Search Results (214)

Chloroplast codon usage bias (CUB) records both maternal phylogeny and selection intensity. Characterizing CUB in the synthetic cereal × Triticosecale and its Triticum and Secale parents is therefore a prerequisite for plastid-based engineering and for tracing the evolutionary consequences of recent allopolyploidy. Complete plastome sequences of five taxa—Triticum monococcum, T. turgidum, T. aestivum, Secale cereale and × Triticosecale sp.—were downloaded. Protein-coding genes were extracted to calculate overall GC, GC1–GC3, SCUO, RSCU, ENC-GC3s, neutrality, and PR2 plots. Optimal codons were defined as RSCU ≥ 1 and △RSCU ≥ 0.8. The results showed that the chloroplast genomes of these five species are low in GC content for the third base of codons, suggesting an end preference for A or U bases. The SCUO values ranged from 0.22 to 0.23, suggesting no significant codon usage bias. GC content was relatively low (38.78–39.16%), with the order GC1 > GC2 > GC3. RSCU analysis indicated that codons ending with A/T are more commonly used. Neutral mapping, ENC-GC3s, and the PR2 plot all showed that the preference of codon usage for the majority of functional genes was influenced by a combination of mutation and natural selection pressure, and the influence of natural selection was predominant. RSCU clustering recovers the expected maternal tree (Triticum clade + triticale). All optimal codons terminate with A or U, yielding identical plastid translation tables for the five species. Despite its recent hybrid origin, triticale plastid CUB is indistinguishable from its wheat maternal ancestor and is governed mainly by selection. The compiled optimal codon set provides an immediate reference for chloroplast transformation and for dissecting selection relaxation in newly synthesized triticale combinations. Full article

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

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development. Full article

The plant Actinostemma tenerum is endemic to East Asia and has been used as a traditional medicinal herb for over 1400 years. Investigating the chloroplast genome characteristics and codon usage bias (CUB) is essential for advancing research on molecular markers and genetic diversity in A. tenerum. In this study, we sequenced the complete chloroplast genome of A. tenerum, revealing a length of 160,579 bp, with a GC content of 36.5%. The genome comprised 132 coding genes, including 87 protein-coding genes (CDSs), 8 rRNA genes, and 37 tRNA genes. Analysis of the 51 selected CDSs showed average GC1, GC2, and GC3 values of 46.95%, 39.52%, and 28.11%, respectively. The effective number of codons (ENC) ranged from 35.34% to 56.23%, with an average of 45.57%, indicating a weak CUB. Nucleotide composition analysis revealed unequal distribution of A, T, C, and G, with codon preference biased towards A or U. Neutrality plots, ENC-plots, and PR2-bias plots indicated that natural selection predominantly influences on CUB. A total of 18 optimal codons were identified. This study contributes genetic insights into A. tenerum and enhances our understanding of codon usage patterns in plant chloroplast genomes. 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

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

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

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

To better understand the mitochondrial genome evolution within the genus Pedicularis, we investigated two representative species, Pedicularis kansuensis and Pedicularis chinensis. We sequenced and assembled the mitochondrial genomes of two Pedicularis species, P. kansuensis and P. chinensis, using Nanopore technology. Both genomes showed irregular morphological characteristics, with P. chinensis measuring 225,612 bp and P. kansuensis 273,598 bp, and GC (guanine and cytosine) contents of 44.42% and 44.29%, respectively. Each genome encodes 36 unique protein-coding genes, 3 rRNA genes, and varying numbers of tRNA genes (P. chinensis: 20; P. kansuensis: 19). Codon usage analysis revealed distinct preferences, while repeat sequence analysis identified significant differences in SSRs, tandem repeats, and dispersed repeats between the two genomes. Structural analyses highlighted genome recombination facilitated by repeat sequences. Phylogenetic analysis confirmed the placement of Pedicularis within Orobanchaceae, clustering P. kansuensis and P. chinensis with Castilleja paramensis and other genera in the family, thus resolving longstanding taxonomic uncertainties regarding their relationship with Scrophulariaceae. RNA editing events were predominantly C-to-U, ccmB and nad4 exhibiting the highest editing frequencies. Synteny analysis revealed frequent rearrangements, underscoring the dynamic evolution of Pedicularis mitochondrial genomes. These findings provide valuable insights into the structure, function, and evolution of mitochondrial genomes in parasitic plants. Full article

The genus Manglietia Blume is an important group of Magnoliaceae that has high economic and ornamental value. Owing to the small morphological differences among most Manglietia species and the limited sample sizes in previous molecular-level studies, its infrageneric classification remains unclear, and interspecific relationships for some species are still contentious. Clarifying the phylogenetic relationships within the genus Manglietia is crucial for species classification, genetic diversity assessment, and evolutionary developmental studies. This study sequenced, assembled, and annotated the chloroplast (cp) genomes of Manglietia guangnanica, Manglietia hookeri, and Manglietia longirostrata. The results indicated that these cp genomes are canonical quadripartite structures with total lengths of 160,067 bp, 160,067 bp, and 160,076 bp, respectively. All three cp genomes were annotated with 133 genes, comprising 88 protein-coding genes, 37 tRNAs, and 8 rRNAs. A total of 31, 30, and 30 dispersed repeats and 53, 53, and 56 SSRs were detected, respectively. ENC plot, neutrality plot, and PR2 plot analyses indicated that codon usage bias was influenced primarily by natural selection. Nucleotide diversity analysis revealed 8 highly variable regions in the cp genomes, among which petA-psbJ, rpl32-trnL, and ccsA-ndhD are recommended as candidate molecular markers for Manglietia species. Phylogenetic analysis revealed four highly supported clades: Clade I (18 species), Clade II (M. decidua only), Clade III (9 species), and Clade IV (M. caveana only). Among these clades, Clade IV is a newly discovered monotypic clade in this study, which differs from the results of all previous studies. Further investigations of Clades I and III, which include multiple Manglietia species, revealed that the presence or absence of hairs on Twigs, Stipules, and the abaxial surface of the leaf are important morphological characteristics for distinguishing species between these two clades. Furthermore, the results revealed that M. guangnanica and M. calcarea are two distinct species, and the treatment of M. longirostrata as a variety of M. hookeri was not supported by our study. This study enriches the cp genome data of Manglietia, provides new insights into infrageneric classification, and lays a foundation for further phylogenetic and evolutionary studies of Manglietia. Full article

Chloroplast genomes are valuable tools for exploring plant evolution, photosynthesis, and molecular systematics due to their relatively conserved structure and gene content. Here, I present a comprehensive comparative analysis of complete chloroplast genomes from 20 taxonomically diverse plant species, focusing on 16 widely used barcoding genes to investigate patterns of genome structure, gene retention, codon usage bias, and phylogenetic relationships. Genome sizes ranged from ~121 kb in Marchantia polymorpha to over 160 kb in Vitis vinifera, with GC content largely conserved across species. A multi-gene Neighbor-Joining phylogenetic framework recovered major taxonomic groupings and revealed gene-specific topological differences, reflecting locus-specific evolutionary histories. Presence/absence profiling showed that 13 of the 16 barcoding genes were consistently retained across species and classified as core genes, while the remaining three exhibited more variable distributions and were considered accessory. This pattern reflects both broad conservation and lineage-specific gene loss across plastomes. Genome-wide similarity analysis revealed high identity among closely related taxa (e.g., Arabidopsis and Brassica) and greater divergence among bryophytes, gymnosperms, and angiosperms. Codon usage analysis revealed generally conserved patterns, with lineage-specific biases observed in Cucumis sativus and Brassica rapa, suggesting influences from mutational pressure and potential translational selection. This integrative analysis highlights the dynamic yet conserved nature of chloroplast genomes and underscores the value of combining multiple genomic features in plastome evolution studies. The resulting dataset and analytical pipeline offer a useful resource for future phylogenomic, evolutionary, and biodiversity research in plant science. Full article

Synonymous codon usage (codon bias) greatly influences not only translation but also mRNA stability. In vertebrates, highly expressed genes preferentially use codons with an optimal tRNA adaptation index (tAI) that mostly end in C or G. Surprisingly, the codon usage of viruses infecting humans often deviates from optimality, showing an enrichment in A/U-ending codons, which are generally associated with slow decoding and reduced mRNA stability. This observation is particularly evident in RNA viruses causing respiratory illnesses in humans. This review analyzes the mutational and selective forces that shape nucleotide composition and codon usage drift in human RNA viruses, as well as their impact on translation, viral fitness, and evolution. It also describes how some viruses overcome suboptimal codon usage to outcompete host mRNA for translation. Finally, the roles of viral tropism and host adaptation in codon usage bias of prototypical viruses are discussed. 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: Collabieae is a medium-sized group within the orchid subfamily Epidendroideae that is distributed primarily across tropical Asia. Most Collabieae species are known for their considerable ornamental and medicinal merits. However, habitat destruction and overharvesting have led to severe decline in their wild populations. Chloroplast (cp) genomes are highly valued in evolutionary studies, due to comparative conservation and accumulation of genomic variations. Elucidating the structure of chloroplast genome is instrumental in conserving genetic diversity within the Collabieae. Methods: we explored the chloroplast genome characteristics of Collabieae. We incorporated three newly sequenced genomes from species (Acanthophippium sylhetense, Eriodes barbata, and Spathoglottis plicata), along with seven related species. Results: all analyzed cp genomes displayed a typical quadripartite circular structure. The total lengths ranged from 157,036 bp to 158,321 bp. Each genome contained 136 genes: 88 protein-coding genes, 38 tRNA genes, eight rRNA genes, and two pseudogenes. Across the ten Collabieae species, gene number, order, orientation, GC content, and codon usage bias were highly consistent, indicative of strong sequence conservation. However, notable structural divergence was observed at the plastome junctions, alongside variations in SSR and repetitive element frequencies. Moreover, six hypervariable regions were identified. Noncoding regions exhibited higher variability compared to protein-coding regions. Phylogenetic analysis indicated that E. barbata forms a distinct, small branch sister to the rest of the Collabieae members. Genera Acanthophippium and Spathoglottis were sister to the remaining groups within the tribe. Conclusions: this overall phylogenetic framework aligns well with previous findings. Our study provides valuable cp genomic resources and advances evolutionary research in Collabieae. Full article