely defined. Oocyte maturation depends on translational control of maternal mRNA synthesized during growth. We performed a computational analysis on human oocytes from women <30 versus ≥40 years and observed that mRNA GC content correlates negatively with half-life in oocytes from young (<30 yr) but positively with oocytes from aged (>40 yr) women. In young oocytes, longer mRNA half-life is associated with lower protein abundance, whereas in aged oocytes GC content correlates positively with protein abundance. During the GV-to-MII transition, codon composition stratifies stability: codons that support rapid translation (optimal) stabilize mRNA, while slow-translating codons (non-optimal) promote decay. With reproductive aging, GC-containing codons become more optimal and align with increased protein abundance. These findings indicate that reproductive aging remodels codon-optimality-linked, translation-coupled mRNA decay, stabilizing a subset of GC-rich maternal mRNA that may be prone to excess translation during maturation. Our analysis is explicitly within human reproductive aging; it does not revisit cross-species stability rules. Instead, it shows that sequence–stability relations are reprogrammed with age within human oocytes, including an inversion of the GC–stability association during GV-to-MII transition. Disruption of the normal mRNA clearance program in aged oocytes may compromise oocyte competence and alter maternal mRNA dosage, with downstream consequences for early embryonic development. Full article

Areca palm velarivirus 1 (APV1), the causal agent of yellow leaf disease (YLD), poses a serious threat to the economically important areca palm industry in the Hainan Province, China, yet its evolutionary dynamics remain poorly understood. Here, we performed a large-scale molecular survey by sequencing the coat protein (CP) gene from 364 APV1-infected samples collected across major cultivation regions of Hainan. Population genetic analyses revealed extremely high haplotype diversity (H_d = 0.997) but very low nucleotide diversity (π = 0.017). Neutrality tests (Tajima’s D = −2.266; Fu’s F_S = −23.697) and a unimodal mismatch distribution supported a scenario of recent demographic expansion from a restricted ancestral pool. Evolutionary analyses indicated that the CP gene is subject to strong purifying selection, although eight codons exhibited episodic positive selection, suggesting ongoing viral adaptation. Furthermore, we identified three distinct genetic clusters with significant geographic structuring, indicating that viral dissemination is shaped by local factors. Together, these results reveal a recent explosive invasion of APV1 characterized by rapid island-wide expansion and emerging local differentiation. This work provides novel insights into the evolutionary trajectory of APV1 and establishes a genomic basis for improved surveillance and management of YLD. Full article

Background/Objectives: Autosomal recessive primary microcephaly is a rare and genetically heterogeneous disorder characterized by congenital non-syndromic microcephaly, with at least 28 causative genes identified to date. Biallelic variants in the CDK5RAP2 gene, an ultra-rare cause of autosomal recessive primary microcephaly, lead to Primary Autosomal Recessive Microcephaly 3 (MCPH3). Methods: We present seven patients from six families diagnosed with MCPH3 in light of clinical and molecular findings using whole-exome sequencing (WES). Furthermore, we investigated the effects of the identified intronic variants on splicing through RNA analysis. Results: Almost all patients had severe microcephaly, mild to moderate intellectual disability, speech delay, and cutaneous pigmentary abnormalities. Four patients presented with postnatal short stature, and two showed weight deficiency. Dysmorphic evaluation revealed that the most prominent features included brachycephaly, hypertelorism, epicanthus, high-arched eyebrows, prominent nasal bridge, and micrognathia. We identified five distinct homozygous CDK5RAP2 variants in our patients, including four novel variants. Segregation analysis verified that the parents were carriers. Two of these variants were intronic (c.3148+5G>C and c.383+4dupA), two were frameshift (c.3168del), and one was a nonsense variant (c.1591C>T). Both intronic variants disrupted splicing, generating a premature stop codon and resulting in a truncated protein. Conclusions: This study broadens the mutational landscape of CDK5RAP2. We also sought to demonstrate the functional consequences of the CDK5RAP2 intronic variants on gene function using RNA analysis. The identification of four novel variants underscores the importance of molecular diagnostics in patients with primary microcephaly and provides valuable data for genetic counseling and future functional studies. Full article

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (O_L), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article

Listeria monocytogenes (L. monocytogenes) is an important foodborne pathogen that poses great risks to food safety and public health, and knowledge about its presence and diversity in potential sources is crucial for effectively tracking and controlling it in the food chain. In this study, we investigated the prevalence, antimicrobial susceptibility, and genomic characteristics of Listeria monocytogenes (L. monocytogenes) collected from retail chicken meat samples in Qingdao, China, in 2022. A total of 38 (10.6%, 38/360) L. monocytogenes isolates were recovered from 360 retail chickens. All 38 isolates were classified into two lineages (I and II), three serogroups (IIa, IIb, IIc), eight sequence types (STs), eight clonal complexes (CCs), eight Sublineages (SLs) and nine cgMLSTs (CTs). ST121 and ST9 were the most prevalent STs in this study. The ST121 strains from China had heterogeneity with those from other countries, while the Chinese ST9 strains had homogeneity with those from other countries. One resistance cassette tet(M)-entS-msr(D) was identified in eight L2-SL121-ST121-CT13265 isolates, the genetic structure of which was identical to that of three reference genomes. All isolates carried the L. monocytogenes pathogenic island (LIPI)-1, with only one carrying LIPI-3 and three carrying LIPI-4. In addition, 11 isolates subtyped as L2-SL121-ST121-CT13265 were found to have a premature stop codon (PMSC) in the inlA gene in this study. Our data revealed the antimicrobial susceptibility, genomic characteristics and evolutionary relationships of L. monocytogenes in retail chicken in Qingdao, China. The characterization of genotypes, virulence, stress and antimicrobial markers of strains circulating in retail chicken in Qingdao, as described in this study, provides the opportunity to improve risk assessments of L. monocytogenes exposure. Full article

Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and antimicrobial properties, showing great potential in medical and food applications. Additionally, its essential oil has substantial commercial value. Mitochondria play a crucial role as organelles within plant cells; however, the mitochondrial genome of E. foetidum remains underexplored. To fill this research gap, we conducted sequencing and assembly of the mitochondrial genome of E. foetidum, aiming to uncover its genetic mechanisms and evolutionary trajectories. Our investigation reveals that the mitochondrial genome of E. foetidum is a circular structure, similar to that of other species, with a length of 241,660 bp and a GC content of 45.35%, which is within the range observed in other organisms. This genome encodes 59 genes, comprising 37 protein-coding sequences, 18 tRNA genes, and 4 rRNA genes. Comparative analysis highlighted 16 homologous regions between the mitochondrial and chloroplast genomes, with the longest segment spanning 992 bp. By analyzing 37 protein-coding genes (PCGs), we identified 479 potential RNA editing sites, which induce the formation of stop codons in the nad3 and atp6 genes, as well as start codons in the ccmFC, atp8, nad4L, cox2, cox1, and nad7 genes. Meanwhile, the genome shows a preference for A/T bases and A/T-ending codons, with 32 codons having a relative synonymous codon usage (RSCU) value greater than 1. The codon usage bias is relatively weak and mainly influenced by natural selection. Most PCGs are under purifying selection (Ka/Ks < 1), while only a few genes, such as rps7 and matR, may be under positive selection. Phylogenetic analysis of mitochondrial PCGs from 21 species showed E. foetidum at the basal node of Apiaceae, consistent with the latest APG angiosperm classification and chloroplast genome-based phylogenetic relationships. In summary, our comprehensive characterization of the E. foetidum mitochondrial genome not only provides novel insights into its evolutionary history and genetic regulation but also establishes a critical genomic resource for future molecular breeding efforts targeting mitochondrial-associated traits in this economically important species. Full article

It is estimated that one in four people worldwide carries Mycobacterium tuberculosis bacteria. MPT64 is a protein exclusively secreted by Mycobacterium tuberculosis complex (MTC) bacteria. It serves as a crucial diagnostic marker and plays a role in the bacterium’s survival by modulating the host immune response. Consequently, the development of innovative diagnostic tools based on MPT64, as well as the production of high-purity MPT64 protein to support research on tuberculosis pathogenesis and the advancement of novel therapeutic strategies, is of great importance. In this study, optimization experiments were conducted to produce this protein in E. coli with high yield and purity. First, a gBlock was designed by codon optimization and then cloned into a plasmid vector using the LIC method. For more efficient production, E. coli BL21(DE3)-R3-pRARE2 strain, which carries rare tRNAs for rare codons, was used as the host. Five different culture media were tested to maximize protein production, with the highest yield obtained in eBHI medium. The resulting protein yield was 4.9 mg/L. To the best of our knowledge, this study provides the most detailed information on the recombinant production and characterization of MPT64 to date. Therefore, these results contribute important data for future studies on the MPT64 protein. Full article

Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC I plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and dN/dS analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC I polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand. Full article

Background/Objectives: Fissidens crispulus Brid. is a dioicous moss with conspicuous axillary hyaline nodules and serrulate leaf margins. It features Neoamblyothallia-type peristome teeth and serves as an ecologically significant model for studying adaptation in the hyperdiverse genus Fissidens (>440 species). Methods: In this study, the complete chloroplast genome of F. crispulus was sequenced and de novo assembled, enabling detailed comparative genomic, phylogenetic, and codon usage bias studies. Results: As the third fully sequenced member of Fissidentaceae, this study deciphers its 124,264–124,440 bp quadripartite genome encoding 129 genes (83 CDS, 32 tRNAs, 8 rRNAs). Repeat analysis identified 125–127 SSRs, dominated by mono-/di-nucleotide A/T repeats (>70%), and dispersed repeats predominantly forward (F) and palindromic (P) (>85%), confirming profound AT-biased composition (GC content: 28.7%). We established 7 hypervariable loci (matK, ycf2, etc.) as novel Dicranidae-wide phylogenetic markers. Codon usage exhibited significant A/U-ending preference, with 12 optimal codons (e.g., GCA, UGU, UUU) determined. Maximum likelihood analyses resolved F. crispulus and F. protonematicola as sister groups with high support value (MBP = 100%). Conclusions: This work provides the foundational cpDNA resource for Fissidens, filling a major gap in bryophyte chloroplast genomics and establishing a framework for resolving the genus’s infrageneric conflicts. Furthermore, it offers critical insights into bryophyte plastome evolution and enables future codon-optimized biotechnological applications. Full article