Search Results (336)

Background: The family Sperchontidae Thor, 1900 is proposed as a transitional group between the “lower” and “higher” water mites (Subcohort Hydrachnidiae), and is important for understanding the evolutionary history of Hydrachnidiae. However, mitogenomic data are lacking. Methods: The first complete mitogenomes of Sperchontidae were sequenced from two species, Sperchon plumifer and Sperchon sp. Structural features were analyzed, gene rearrangements were compared with five published water mite mitogenomes, and phylogenetic relationships among 31 species within the order Trombidiformes were reconstructed. Results: Both mitogenomes contained the typical 37 genes and exhibited a strong A+T bias (73.1–73.6%), positive AT-skew, and negative GC-skew. Protein-coding genes (PCGs) were generally initiated with ATN/TTG codons and terminated with TAA/TAG or incomplete T–, with codon usage biased toward T/U-ending codons; all PCGs were under purifying selection (Ka/Ks < 1). Most tRNAs lacked canonical cloverleaf structures due to D- or T-arm loss. Gene rearrangements occurred in all examined water mite mitogenomes, with intrageneric rearrangements restricted to tRNAs in Hygrobatidae and Unionicolidae but involving both tRNAs and PCGs in Sperchontidae. Phylogenetic analyses using ML and BI (13 PCGs + 2 rRNAs) strongly supported a close relationship between Hydrachnidiae and Trombidiae (BS = 100%, PP = 1.00) and confirmed the three supercohorts in Trombidiformes (Eleutherengonides, Anystides, Eupodides), though relationships among them remained unresolved. Conclusions: This study reports the first two complete mitogenomes of Sperchontidae, providing preliminary insights into gene rearrangement patterns in water mites. The phylogenetic analyses based on mitochondrial genomes provide additional support for the consistency with traditional morphology at lower taxonomic levels, such as within genera and families, whereas relationships among supercohort-level taxa remain unstable and require additional data for further clarification. Full article

Introduction: Stevia rebaudiana Bertoni has recently gained significant attention due to the presence of intensely sweet yet low-calorie steviol glycosides (SGs) in its leaves, making it a promising natural sugar alternative with applications in the food, pharmaceutical, and cosmetics industries. The primary goal of this study was to determine whether generating somaclonal variation from plant material obtained by indirect regeneration results in further genetic changes identifiable using the SCoT marker (Start Codon Targeted). Methods: In the first stage, callus tissue was initiated from first-generation somaclones on MS medium supplemented with 4.0 mg/L 6-benzylaminopurine (BAP), 2.0 mg/L 1-naphthaleneacetic acid (NAA), and 2.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D). Their morphogenetic potential was analyzed on four media with different BAP and Kinetin concentrations. Donor plants, first and second generation somaclones, were also analyzed for genetic diversity using SCoT markers. Results: All first-generation somaclones demonstrated a very high callus initiation capacity, ranging from 95 to 100%. It was found that for most of the studied somaclones, the greatest number of shoots were developed by explants grown in a medium supplemented with 0.5 mg/L BAP and 0.25 mg/L Kin. The studied group of somaclones exhibits a high degree of polymorphism (55.2%). The analysis of genetic similarity of somaclones presented in the form of individual dendrograms indicates that in most cases, greater genetic diversity was revealed as a result of indirect regeneration in the first generation of somaclones compared to the second. Indirect organogenesis allows for the production of subsequent generations of genetically unstable somaclones, creating the potential for obtaining new phenotypic variants useful in plant breeding. Full article

The alloherpesvirus esocid herpesvirus 1 (EsHV-1) causes epidermal hyperplasia on the skin and fins of northern pike (Esox lucius). For the first time, we present a near-complete genome sequence of EsHV-1, directly obtained from a pike skin sample. The 223,553 bp sequence of the genome has a GC-content of 56.47% and is organised into a long, unique segment (148,159 bp) and a short, unique segment (45,925 bp). The short segment is flanked by inverted repeat sequences (IRSs) of 14,733/6 bp, with the IRS length difference attributed to a codon deletion. The genome is predicted to contain 144 open reading frames, including eight duplicated within the IRSs. The leftmost third of the genome contains genes of unknown function, but many of which exhibit extensive inter-gene homology, suggesting gene duplication. Six paralogous groups were identified, each containing two to thirteen gene members. Homologues of all twelve alloherpesvirus core genes are present. The ATPase subunit of the terminase and the DNA polymerase is composed of three and two exons, respectively. However, an alternate splicing pattern is found, for which, speculatively, a role is suggested in the terminase assembly at the capsid portal. Full article

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

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

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

Colletotrichum spp. are the causative agents of anthracnose of rubber trees, one of the most destructive diseases, resulting in substantial economic losses. To investigate the evolutionary characteristics of these pathogenic species, we first assembled the complete mitogenomes of four dominant pathogens, i.e., C. siamense, C. fructicola, C. wanningense and C. bannaense. Comparative analyses revealed that variations in their mitogenome size were primarily driven by intron expansion and expansion/contraction within the cox1, cob and nad genes. Moreover, we observed the strong conservation of gene content, mitochondrial DNA copy number, gene order and intron features within species complexes, but a clear divergence between them. Notably, further studies indicated that patterns such as genomic organization, selective pressures and codon usage were consistent across the genus, suggesting that Colletotrichum species complexes had followed distinct evolutionary trajectories, particularly in the arrangement of protein-coding genes. Therefore, this study systematically characterized the mitogenomes of the four major Colletotrichum species associated with rubber tree anthracnose and provided novel insights into the broad evolutionary mechanisms shaping Colletotrichum species complexes. Full article

Mitochondrial genomes are powerful tools for taxonomic delimitation and species identification, yet they remain scarce for Chironomidae (Diptera). In this study, we assembled and annotated 63 new mitochondrial genomes, encompassing 63 species within 39 genera in Orthocladiinae sensu lato (including Prodiamesinae and Orthocladiinae) and Chironominae by whole-genome sequencing, marking the first report of mitochondrial genome data for the Xiaomyini. Comparative analyses revealed structural variation, including transfer RNA gene rearrangements, along with strong nucleotide composition bias, codon usage patterns, and gene-specific selection pressure differences. Distinct evolutionary dynamics were detected among protein-coding genes, ribosomal RNAs, transfer RNAs, and the control region. Heterogeneity analyses and phylogenetic analyses showed that amino acid datasets perform better for basal branch of Orthocladiinae relationships, although the resolution within non-basal branches of Orthocladiinae remains limited. By substantially increasing both the number and taxonomic breadth of mitochondrial genomes in Chironomidae, this study delivers a vital foundation for future multi-marker phylogenetic reconstruction, taxonomic revision, and rapid species identification, with direct applications to biodiversity conservation and freshwater ecosystem monitoring. Full article

Background: The chloroplast genome provides rich genetic information for plant evolutionary studies. This study aimed to assemble, annotate, and analyze the complete chloroplast genome of flax cultivar ‘Longya 15’ (Linum usitatissimum L.) and clarify its phylogenetic relationships with other Linaceae species. Methods: We assembled and annotated the chloroplast genome of ‘Longya 15’ and retrieved chloroplast genomes of related species (e.g., Linum grandiflorum NC_058845.1, Linum lewisii NC_058799.1) from the NCBI database for phylogenetic analysis. Results: The chloroplast genome of ‘Longya 15’ was a 157,074-bp quadripartite structure with 37.42% GC content, encoding 128 genes (83 mRNAs, 37 tRNAs, 8 rRNAs) without pseudogenes. It showed codon bias for leucine (28 codons with RSCU > 1, ending in A/U), 260 dispersed repeats, and 240 SSRs. Ka/Ks analysis revealed purifying selection for most genes, while rps18 and ycf2 had positive selection. ycf1 was identified as the hypervariable region (pi = 0.25024). Phylogenetically, it clustered closest with Linum grandiflorum, followed by L. lewisii and L. perenne, and was related to Hypericum species. Conclusions: This is the first fine assembly and annotation of ‘Longya 15’ chloroplast genome, confirming no pseudogenes in flax chloroplast. It elucidates flax chloroplast genome conservation and evolutionary dynamics, enriches the database, and provides a foundation for Linaceae phylogenetics, germplasm development, and stress-resistant breeding. Full article

KRAS is the most frequently mutated oncogene in cancer. Its activating mutations are associated with aggressive tumor behavior and resistance to certain therapies, including anti-EGFR treatments in colorectal cancer. In particular, the KRAS G12C mutation, which accounts for approximately 3–4% of colorectal cancers (CRCs) and 12–14% of non-small cell lung cancers (NSCLCs), involves a cysteine substitution at codon 12. This has provided the opportunity to develop selective covalent inhibitors that trap the mutant protein in its inactive state. The first targeted therapies for KRAS G12C-mutant cancers comprise sotorasib and adagrasib, both of which have been authorized for use in patients with previously treated NSCLC and CRC. Nevertheless, despite the evidence of clinical activity for this class of agents, primary and acquired resistance, dose optimization, and toxicity management remain significant open challenges. In this review, we summarize recent advances in KRASG12C tumor biology and pharmacological targeting. We also provide additional insights to guide future efforts to overcome the limitations of the current approaches and implement the treatment of KRASG12C-mutant cancers. Full article

Listeria monocytogenes is a Gram-positive bacterial species that causes listeriosis, a major foodborne disease worldwide. The virulence factor inlA facilitates the invasion of L. monocytogenes into intestinal epithelial cells expressing E-cadherin receptors. Naturally occurring premature stop codon (PMSC) mutations in inlA have been shown to result in the production of truncated proteins associated with attenuated virulence. Moreover, different L. monocytogenes strains contain distinct inlA variants. In this study, we first characterized inlA in 546 L. monocytogenes strains isolated from various foods in Shanghai. The results showed that 36.1% (95% Confidence Interval: 32.0~40.2%) of the food isolates harbored inlA with PMSC, which was found to be associated with clonal complex (CC) types, with the highest proportions observed in CC9 and CC121. To investigate the function of inlA, we first used the dominant CC87 isolated from patients as the test strain and constructed an inlA-deleted strain via homologous recombination. Resistance tests and virulence tests showed that while inlA did not affect the resistance of L. monocytogenes, it significantly influenced cell adhesion and invasiveness. To further explore the function of inlA, we performed virulence tests on five CC-type strains carrying inlA with PMSC and their corresponding strains with intact inlA. We found that the virulence of L. monocytogenes strains carrying inlA or inlA with PMSC was associated with their CC type. Our preliminary results showed that premature termination of inlA did not significantly affect the adhesion and invasion abilities of low-virulence CC-type L. monocytogenes strains in Caco-2 cells, but substantially promoted those of high-virulence strains such as CC8 and CC7. In summary, this study preliminarily evaluated the effects of inlA integrity and PMSC mutation variation on the virulence of L. monocytogenes, providing a foundation for further research on inlA-related pathogenic mechanisms. Full article

Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species. Full article

Gastrodia elata Blume is an important medicinal orchid, yet its large-scale cultivation is increasingly threatened by fungal diseases. The 4-coumarate–CoA ligase (4CL) gene family directs a key step in phenylpropanoid metabolism and plant defence, but its composition and function in G. elata have not been investigated. We mined the G. elata genome for 4CL homologues, mapped their chromosomal locations, and analysed their gene structures, conserved motifs, phylogenetic relationships, promoter cis-elements and codon usage bias. Publicly available transcriptomes were used to examine tissue-specific expression and responses to fungal infection. Subcellular localisation of selected proteins was verified by transient expression in Arabidopsis protoplasts. Fourteen Ge4CL genes were identified and grouped into three clades. Two members, Ge4CL2 and Ge4CL5, were strongly upregulated in tubers challenged with fungal pathogens. Ge4CL2 localised to the nucleus, whereas Ge4CL5 localised to both the nucleus and the cytoplasm. Codon usage analysis suggested that Escherichia coli and Oryza sativa are suitable heterologous hosts for Ge4CL expression. This study provides the first genome-wide catalogue of 4CL genes in G. elata and suggests that Ge4CL2 and Ge4CL5 may participate in antifungal defence, although functional confirmation is still required. The dataset furnishes a foundation for functional characterisation and the molecular breeding of disease-resistant G. elata cultivars. Full article

Zinc finger proteins are frequently implicated in a wide range of neurodevelopmental disorders (NDDs). In this study, we report a case of mild intellectual disability (ID), global developmental delay (GDD), and developmental coordination disorder (DCD) in an individual with unaffected parents. Trio-based whole-exome sequencing (WES) identified a de novo variant (c.1530dup, p.Glu511ArgfsTer16) in the ZNF496 gene of the proband. According to ACMG guidelines, this novel variant is classified as pathogenic. It creates a frameshift that introduces a premature stop codon, resulting in a truncated protein of 525 amino acids (compared to the wild-type 587 residues). Notably, NMDEscPredictor analysis predicted that the transcript escapes nonsense-mediated decay (NMD) despite the frameshift. Computational analyses suggest the potential pathogenetic effects of the identified variant. As documented, ZNF496 interacts with JARID2, a gene associated with NDDs, ID and facial dysmorphism (MIM: #620098). In silico analyses suggest that the identified mutation disrupts this interaction by deleting ZNF496’s C2H2 domain, potentially dysregulating JARID2 target genes. To our knowledge, this is the first reported association between ZNF496 and NDDs, and the variant has been submitted to the ClinVar database (SCV006100880). Functional studies are imperative to validate ZNF496’s role in NDDs and confirm the mutation’s impact on ZNF496-JARID2 interactions. Full article

African ground squirrels (Xerus spp.), the inhabitants of African arid zones, face extreme heat and water scarcity driving selection for metabolic optimization. We assembled and annotated the first mitogenomes of Xerus inauris and Xerus rutilus (16,525–16,517 bp), revealing conserved vertebrate architecture with genus-specific traits. Key features include Xerus rutilus’s elongated ATP6 (680 vs. 605 bp), truncated ATP8–ATP6 spacers (4 vs. 43 bp), and tRNA-Pro control regions with 78.1–78.3% AT content. Their nucleotide composition diverged from that of related sciurids, marked by reduced T (25.78–26.9%) and extreme GC skew (−0.361 to −0.376). Codon usage showed strong Arg-CGA bias (RSCU = 3.78–3.88) and species-specific elevations in Xerus rutilus’s UGC-Cys (RSCU = 1.83 vs. 1.17). Phylogenetics positioned Xerus as sister to Ratufa bicolor (Bayesian PP = 0.928; ML = 1.0), aligning with African biogeographic isolation. Critically, we identified significant signatures of positive selection in key mitochondrial genes linked to arid adaptation. Positive selection signals in ND4 (ω = 1.8 × background), ND1, and ATP6 (p < 0.0033) correspond to enhanced proton gradient efficiency and ATP synthesis–molecular adaptations likely crucial for optimizing energy metabolism under chronic water scarcity and thermoregulatory stress in desert environments. Distinct evolutionary rates were observed across mitochondrial genes and complexes: Genes encoding Complex I subunits (ND2, ND6) and Complex III (Cytb) exhibited accelerated evolution in arid-adapted lineages, while genes encoding Complex IV subunits (COXI) and Complex V (ATP8) remained highly conserved. These findings resolve the Xerus mitogenomic diversity, demonstrating adaptive plasticity balancing arid-energy optimization and historical diversification while filling critical genomic gaps for this xeric-adapted lineage. Full article