Search Results (189)

Plant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of Trichopus zeylanicus, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Illumina short-read and PacBio long-read sequencing technologies, followed by extensive annotation and comparative analysis. The circular mitogenome spans 709,127 bp with a GC content of 46%, encoding 32 protein-coding genes, 17 tRNAs, and three rRNAs. Comparative analysis with other monocot mitochondrial genomes revealed conserved gene clusters but also significant lineage-specific rearrangements. Despite genome size similarities, T. zeylanicus displayed marked divergence in gene order, suggesting that genome size does not necessarily correlate with structural conservation. The genome contains 6.7% chloroplast-derived sequences and 324 predicted RNA-editing sites, predominantly in the first and second codon positions. Phylogenetic analysis based on mitochondrial genes placed T. zeylanicus as a distinct lineage within Dioscoreales, supporting its evolutionary uniqueness. This work provides the first mitogenomic resource for Dioscoreales and advances our understanding of mitochondrial diversity and evolution in monocots. Full article

Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first complete assembly and comprehensive analysis of the P. ludlowii mitochondrial genome. Most remarkably, we discovered that the P. ludlowii mitogenome exhibits an atypical dual-circular structure, representing the first documented occurrence of this architectural feature within the genus Paeonia. The assembled genome spans 314,371 bp and encodes 42 tRNA genes, 3 rRNA genes, and 31 protein-coding genes, with a pronounced adenine–thymine bias. This multipartite genome structure is characterized by abundant repetitive elements (112 functionally annotated SSRs, 33 tandem repeats, and 945 dispersed repeats), which potentially drive genome rearrangements and facilitate adaptive evolution. Analyses of codon usage bias and nucleotide diversity revealed highly conserved gene expression regulation with limited variability. Phylogenetic reconstruction confirms that P. ludlowii, P. suffruticosa, and P. lactiflora form a monophyletic clade, reflecting close evolutionary relationships, while extensive syntenic collinearity with other Paeonia species underscores mitochondrial genome conservation at the genus level. Extensive inter-organellar gene transfer events, particularly from chloroplast to mitochondrion, suggest that such DNA exchanges enhance genetic diversity and promote environmental adaptation. The discovery of the dual-circular architecture provides novel insights into plant mitochondrial genome evolution and structural plasticity. This study elucidates the unique structural characteristics of the P. ludlowii mitochondrial genome and establishes a crucial genetic foundation for developing targeted conservation strategies and facilitating molecular-assisted breeding programs for this endangered species. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article

Background:Ants are among the most widely distributed eusocial insects, and desert ants, in particular, serve as important model organisms for studying animal navigation. Methods: In this study, we provide high-quality de novo transcriptomes for eight ant species: Cataglyphis aenescens (Nylander, 1849), Formica approximans Wheeler, 1933, Lasius coloratus Santschi, 1937, Proformica mongolica (Emery, 1901), Proformica muusensis Zhu, Wu, Duan & Xu, 2022, Tapinoma geei Wheeler, 1927, Tapinoma rectinotum Wheeler, 1927, and Tetramorium tsushimae Emery, 1925. Results: The GC content of coding sequences (CDSs) ranged from 43.61% to 46.20%, indicating a slightly AT-rich composition. Codon usage analysis identified 27 to 33 optimal codons per species, the majority of which ended with A or U. Conclusions: These transcriptomic resources provide critical insights into codon usage bias and establish a foundation for future research on molecular evolution, gene regulation, and environmental adaptation in ants inhabiting fragile desert ecosystems. Full article

Background: Siphonaria is a genus of false limpets belonging to the Gastropoda class. Only two species of this genus have been described with mitochondrial genomes. Moreover, the codon usage patterns and factors influencing them have not been studied. This study aims to expand the mitochondrial genome data of this genus and clarify the codon usage patterns. Methods: The complete mitochondrial genome of Siphonaria japonica was sequenced using next-generation sequencing. The gene arrangement and phylogenetic status were compared with Siphonaria gigas and Siphonaria pectinata. The codon usage bias of the three mitochondrial genomes was analyzed based on the relative synonymous codon usage (RSCU), the effective number of codons (ENC) plot, the parity rule 2 (PR2)-bias plot, and neutrality plot analyses. Results: The gene arrangement and maximum-likelihood phylogenetic tree support a close relationship between S. japonica and S. pectinata. The codon usage bias analysis indicated that the codon usage bias of mitochondrial PCGs in the three species was primarily influenced by natural selection. Conclusions: This study offers significant evolutionary insights into the phylogenetic relationships and molecular adaptation strategies among Siphonaria species. Full article

This study presents the first complete mitochondrial genome characterization of Elops machnata (Teleostei: Elopiformes: Elopidae), a basal teleost lineage critical for understanding early actinopterygian evolution. The assembled mitogenome, deposited under GenBank accession number PV294982, spans 16,712 bp and exhibits the canonical vertebrate mitochondrial gene organization, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Base composition analysis revealed 22.71% A, 17.36% C, 29.82% T, and 30.11% G, with a slight AT bias (A + T = 52.53%). Codon usage analysis of the 13 protein-coding genes identified CUA (L), CGA (R), GCC (A), and GGA (G) as the most frequent codons, with a pronounced preference for adenine at the third codon position. Amino acid composition analysis across 23 Elopomorpha species revealed consistently high leucine contents, and tRNA secondary structure prediction showed 21 tRNAs forming typical cloverleaf structures, except for trnS1(gct), which lacks the dihydrouridine (DHU) arm. Phylogenetic reconstruction using maximum likelihood and Bayesian inference methods, based on concatenated mitochondrial protein-coding genes from 23 Elopomorpha species, placed E. machnata in a well-supported clade with Elops hawaiensis, confirming their close evolutionary relationship. This study not only provides essential genomic resources for E. machnata but also resolves key gaps in the mitochondrial genome and improves phylogenetic understanding of Elopomorpha. Full article

Tomato spotted wilt virus (TSWV), belonging to the genus Orthotospovirus, is a significant pathogen through its infection of economically vital crops including tomato, tobacco, pepper, and other species worldwide. Given its substantial influence on the agricultural industry, in-depth research on TSWV is of great necessity. Several studies have been conducted on the dinucleotide preference of TSWV previously; however, the information regarding codon usage bias (CUB) and the virus’s adaptive evolution remains inconclusive. Here, a thorough analysis of TSWV was performed by utilizing five protein-coding sequences in order to investigate the characteristics of CUB. It has been observed that the TSWV protein-coding sequences are AU-rich, and codons ending with A or U are also preferred in these sequences. A consistently stable and preserved genomic composition characterized by a lower codon usage preference was also observed. Principal Component Analysis (PCA), neutrality analysis, and ENC-plot indicated that, in comparison to mutational pressure, natural selection has a more dominant influence on the CUB of TSWV. The codon adaptation index (CAI) demonstrated a more significant correlation between TSWV and Nicotiana tabacum. Meanwhile, the relative codon deoptimization index (RCDI) indicated a stronger correlation between TSWV and Solanum lycopersicum. This study is the first to systematically characterize the CUB of TSWV based on its protein-coding sequences, providing critical insights into viral genetic diversity, evolution mechanisms, and host adaptation. The findings advance understanding of plant-virus coevolution and inform virus-resistant crop breeding and antiviral strategies. Full article

Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ^UUG, psbB-psbT, trnT^UGU-trnL^UAA, trnF^GAA-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article

Objectives: Codon usage bias is a fundamental feature of gene expression that can influence evolutionary processes and genetic diversity. This study aimed to investigate the mitochondrial codon usage characteristics and their driving forces in three Medicago species: Medicago polymorpha, Medicago sativa, and Medicago truncatula. Methods: The complete mitochondrial genome sequences of the three species were downloaded from GenBank, and 21 shared coding sequences were screened. Codon usage patterns were analyzed using CodonW 1.4.2 and CUSP software. Key parameters, including the relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (Fop), were calculated. Phylogenetic trees and RSCU clustering maps were constructed to explore evolutionary relationships. Results: The GC contents of the mitochondrial genomes followed the order of GC1 > GC2 > GC3. ENC values averaged above 35, while CAI, CBI, and Fop values ranged from 0.160 to 0.161, −0.078 to −0.076, and 0.362 to 0.363, respectively, indicating a weak preference for codons ending with A/U. Correlation and neutrality analyses suggested that codon usage bias was influenced by both mutation pressure and natural selection, with natural selection being the dominant factor. Fifteen optimal codons, predominantly ending with A/U, were identified. Phylogenetic analysis confirmed the close relationship among the three Medicago species, consistent with traditional taxonomy, whereas the RSCU clustering did not align with the phylogenetic relationships. Conclusions: This study provides insights into the mitochondrial codon usage patterns and their evolutionary determinants in Medicago species, highlighting the predominant role of natural selection in shaping codon usage bias. The findings offer a foundation for comparative genomic studies and evolutionary analyses and may be beneficial for improving genetic engineering and breeding programs of Medicago species. Full article

Background: Ulva is a globally distributed genus with ecological and economic significance, yet the codon usage bias of the Ulva chloroplast genome remains poorly understood. Methods: We assessed the Ulva chloroplast genome codon usage patterns and their drivers by analyzing 30 genomes across 16 Ulva species. Results: The nucleotide composition analysis demonstrated that Ulva chloroplast genomes are rich in A/T, and prefer to use codons that ended with A/T. The relative synonymous codon usage analysis suggested that related species have similar codon usage patterns. A total of 25 high-frequency codons and 7–14 optimal codons were identified in these chloroplast genomes. The ENC values ranged from 31.40 to 32.76, all of which are less than 35, illustrating a strong codon bias of the Ulva genus. Our comparative analyses suggested that natural selection played the main role in the formation of the codon usage bias. Furthermore, the correlation analysis indicated that an influence of the base composition and gene expression levels on the codon usage bias. Conclusions: This study provides the first comprehensive analysis of the codon usage patterns in Ulva chloroplast genomes, improving our understanding of the genetics and evolution of these economically and ecologically important macroalgae. Full article

Although Cervus elaphus (Linnaeus, 1758) has been well studied, the subspecific taxonomy of Cervus canadensis populations in Qinghai and Gansu, China, is still controversial, and the mitochondrial characteristics of Cervus elaphus (Linnaeus, 1758) remain incompletely understood. We assembled 89 mitogenomes of C. canadensis from five geographical populations across Qinghai and Gansu. Phylogenetic analysis confirmed that the 89 individuals are taxonomically classified as C. c. kansuensis. Nucleotide compositions showed a higher abundance of adenine and cytosine compared to guanine and thymine in both complete mitogenomes and mitochondrial PCGs. Codon usage analysis revealed a strong preference towards A-ending codons (68.04% of over-represented codons, RSCU > 1.6) in mitochondrial PCGs, with systemic avoidance of G-ending codons (53.30% of unused codons, RSCU = 0). The CAMs of 13 PCGs are reported for the first time. Furthermore, the ENC plot showed that the codon usage of all PCGs was biased except for gene ATP8. The PR2 bias plot showed that gene ND6 exhibited bias towards T3 and G3, whereas the other genes preferred A3 and C3. Both the ENC-plot and PR2 bias plot suggested that natural selection played an important role in the forces driving codon usage bias in mitochondrial PCGs. Our results demonstrate the subspecific status of C. canadensis distributed in Qinghai and Gansu as C. c. kansuensis, and provide insights into the mitochondrial characteristics of C. c. kansuensis. The mitogenome sequences assembled in this study provide valuable data for further understanding of the Cervus elaphus (Linnaeus, 1758) mitogenome. Full article

This study reports the first complete mitochondrial genomes of three egg parasitoid wasps parasitizing Nilaparvata lugens—Pseudoligosita nephotetticum, Anagrus frequens, and Anagrus nilaparvatae. Genome sizes ranged from 15,429 to 15,889 bp, with all three mitogenomes displaying strong A + T bias, standard gene content, and characteristic strand asymmetries. While A. frequens and A. nilaparvatae exhibited conserved gene orders, extensive gene rearrangements, including multiple inversions in both protein-coding genes (PCGs) and tRNAs, were observed in P. nephotetticum. Codon usage analyses revealed a preference for codons ending in A or U. The non-synonymous (Ka) to synonymous (Ks) substitution ratio analysis identified signs of positive selection in multiple PCGs, particularly in atp8, nad6, and nad3, suggesting possible adaptive evolution related to host-searching behavior. Secondary structure analyses showed the loss of trnL1 in all Anagrus species, while trnS1 and trnR lacked the DHU arm, indicating possible derived traits in Mymaridae. Phylogenetic analysis was the first time to describe the relationship of the genus Anagrus within Mymaridae from the perspective of 13 protein genes. Furthermore, the grouping of (Pseudoligosita + Megaphragma) + Trichogramma was supporting the distinct evolutionary lineage of Pseudoligosita. This work provides new molecular resources and phylogenetic insight for Chalcidoidea, with implications for parasitoid evolution and biological control strategies. Full article

With increasing demand for stingless bee honey, meliponiculture has gained widespread attention. Heterotrigona itama is one of the most economically important species. However, excessive exploitation for commercial purposes has led to population declines, and the species is now considered vulnerable in Thailand. Despite its ecological and economic significance, genomic and taxonomic information on H. itama remains limited. In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of H. itama to explore its genome structure and phylogenetic position. The circular mitogenome is 15,318 bp in length and consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The genome exhibits a strong A+T bias (75.41%), which affects codon usage and amino acid composition. Isoleucine, methionine, and phenylalanine were the most commonly encoded amino acids. Gene arrangement was highly conserved and closely resembled that of Tetragonula species. Phylogenetic analyses confirmed that H. itama clusters with other stingless bees and is more closely related to bumblebees than to honeybees. Several gene rearrangements suggest a high degree of mitogenomic plasticity. This study provides essential genomic resources for future studies in systematics, phylogenetics, population genetics, and conservation of stingless bees in the Meliponini tribe. Full article

The non-random usage of synonymous codons encoding the same amino acid—referred to as codon usage bias (CUB)—varies substantially across genomes and significantly affects translational efficiency by modulating transcriptional and post-transcriptional processes. In chloroplast genomes, the optimization of CUB is critical for improving the efficacy of genetic engineering approaches. However, comprehensive analyses of CUB in Fagopyrum chloroplast genomes remain scarce. In this study, we performed an in-depth comparative analysis of codon usage patterns in the chloroplast genomes of nine Fagopyrum species. Our results revealed a marked AT-rich nucleotide composition, with base content in the order T > A > C > G. We identified 23 optimal codons and 29 high-frequency codons, most of which ended with A or U. Correlation analyses demonstrated that codon usage is strongly influenced by nucleotide skewness (GC and AT skews), protein properties (such as amino acid composition and the number of synonymous codons), and gene expression levels. Neutrality plot analysis (PR2 bias) and evaluations based on the effective number of codons (ENc) indicated that both mutational pressure and natural selection contribute to shaping CUB, with natural selection identified as the predominant evolutionary force. Comparative analyses with four model organisms indicated that Arabidopsis thaliana shares the highest codon usage compatibility with Fagopyrum chloroplast genomes, highlighting its suitability as a potential heterologous expression system. Phylogenetic reconstruction based on codon usage profiles yielded a fully resolved topology with 100% bootstrap support at all nodes, reinforcing the utility of codon usage data in evolutionary inference. This study elucidates the evolutionary determinants of codon usage variation in Fagopyrum plastomes and provides a robust methodological foundation for codon optimization in chloroplast-based synthetic biology. The validated codon adaptation metrics offer promising tools for improving heterologous protein expression and guiding transgene design in advanced breeding strategies. Full article