Search Results (72)

Background/Objectives: Scutiger ningshanensis (Fang, 1985) is an endemic Chinese amphibian species within the genus Scutiger (Megophryidae). Despite its ecological significance, its mitochondrial genome architecture and evolutionary relationships remain poorly understood. Given the high structural variability in Megophryidae mitogenomes and unresolved phylogenetic patterns in Scutiger, this study aims to (1) characterize the complete mitogenome of S. ningshanensis, (2) analyze its molecular evolution, and (3) clarify its phylogenetic position and divergence history within Megophryidae. Methods: The complete mitochondrial genome was sequenced and annotated, followed by analyses of nucleotide composition, codon usage bias, and selection pressures (Ka/Ks ratios). Secondary structures of rRNAs and tRNAs were predicted, and phylogenetic relationships were reconstructed using maximum likelihood and Bayesian methods. Divergence times were estimated using molecular clock analysis. Results: The mitogenome of S. ningshanensis is 17,282 bp long, encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region, with a notable AT bias (61.05%) with nucleotide compositions of T (32.51%), C (24.64%), G (14.3%), and A (28.54%). All tRNAs exhibited cloverleaf structures except trnS1, which lacked a DHU stem. Phylogenetic analysis confirmed the monophyly of Scutiger, forming a sister clade to Oreolalax and Leptobrachium, and that S. ningshanensis and S. liubanensis are sister species with a close evolutionary relationship. Positive selection was detected in Atp8 (Ka/Ks > 1), suggesting adaptation to plateau environments, while other PCGs underwent purifying selection (Ka/Ks < 1). Divergence time estimation placed the origin of Megophryidae at~47.97 MYA (Eocene), with S. ningshanensis diverging~32.67 MYA (Oligocene). Conclusions: This study provides the first comprehensive mitogenomic characterization of S. ningshanensis, revealing its evolutionary adaptations and phylogenetic placement. The findings enhance our understanding of Megophryidae’s diversification and offer a genomic foundation for future taxonomic and conservation studies. Full article

Chionea is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of Chionea (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed by integrating these sequences with 30 additional Tipuloidea mitogenomes retrieved from NCBI. Unlike other Tipuloidea species, which are predominantly distributed in relatively warmer regions, this research investigates whether positive selection has acted on the mitogenomes of these three Chionea species due to environmental pressures, thereby elucidating key evolutionary drivers for Chionea. The three mitogenomes of Chionea exhibit characteristic features typical of insect mitogenomes, comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA genes (tRNA), and a single non-coding control region (D-loop). Notably, the secondary structure of trnS1 lacks the DHU arm in all three samples, and UUA (Leu) emerges as the most frequently utilized codon. Furthermore, the COX2 and ND5 genes utilize incomplete stop codons “T”. Utilizing these 13 PCGs, we reconstructed the internal phylogenetic relationships within Tipuloidea, revealing that Chionea tianhuashana and C. sphaerae form sister branches, while (C. tianhuashana + C. sphaerae) constitutes a sister branch to C. crassipes. Moreover, our analysis confirms the monophyly of Tipulidae, Tipula, and Nephrotoma as well as the polyphyly of Tipulinae, Chioneinae, and Limoniidae. In the branch site model analysis, three positively selected sites were detected when Chionea was designated as the foreground branches: COX3 (at position 242), ND5 (at position 535), and ND6 (at position 138). 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

In this study, we sequenced and characterized the complete mitochondrial genome of Acorssocheilus spinifer, an endemic stream-dwelling cyprinid species from South China first described in 2006. The mitogenome is 16,591 bp in length and contains the standard set of 37 genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes) plus a control region. The genome exhibits typical cyprinid characteristics, with most genes encoded on the H-strand and a nucleotide composition biased toward A + T (55.9%). All tRNA genes display the typical cloverleaf secondary structure, except for tRNA^Ser (GCU), which lacks the dihydrouridine (DHU) arm. Phylogenetic analysis using complete mitogenomes from 14 Acrossocheilus species revealed that 12 species form a monophyletic assemblage with three distinct clades. Within this framework, A. spinifer clusters closely with A. beijiangensis, supporting previous morphological observations. Our findings provide valuable genetic data for further taxonomic refinement and conservation efforts for Chinese barred species of Cyprinidae. 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

Background: The mitochondrial genome has been used for understanding higher-level phylogenetic relationships within Coccomorpha. we sequenced and analyzed the first mitochondrial genome of Xylococcus castanopsis Wu & Huang, 2017 to elucidate its genomic features and phylogenetic position. Methods: The complete mitogenome was assembled using NOVOPlasty and annotated with MITOS. We analyzed genome organization, codon usage, and tRNA structures. Phylogenetic relationships were reconstructed using 13 protein-coding genes from 19 scale insect species with Bayesian Inference and Maximum Likelihood methods. Result: The mitochondrial genome is 16,363 bp in size and contains the typical 37 mitochondrial genes, with an A + T content of 89.2%. All protein-coding genes start with the ATN and end with TAA/TAG or a single T- residue. Sixteen tRNAs exhibit the typical cloverleaf structure, while the remaining six lack either the dihydrouridine (DHU) or TΨC (T) arm. Gene rearrangements occur only in individual tRNAs and transpositions between the gene clusters trnS2-ND1 and trnL1-rrnL-trnV-rrnS. Phylogenetic analysis consistently place Xylococcidae as a sister group to all scale insects except Matsucoccidae. Conclusions: This study provides the first complete mitogenome for Xylococcidae, revealing characteristic gene rearrangements. Phylogenetic reconstruction resolves the phylogenetic position of Xylococcidae as a distinct lineage sister to all scale insects except Matsucoccidae, providing critical evolutionary insights. Full article

Background/Aims: Ledrinae comprises about 460 described species across five tribes and represents an early-branching, morphologically distinctive lineage of leafhoppers, yet its intra-subfamilial relationships remain ambiguous owing to limited mitogenomic sampling. Here, we sequence and annotate the complete mitochondrial genome of Petalocephala arcuata—only the 18th Ledrinae mitogenome—to broaden taxon coverage within the genus and furnish critical molecular data for rigorously testing Ledrinae monophyly and refining tribal and genus level phylogenetic hypotheses. Methods: In this study, we sequenced and annotated the complete mitochondrial genome of P. arcuata via Illumina sequencing and de novo assembly, and reconstructed the phylogeny of 62 Cicadellidae species using maximum likelihood and Bayesian inference methods. Results: The 14,491 bp circular mitogenome of P. arcuata contains 37 genes with 77.4% A+T. All PCGs use ATN start codons except ND5 (TTG), and codon usage is A or U biased. Of 22 tRNAs, only trnS1 lacks a DHU arm, while the others adopt the canonical cloverleaf structure. Bayesian inference and maximum likelihood analyses produced broadly congruent topologies with mostly high nodal support, recovering Ledrinae as monophyletic and clustering all Petalocephala species into a well-supported clade. Conclusions: In this study, we enriched the molecular resources for the genus Petalocephala by sequencing, annotating, and analyzing the complete mitochondrial genome of P. arcuata. Phylogenetic reconstructions based on these genomic data align closely with previous morphological diagnoses, further confirming the monophyly of the genus Petalocephala. Full article

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene–Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies. Full article

Satyrinae, one of the most species-rich groups within the Nymphalidae family, has traditionally relied on morphological characteristics for classification. However, this approach encounters challenges due to issues such as cryptic species and paraphyletic groups. Recent molecular phylogenetic studies have revealed the complex evolutionary history of Satyrinae, leading to the reclassification of the originally polyphyletic Satyrini into multiple independent tribes and confirming the monophyletic status of groups such as Amathusiini. Nevertheless, the phylogenetic relationships and divergence times of certain tribes remain contentious. This study focuses on three species of the Amathusiini tribe (Faunis aerope, Stichophthalma howqua, and Aemona lena), constructing a phylogenetic tree by sequencing the complete mitochondrial genome and integrating 13 protein-coding genes, including COI and ND5. The results indicate that the mitogenome lengths for the three satyrid species are 15,512 bp for Faunis aerope, 13,914 bp for Stichophthalma howqua, and 15,288 bp for Aemona lena. The genetic composition and sequencing of the newly obtained mitogenomes exhibit high conservation and are distinctive to this group of butterflies. Each of the three mitogenomes contains a characteristic collection of 37 genes along with an AT-rich region. Notably, the tRNA genes across these mitogenomes display a conventional cloverleaf configuration; however, the tRNA^Ser stem (AGN) lacks the dihydrouridine (DHU) arm. The three species exhibit varying lengths of AT-rich regions, resulting in differences in their mitochondrial genome sizes. Finally, the phylogenetic analysis supports the relationships among the four tribes of Satyrinae as: (Satyrini + (Amathusiini + Elymniini)) + Melanitini. Full article

The mitochondrial genomes of three species of Elmidae were sequenced. The sizes were 16,309 bp (C. jaechi), 16,291 bp (G. longiusculus), and 15,480 bp (S. punctulata). Each genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). All three mitogenomes show AT bias. Except for trnS1, lacking the dihydrouridine (DHU) arm, all tRNA genes had a typical cloverleaf structure. The codon usage preferences of the three species showed high similarity. The arrangement of the genes in the three mitogenomes was consistent among them but differed from that in the typical mitogenomes of Coleoptera. The Ka/Ks ratio indicated that COX1 and nad4L had a lower evolutionary rate, being relatively conserved genes among 13 PCGs. The phylogenetic analysis revealed that Elmidae belongs to the superfamily Dryopoidea within the suborder Polyphaga and is monophyletic. The results preliminarily indicate that the taxonomic groups at the subfamily, tribe, and genus levels within Elmidae are ambiguous, and further revisions may be required in the future. Full article

Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for the hydrolysis of the phosphodiester bond on the 5′ side of an apurinic/apyrimidinic site during base excision repair. Moreover, in DNA, this enzyme can recognize nucleotides containing such damaged bases as 5,6-dihydro-2′-deoxyuridine (DHU), 2′-deoxyuridine (dU), alpha-2′-deoxyadenosine (αA), and 1,N6-ethenoadenosine (εA). Previously, by pulsed electron–electron double resonance spectroscopy and pre-steady-state kinetic analysis, we have revealed multistep DNA rearrangements during the formation of the catalytic complex. In the present study, the modeling of the eversion trajectory of nucleotides with various damaged bases was performed by directed molecular dynamics simulations. It was found that each damaged base at the beginning of the eversion interacts with protein loop Val196-Arg201, which should be moved to enable further nucleotide eversion. This movement involves a shift in loop Val196-Arg201 away from loop Asn253-Thr257 and requires the disruption of contacts between these loops. The Glu260Ala substitution facilitates the separation of the two loops. Moreover, conformational changes in the Asn253-Thr257 loop should occur in the second half of the lesion eversion trajectory. All these perturbations within the protein globule tend to reduce steric interactions of each damaged base with the protein during the eversion of the nucleotide from DNA and movement to the active site. These perturbations are important determinants of substrate specificity of endonuclease APE1. Full article

Sugarcane thrips, Fulmekiola serrata (Kobus) (Thysanoptera: Thripidae), is a common foliar pest that infests sugarcane and is found throughout tropical and subtropical countries. In this study, we obtained and analyzed the complete mitochondrial genome of F. serrata for the first time and explored the phylogenetic relationships of the higher-order elements of Thysanoptera members at the mitochondrial level. The complete mitochondrial genome of F. serrata is 16,596 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 noncoding control region. A+T accounted for 75% of the total bases in the mitochondrial genome of F. serrata, revealing an obvious AT bias. Among the 13 PCGs, except for nad5, which had a start codon of TTG, the remaining genes had ATNs typical of insects (ATA, ATT, ATC, and ATG); nad1, nad2, nad3, and atp8 had incomplete termination codons of TA or T. The remaining nine PCGs were complete with the termination codon TAA. Of the 22 tRNA secondary structures, all were typical cloverleaf secondary structures except for trnS1, which was missing the DHU arm. Compared with the hypothetical ancestral gene arrangement of arthropods, F. serrata presented extensive gene rearrangement, with 23 translocated genes, 8 inverted genes, and 5 shuffled genes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies: ((Thripidae + (Stenurothripidae + Aeolothripidae)) + Phlaeothripidae), with Thripidae, Aeolothripidae and Phlaeothripidae being monophyletic groups, whereas F. serrata is closely related to Thrips palmi, and the two are sister groups. Full article

Fulgoraria rupestris is a predatory marine gastropod belonging to Neogastropoda and possessing considerable taxonomic significance. However, research on this species remains limited. We acquired the complete mitochondrial genome of F. rupestris through second-generation sequencing and conducted an analysis of its genome structural features. The mitochondrial genome of F. rupestris spans a total length of 16,223 bp and encompasses 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs). Notably, most tRNAs exhibit the typical cloverleaf structure, but there is an absence of the Dihydrouridine (DHU) arm in the trnS1 and trnS2 genes. The A + T content is 68.67%, indicating a pronounced AT bias. Additionally, we conducted a selection pressure analysis on the mitochondrial genomes of four species within Volutidae, revealing that all PCGs are subjected to purifying selection. In comparison to other species within Neogastropoda, F. rupestris shares an identical gene arrangement. Additionally, based on mitochondrial genome sequences of the 13 PCGs from 50 species within Neogastropoda, we constructed a phylogenetic tree. The phylogenetic tree indicates F. rupestris forms a clade with species within the family Volutidae (Cymbium olla, Neptuneopsis gilchristi, and Melo melo). This study serves as a valuable reference for future research on F. rupestris, offering insights for the upcoming phylogenetic and taxonomic classification within Neogastropoda. Furthermore, the findings provide valuable information for the development of genetic resources in this context. Full article

The complete mitochondrial genome has been extensively utilized in studies related to phylogenetics, offering valuable perspectives on evolutionary relationships. The mitochondrial genome of the fine-eyed plateau loach, Triplophysa microphthalma, has not attracted much attention, although this species is endemic to China. In this study, we characterized the mitochondrial genome of T. microphthalma and reassessed the classification status of its genus. The complete mitochondrial genome of T. microphthalma was 16,591 bp and contained thirty-seven genes, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and twenty-two transfer RNA genes (tRNAs). All but one of the thirteen PCGs had the regular start codon ATG; the gene cox1 started with GTG. Six PCGs had incomplete stop codons (T--). These thirteen PCGs are thought to have evolved under purifying selection, and the mitogenome shared a high degree of similarity with the genomes of species within the genus Leptobotia. All tRNA genes exhibited the standard clover-shaped structure, with the exception of the trnS1 gene, which lacked a DHU stem. A phylogenetic analysis indicated that T. microphthalma was more closely related to species within the genus Triplophysa than to those in Barbatula. The present study contributes valuable genomic information for T. microphthalma, and offers new perspectives on the phylogenetic relationships among species of Triplophysa and Barbatula. The findings also provide essential data that can inform the management and conservation strategies for T. microphthalma and other species of Triplophysa and Barbatula. Full article

The mitochondrial genomes of three species of Yangiella were sequenced, annotated, and analyzed. The genome length of the three species of the genus is 15,070–15,202 bp, with a typical gene number, including a control region, 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs). It was found that the mitochondrial genome of Yangiella had AT bias. Except for the lack of a DHU arm of the trnS1 gene, the other tRNAs had a typical cloverleaf structure, and the codon usage preferences of the three species exhibited high similarity. In addition, tRNA gene rearrangements were observed among the three subfamilies of Aradidae (Mezirinae, Calisiinae, Aradinae), and it was found that codon usage preferences appeared to be less affected by base mutation and more by natural selection. The Pi and Ka/Ks values indicated that cox1 was the most conserved gene in the mitochondrial genome of Aradidae, while atp8 and nad6 were rapidly evolved genes. Substitution saturation level analysis showed that the nucleic acid sequence of mitochondrial protein-coding genes in Aradidae did not reach saturation, suggesting the rationality of the phylogenetic analysis data. Bayesian and maximum likelihood methods were used to analyze the phylogeny of 16 species of Hemiptera insects, which supported the monophyly of Aneurinae, Carventinae, and Mezirinae, as well as the monophyly of Yangiella. Based on fossils and previous studies, the differentiation time was inferred, indicating that Yangiella diverged about 57 million years ago. Full article