Search Results (239)

Flemingia philippinensis Merr. et Rolfe (F. philippinensis) is a Chinese herbal medicine rich in polyphenols, especially isoflavone derivatives. It exhibits potent anti-inflammatory properties and is widely used in the treatment of various diseases. In this study, we aim to sequence, assemble, and analyze the mitogenome of F. philippinensis in detail to understand the genetic structure of their organelles and their gene expression. The results showed that the mitogenome of F. philippinensis possesses a circular architecture with a total length of 427,353 bp and a GC content of 44.90%. Annotation results revealed 33 unique protein-coding genes (PCGs), 16 transfer RNA (tRNA), and 3 ribosomal RNA (rRNA) genes in the mitogenome. Furthermore, comparative analysis of mitogenome andchloroplast gemone (cpgemone) sequences identified six mitochondrial plastid sequences (MTPTs), including one partial PCG and five complete tRNA genes. Subsequent collinearity analysis indicated that numerous homologous collinear blocks were detected between F. philippinensis and its closely related species, and have undergone a large number of genomic rearrangements in the F. philippinensis mitogenome. Finally, RNA editing analysis identified 498 C -to- U editing sites, notably enriched in nad4 (44 sites) and ccmB (33 sites). Codon usage bias analysis indicated that leucine (Leu 10.66%) and serine (Ser 9.19%) were the most frequently used amino acids. This study lays a theoretical foundation for further elucidating the structural characteristics and understanding the evolution, classification, and identification of F. philippinensis. Full article

Alveolar macrophages orchestrate phagocytosis and inflammatory programs during respiratory infection. CD2-associated protein (CD2AP) and BTB and CNC homology 2 (BACH2) are immune-related genes involved in cytoskeletal organization/vesicular trafficking and transcriptional regulation, respectively, but the coding-level constraints shaping their synonymous-site architecture remain unclear. Here, we profiled codon usage bias (CUB) of CD2AP and BACH2 across 49 vertebrate species using nucleotide composition, relative synonymous codon usage, and complementary codon bias diagnostics. Across species, BACH2 preferentially used G/C-ending codons with higher GC3s, whereas CD2AP was enriched for A/T-ending codons with lower GC3s. Both genes showed weak-to-moderate CUB (high ENC and modest CAI). ENC–GC3s and PR2 analyses indicated a strong compositional background at third codon positions, while neutrality analysis yielded shallow GC12–GC3 slopes, suggesting overall coding constraints, with compositional effects acting as a background influence and selective constraints possibly contributing to GC1/GC2 patterns. CD2AP deviated more from composition-only expectations than BACH2, suggesting greater gene-specific modulation. Phylogenetic reconstruction placed Sus scrofa within mammalian clades for both genes. In conclusion, CD2AP and BACH2 display opposite third-base codon-ending preferences across vertebrates, with CD2AP favoring A/T-ending codons and BACH2 favoring G/C-ending codons. This provides a comparative baseline for codon usage analyses of macrophage-relevant immune genes. Full article

Iguanodectes geisleri and I. adujai are freshwater fish from South America. Their taxonomic status and phylogenetic relationships are uncertain due to limited molecular data. High-throughput sequencing was applied to obtain and annotate for the first time the complete mitochondrial genomes of I. geisleri and I. adujai to clarify their phylogenetic positions. Mitochondrial genome sequences of 73 Characoidei species were retrieved from GenBank, with Gyrinocheilus aymonieri and Microphysogobio alticorpus designated as outgroups. Phylogenetic trees were constructed using a mitochondrial protein-coding gene dataset and Maximum Likelihood and Bayesian Inference methods. The complete mitochondrial genome measured 16,774 and 16,802 bp, respectively. Both genomes exhibited highly conserved structures. Despite morphological similarities and a close phylogenetic relationship, differences were detected in genomic structure, base composition, codon usage bias, and the control region between the two species. The two species comprise a strongly supported monophyletic clade and are sister species but represent distinct, independent branches. I. geisleri and I. adujai have been recognized as distinct species based on morphological differences, and this study provides molecular confirmation of their separate taxonomic status. The study provides molecular data for the taxonomic identification of fishes of the genus, Iguanodectes, and foundational mitochondrial genomic data for Characiformes. The study advances research on the genetic evolution of this group and resource conservation. Full article

Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome features and evolutionary position are still unclear. This study aims to assemble and characterize its complete chloroplast genome and clarify its phylogenetic placement within Delphinium. Methods: Using Illumina NovaSeq data, we de novo assembled the D. densiflorum plastome, annotated it with CPGAVAS2, and compared it with 12 published Ranunculaceae plastomes. We analyzed IR-boundary dynamics, genome-wide sequence variation, and codon-usage bias and constructed a maximum-likelihood phylogeny based on 69 shared protein-coding genes. Results: The plastome is 154,161 bp (GC 38.24%) with a canonical quadripartite structure, encoding 131 genes (87 CDS, 8 rRNA, 37 tRNA). An IR expansion into the SSC region yields the shortest SSC reported among the compared Delphinium species and produces unique structural variants. Photosynthetic genes are extremely conserved (nucleotide diversity Pi ≤ 0.01), whereas several loci (e.g., ycf1 and psaC) are highly divergent (Pi ≥ 0.05). Codon usage shows a strong bias toward AU-ending triplets. Phylogenetically, D. densiflorum forms a 100%-bootstrap clade with other high-altitude congeners, supporting the non-monophyly of Delphinium. Conclusions: This study delineates the plastome architecture and putative adaptive signatures of D. densiflorum, identifies robust candidate loci for DNA barcoding, and provides molecular evidence for taxonomic revision and conservation strategies in Delphinium. Full article

Ophiocordyceps sinensis, a fungus parasitic on insects, attracts interest due to its unique medicinal applications and complex ecological interactions. The potential relationship between codon usage bias and the parasitic relationship between O. sinensis and Thitarodes xiaojinensis was explored by analyzing the nuclear genomes and mitochondrial genomes of the two. The nuclear genomes showed contrasting preferences: O. sinensis sclerotium exhibited strong GC-ending codon bias (GC3 = 66.13%), while T. xiaojinensis favored AT-ending codons (GC3 = 49.14%). Conversely, both mitochondrial genomes displayed a strong preference (>70% AT) for AT-ending codons. Optimal codon analysis revealed 25 (GC-ending) in O. sinensis and 28 (GC-ending) in T. xiaojinensis nuclear genomes, with overlaps for Leu, Val, Ser, and Pro. The mitochondrial genomes had fewer optimal codons (16 and 13, AT-ending), showing limited overlap (Phe, Leu, Asp, Ser). Neutral plotting analysis, effective number of codons analysis, relative synonymous codon usage analysis, and parity bias analysis showed that the codon usage preferences of the nuclear genomes and mitochondrial genomes of O. sinensis and T. xiaojinensis are jointly affected by selection and mutation pressure. Natural selection predominates in nuclear genomes, while mutation pressure dominates in mitochondrial genomes. This provides new molecular insights into their host–parasite specificity. Full article

Starch biosynthesis is a fundamental process influencing yield and fruit quality in banana, with ADP-glucose pyrophosphorylase (AGPase) serving as the rate-limiting enzyme catalyzing sucrose conversion into starch. However, the mechanisms underlying functional differentiation of AGPase family genes following polyploidization remain largely unexplored. In this study, eight AGPase genes, including large (MaAPL) and small subunit (MaAPS) members, were identified from the banana (Musa acuminata) genome, all harboring the conserved ADP-glucose pyrophosphorylase domain. Phylogenetic analysis traced their evolutionary origin to the ancient moss Physcomitrella patens, with polyploidization identified as the primary driver of gene family expansion. These genes exhibit conserved codon usage bias and have undergone strong purifying selection. Among them, MaAPS1 displayed distinct functional differentiation, increased intron number, enriched promoter cis-elements, and significantly elevated expression—features likely contributing to its adaptation for enhanced starch accumulation in fruit. Furthermore, the MaAPS1 protein was predominately localized in the chloroplast. Functional validation supported its regulatory involvement: transient silencing in banana fruit reduced starch content, while transient overexpression in banana fruit increased starch levels. Co-expression and molecular docking analyses revealed that transcription factors ERF1, C3H1, bZIP1, and bZIP3 may interact with the MaAPS1 promoter, indicating a multifactorial regulatory network. Overall, this study provides insights into polyploidy-driven functional innovation and transcriptional regulation of MaAPS1 in banana starch biosynthesis, providing valuable molecular targets for genetic improvement of yield and fruit quality. Full article

Background: The subtribe Pleurothallidinae is a diverse group within Orchidaceae with a complex taxonomic history. Comparative plastome analysis can provide insights into genome evolution and facilitate phylogenetic reconstruction. Methods: Here we analyzed 25 complete chloroplast genomes representing 15 genera, including 14 newly assembled genomes, to investigate plastome evolution in this subtribe. Results: All genomes exhibited the typical quadripartite structure (148, 246–158, 138 bp) with conserved gene content (128–134 genes). While most protein-coding genes were under purifying selection, we detected signatures of positive selection in specific lineages. Notably, ndhF in Lepanthes tachirensis showed a markedly elevated Ka/Ks ratio (3.65), which may be associated with adaptation to an extensive distributional range. ENC-plot analysis indicated that natural selection, rather than mutation pressure alone, shapes codon usage bias, with patterns varying among species from different geographic regions. Nucleotide diversity analysis identified eight hypervariable intergenic regions (psbK-psbI, atpI-rps2, petN-psbM, psbB-psbT, petD-rpoA, rpoA-rps11, rps3-rpl22, ccsA-ndhD) suitable as candidate molecular markers. Phylogenetic analysis confirmed that Lepanthes and Pleurothallis are non-monophyletic as traditionally defined. Conclusions: These findings expand plastome resources for Pleurothallidinae, reveal lineage-specific patterns of selection, and provide molecular markers for future taxonomic and evolutionary studies. Full article

Background: Hemiboea yongfuensis is a recently discovered critically endangered species. It is exclusive to the limestone regions of Yongfu County, Guilin, Guangxi. Currently, there is a lack of mitogenome data for Hemiboea species, hindering the potential of disclosing the evolutionary processes of the mitochondrial genome, which has been far less assembled and shown to be complex in the plant kingdom. Moreover, it prevents potential applications of mitochondrial genome data in phylogenetics and plant adaption, breeding, and conservation. Results: In order to reveal the mitochondrial features and variations and explore the usefulness of mitochondrial genes in phylogenetics, in this study, we assembled the complete mitogenome of H. yongfuensis using PacBio HiFi long reads, and analyzed its codon usage bias, RNA editing sites, repetitive sequences, sequence lateral transfer, phylogenetic relationships, and synteny. The linear mitochondrial genome assembly we obtained has a length of 619,997 bp and a GC content of 43.63%. The assembly encompasses 61 genes, which include 37 protein-coding genes (PCGs), 21 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Importantly, our analysis uncovered a significant presence of repetitive sequences with a high proportion of forward repeats in the mitogenome and significant transposition of sequences from the chloroplast to mitochondrion. Additionally, we revealed the codon usage characteristics of protein-coding genes and identified numerous RNA editing events. Furthermore, we assessed the collinearity of the species in the Gesneriaceae family and found rampant reorganizations. The phylogenetic analyses based on the mitochondrial PCGs for the entire Lamiales order show the monophyly of Gesneriaceae as well as other families and a general high phylogenetic resolution. Conclusions: Our study provides the first mitogenome data for H. yongfuensis and the genus Hemiboea, expanding the rapidly increasing but yet limited plant mitogenome resources. It enhances our understanding of the mitogenome and Lamiales evolution, whereas more potentials of the mitogenome data, such as its possible functions in adaptation to limestone habitats, conservation, and germplasm breeding, remain under-exploited. This first reported Hemiboea mitogenome in addition to more mitogenomes from the same and related species would shed further light on these unresolved issues in future studies. Full article

Background/Objectives: The Fagopyrum dibotrys complex is a specialized high-altitude lineage in southwestern China with medicinal and breeding potential, but species delimitation remains unresolved. Methods: We sequenced 26 complete chloroplast genomes from the Hengduan Mountains to the Yunnan–Guizhou Plateau, analyzing genomic structures, variation patterns, and phylogenetic relationships. Results: All genomes exhibited typical quadripartite structures (152,213–160,302 bp), containing 133 genes (88 protein-coding, 8 rRNA, and 37 tRNA) with GC content of 37.9%. Collinearity analysis revealed highly conserved structures without structural rearrangements. Variations were concentrated in the large single-copy(LSC)/small single-copy(SSC) non-coding regions, with hotspots at ycf4–cemA and ndhF–rpl32. Codon usage showed an A/U bias, with leucine being most abundant and cysteine the least. Simple sequence repeats (SSRs) were predominantly mononucleotide repeats enriched in the LSC, while long repeats were mainly palindromic/forward. Maximum likelihood and Bayesian phylogenies consistently resolved three clades: Tibetan high-altitude specialists, limestone specialists, and a widespread Hengduan–Yunnan–Guizhou clade, with geographic clustering indicating isolation as the primary differentiation driver. Conclusions: This study refines the phylogenetic resolution of the F. dibotrys complex and identifies informative chloroplast markers, providing a genomic foundation for reliable species delimitation, evolutionary inference, and conservation management of this medicinal lineage. Full article

Cleisthenes herzensteini is a commercially important demersal fish in the Northwest Pacific. However, the resource stock of this species has undergone a drastic decline due to overfishing and habitat degradation. As a representative taxon for benthic adaptation in the order Pleuronectiformes, the molecular mechanisms underlying its specialized phenotypic traits remain poorly elucidated. Furthermore, population-level studies focusing on the mitochondrial genome of Cleisthenes herzensteini are currently scarce. Given that the mitochondrial genome serves as an ideal genetic tool for deciphering species evolution and population genetics, sequencing of its mitogenome will help fill critical gaps in genetic resources and provide essential support for species conservation and phylogenetic research. In this study, we sequenced, assembled, and annotated its complete mitochondrial genome. The circular mitogenome is 17,171 bp in length and exhibits a typical A + T bias (54.04%). Repeat sequence analysis identified 35 dispersed repeats. Codon usage analysis revealed that leucine was the most frequently encoded amino acid, with CUU being the preferred codon. Several protein-coding genes possessed incomplete stop codons (T--/TA-), and a nucleotide preference for A and C was observed at the third codon position. Phylogenetic reconstruction based on mitogenomes from 23 species supported the monophyly of the order Pleuronectiformes. C. herzensteini showed the closest relationship with Dexistes rikuzenius, forming a distinct clade alongside Hippoglossoides dubius and Limanda aspera. These results provide essential genetic resources for understanding the evolution and population genetics of C. herzensteini and related flatfishes. According to the investigation, this study represents the first report on the sequencing and analysis of the complete mitochondrial genome of the Cleisthenes herzensteini. This not only fills the gap in mitochondrial genetic information for this species but also provides a reference for subsequent investigations into the phylogenetic relationships and evolutionary processes within the family Pleuronectidae. Full article

The genus Pseudobagrus represents a group of economically and ecologically significant freshwater bagrid catfishes in East Asia, yet its taxonomy remains contentious. This study employed the complete mitochondrial genomes of 15 Pseudobagrus species to clarify their phylogenetic relationships. The mitogenomes ranged from 16,526 to 16,647 bp, exhibiting a conserved gene order and significant AT bias (average A + T = 57.85%). All genomes contained 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and a control region. Start codons were predominantly ATG, except for COI (GTG), while stop codons varied among TAA, TAG, and incomplete T--. Codon usage bias favored NNU and NNA codons, and 12 optimal codons were identified in P. albomarginatus. The phylogenetic trees based on concatenated PCGs revealed two major clades. Clade I contained 14 species. Within this clade, P. albomarginatus, P. tenuis, and P. brevicorpus clustered together first, and then this trio grouped with P. ussuriensis. Pseudobagrus trilineatus formed the separate Clade II. These results provide a molecular foundation for species delimitation and systematic revision within Pseudobagrus, supporting the monophyly of the genus while highlighting cryptic diversity and taxonomic complexity. Full article

This study investigates the codon usage characteristics of Japanese encephalitis virus (JEV) genotype 5 (G5). Based on 339 complete JEV genome sequences, we systematically compared the codon usage patterns of G5 with other genotypes (G1–G4) using a multi-faceted approach, including evolutionary analysis, nucleotide composition, Relative Synonymous Codon Usage (RSCU), Principal Component Analysis (PCA), Effective Number of Codons Plot analysis (ENC-Plot), Parity Rule 2 analysis (PR2), Neutrality plot analysis, dinucleotide abundance analysis and Codon Adaptation Index analysis (CAI). The results indicate that G5 forms a distinct evolutionary branch, with both its overall GC content (50%) and GC content at the third codon position (GC3, 53%) being lower than those of other genotypes. RSCU analysis revealed a preferential use of A/U-ended codons in G5, indicating a trend towards reduced GC3 usage. ENC analysis demonstrated a stronger codon usage bias in G5 (mean ENC = 54.2). Furthermore, ENC-plot, PR2, and neutrality plot analyses collectively suggested that G5 is subject to stronger natural selection pressure. Analysis of dinucleotide abundance showed a significant increase in CA values in G5, while CAI analysis indicated higher translational efficiency in human hosts compared to Culex mosquito hosts. Our findings suggest that G5 JEV, potentially through reduced Cytosine-phosphate-Guanine (CpG) usage and optimized codon preference, may enhance its capabilities for immune evasion and host adaptation, and could possess the potential for efficient replication in humans or other mammalian hosts. This research provides crucial theoretical insights into the molecular evolutionary mechanisms of G5 JEV and informs related vaccine development. Full article

Background/Objectives: Soroseris hookeriana, a Tibetan medicinal plant endemic to the high-altitude Qinghai–Tibet Plateau, possesses significant pharmacological value but lacks fundamental genomic characterization. This study aims to generate and comparatively analyse its complete chloroplast genome. Methods: Total DNA was sequenced, assembled with GetOrganelle, annotated with CPGAVAS2, and compared with eight Asteraceae species; phylogenetic placement was inferred with IQ-TREE from 21 complete plastomes. Results: The circular chloroplast genome is 152,514 bp with a typical quadripartite structure (LSC 84,168 bp, SSC 18,528 bp, two IRs 24,909 bp each). It contains 132 unique genes (87 protein-coding, 37 tRNA, 8 rRNA; 18 duplicated in IRs yield 150 total copies). Twenty-three genes harbour introns; clpP and ycf3 have two. Overall GC content is 37.73%, elevated in IRs (43.12%). Codon usage shows strong A/U bias at the third position; 172 SSRs and 39 long repeats are detected. IR-SC boundaries exhibit the greatest inter-specific variation, notably in ycf1 and ndhF. Conclusions: The complete plastome robustly supports S. hookeriana and Stebbinsia umbrella as sister species (100% bootstrap) and provides essential genomic resources for species identification, population genetics, and studies of high-altitude adaptation. Full article

Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of O. marmorata from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among Oxyeleotris species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of O. marmorata (from both native and cultured habitats) and Oxyeleotris lineolata mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that Oxyeleotris forms a monophyletic clade and is closely related to Bostrychus sinensis. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 Oxyeleotris species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems. Full article

Tarantulas (family Theraphosidae) are ecologically significant invertebrate predators in terrestrial ecosystems, but many species face threats from habitat fragmentation and unsustainable collection for the international pet trade. Brachypelma albiceps, a CITES Appendix II-listed species, lacks comprehensive mitochondrial genome characterization, limiting phylogenetic and evolutionary studies. Here, we report a complete mitochondrial genome sequence for B. albiceps (13,856 bp; GC content 32.84%) and provide detailed annotation. The genome exhibits typical metazoan mitochondrial organization, containing 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs, with an AT-rich nucleotide composition (67.16%) characteristic of arthropod mitochondria. Comparative analyses of B. albiceps and six other Mygalomorphae species revealed strong biases toward A/T-ending codons and avoidance of G/C-ending codons. ENC–GC3s, neutrality, and PR2 analyses consistently indicate that natural selection plays a dominant role in shaping synonymous codon usage, with mutation pressure also contributing. Phylogenetic reconstruction based on 10 high-quality mitochondrial protein-coding genes from 23 spider species confirmed the placement of B. albiceps within the family Theraphosidae and its close phylogenetic relationship to Cyriopagopus species. These results provide valuable genomic resources for the Theraphosidae systematics, enhance our understanding of codon bias evolution, and provide critical DNA barcode data for forensic identification of CITES-regulated specimens in the illegal wildlife trade. Full article