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At least 19 recordsLinked to original sources
PubMed2026

Assembly and Characterization of the First Complete Mitochondrial Genome of Tussilago farfara L.: Insights into Biological Functions and Phylogenetic Relationships within the Asteraceae Family.

Tussilago farfara L., a member of the Asteraceae family, is an economically valuable species due to its edible and medicinal properties. To elucidate the structural characteristics, genetic mechanisms, and evolutionary pathways of the organelle genomes of T. farfara, we sequenced, assembled, and annotated its mitochondrial genome for the first time. The complete mitochondrial genome of T. farfara spans 306,024 bp and contains 33 mitochondrial protein-coding genes (PCGs), 3 rRNAs, and 22 tRNAs. Analysis of the nucleotide substitution rate and genetic diversity revealed that most mitochondrial genome genes may have undergone purifying selection, indicating a slow evolutionary rate and a relatively conserved genomic structure. We further identified 13 fragments of chloroplast-derived DNA integrated into the mitochondrial genome, evidencing intracellular gene transfer. Collinearity analysis showed that Arctium lappa shares the most extensive mitochondrial homologous sequences and the highest sequence similarity with T. farfara. Phylogenetic analysis based on the mitochondrial genome helped to clarify the evolutionary and taxonomic position of T. farfara within the Asteraceae family. The mitochondrial genome sequence of T. farfara provides a valuable genomic resource for species identification and for evolutionary studies within the Asteraceae family.

Genome, Mitochondrial↗
PubMed2026

The Complete Mitochondrial Genome of a Newly Recorded Chinese Species of Diglyphus sabulosus (Hymenoptera: Eulophidae) and Insights into Its Phylogenetic Position.

Diglyphus Walker, 1844 is an economically important genus which many species acting as biocontrol agents against agromyzid leafminer pests, but there is a lack of mitogenomic data on the evolutionary relationships within this genus, hindering a comprehensive understanding of its evolutionary history. We used traditional morphological methods to identify species, and present the first complete mitochondrial genome sequence and characterization of features of Diglyphus sabulosus and further infer its phylogenetic position based on the amino acid sequences of 13 protein-coding genes (PCGs). The complete mitochondrial genome of D. sabulosus is 15,690 bp in length, including 13 PCGs, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. The AT content of the whole genome sequence was 81.0%, indicating a significant AT bias. All protein-coding genes have the typical ATN as the start codon and TAA as the stop codon. Phylogenetic analysis inferred from the amino acid sequences of 13 PCGs revealed that all species within the family Eulophidae constituted a monophyletic clade, supporting the monophyly of this family. D. sabulosus and D. poppoea form a well-supported sister group, representing the species with the closest phylogenetic relationship within the analyzed taxa. In this study, the mitogenome structure was analyzed and the taxonomic status of D. sabulosus was clarified, thus providing a theoretical basis for understanding the phylogenetic relationships of Diglyphus.

Animals↗
PubMed2025

Complexity of schistosome vector bulinine snails in Kenya: Insights from nuclear genome size variation, complete mitochondrial genome sequence, and morphometric analysis.

Investigations of nuclear genome size, complete mitochondrial genome (mitogenome) sequence, and morphometrics were conducted on specimens of Bulinus snails (Gastropoda: Planorbidae) collected from 14 locations across the east coast, central Kenya, and western Kenya around the Lake Victoria region (November 2013 and January 2024). Flow cytometry measurements of DNA content (C-value) revealed unexpected variation in nuclear genome size, with diploid Bulinus africanus and B. forskalii species groups showing C-values ranging from 0.76 to 1.98 pg, while tetraploid B. truncatus had a C-value of 1.82 pg. Additionally, C-values for six B. globosus specimens from different localities ranged from 1.43 to 1.98 pg. These findings suggest that bulinine snails, particularly the B. africanus species group, have undergone genome expansion, whole genome duplication (polyploidization), or both, which have not been previously recognized. Next-generation sequencing was performed to determine and annotate 14 complete mitogenome sequences. Despite the well-conserved arrangement of protein-coding genes, two versions of mtDNA genome structure, distinguished by the tRNA-D (Asp) location, were found, designated as DCF (Asp-Cys-Phe) type (in the B. forskalii group and the B. truncatus/tropicus complex) and CF (Cys-Phe) type (in the B. africanus group). Phylogenetic analyses based on complete mtDNA sequences of bulinines from Kenya, along with cytochrome c oxidase subunit I (COX1) sequences from various localities across Africa, contributed to resolving species identities and provided further support for the presence of multiple or cryptic species in the taxon B. globosus. A landmark-based morphometric analysis was ineffective in distinguishing these species. This study reveals unexpected nuclear genome size variation, provides new mitogenome sequences, and highlights the limitations of morphological analysis. It offers valuable insights into the cytogenetics, polyploidy, genomics, taxonomy, and evolution of bulinines, which serve as intermediate hosts for schistosomes responsible for human urogenital schistosomiasis and intestinal schistosomiasis in domestic and wild mammals.

Animals↗
PubMed2026

The complete mitochondrial genome of Ramulus bifarius (Phasmida: Phasmatidae; Clitumninae).

We successfully acquired the complete mitochondrial genome information of Ramulus bifarius (S. C. Chen and Y. H. He, p. 476, Phasmatodea of China, 2008), which can be used for subsequent related molecular studies. The mitogenome of R. bifarius exhibits a circular duplex structure, with a total length of 16,915 bp and a high adenine and thymine bias of 76.7%. It contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a single control region.

China↗
PubMed2026

Complete mitochondrial genomic sequence of Lenzites betulinus (Polyporales, Basidiomycota).

Lenzites betulinus is a medicinal fungus in the Polyporaceae. Here, we report the first complete mitochondrial sequencing of this species. The circular genome is 61,288 bp in length, with a GC content of 26.32% and base composition of A (36.98%), T (36.70%), G (12.96%), and C (13.36%). It contains 14 core protein-coding genes (PCGs), 26 tRNA genes, two rRNA genes, and nine intronic ORFs within the cox1 gene. A maximum-likelihood phylogenetic tree based on 14 PCGs from 17 mitochondrial genomes confirmed that L. betulinus clusters within the Polyporaceae, closely related to Trametes and Fomitopsis. This served as a significant reference for ongoing research into other species within the Polyporales order.

Mitochondrial genome↗
PubMed2026

Insights Into the Structural Features, Codon Usage Patterns, and Phylogenetic Analysis in Neoniphon argenteus (Teleostei: Holocentriformes) Based on Complete Mitochondrial Genome.

Neoniphon argenteus, a widely distributed nocturnal coral reef fish in the family Holocentridae, plays an important role in maintaining coral reef ecosystem health, yet its phylogenetic position remains poorly resolved. To bridge this gap, we sequenced and analyzed the complete mitochondrial genome of a specimen from the South China Sea to characterize its structural features, codon usage patterns, and phylogenetic relationships. The 16,569 bp mitogenome (GenBank: PP190474.1) encodes 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions, exhibiting a distinct A + T bias. All tRNAs fold into typical cloverleaf secondary structures except tRNA-Ser (AGN), which lacks the dihydrouridine (DHU) arm. The control region contains palindromic motifs (TACAT/ATGTA) capable of forming hairpin structures and five conserved sequence blocks, whereas the OL region harbors a conserved 5'-GCCGG-3' motif. RSCU analysis revealed 31 frequently used codons (RSCU > 1) with a pronounced preference for A/C-ending codons. The ΔRSCU method identified 10 candidate optimal codons (GCA, CAA, GAA, GGA, AUU, CUA, CCA, CGA, ACA, and GUC). Selection pressure analysis using EasyCodeML and site-specific models indicated that all PCGs are predominantly under purifying selection, with no significant evidence of pervasive positive selection. ND6 exhibited elevated pairwise Ka/Ks ratios (mean = 1.209 ± 0.047), consistent with reduced selective constraint rather than adaptive evolution. Phylogenetic analysis of 19 Holocentriformes species using maximum likelihood and Bayesian inference with partitioned models based on 13 PCGs and two rRNA genes (12S and 16S) assigned all taxa to two well-supported subfamilies (Holocentrinae and Myripristinae). Within Holocentrinae, Neoniphon species form a monophyletic clade nested within a paraphyletic Sargocentron, suggesting that the genus Sargocentron as currently defined is not monophyletic. This study provides useful baseline molecular data for further exploration of the evolutionary history of N. argenteus and other members of Holocentriformes.

Holocentridae↗
PubMed2026

The first two complete mitochondrial genomes for the genus Neotrichoporoides (Hymenoptera, Eulophidae) and their phylogenetic analysis.

Neotrichoporoides belongs to the family Eulophidae (Hymenoptera: Chalcidoidea). As a group of parasitic wasps, it plays an indispensable role in the biological control of agricultural and forest pests and in maintaining ecosystem balance. To date, only nine complete mitochondrial genomes of Eulophidae have been sequenced worldwide, including the two newly sequenced species in this study. To enrich our understanding of the mitochondrial genomic diversity of Eulophidae and to provide preliminary insights into its phylogenetic relationships, we sequenced and comparatively analyzed the mitochondrial genomes of two Neotrichoporoides species. The mitogenomes of N. nyemitawus (GenBank: PZ188956; 15,164 bp) and N. viridimaculatus (GenBank: PX794932; 15,297 bp) contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR), and exhibit a strong AT bias, with AT contents of 85.5% and 85.0%, respectively. We further analyzed mitochondrial gene rearrangements across 17 species from Encyrtidae, Eulophidae and Pteromalidae and summarized family-specific rearrangement characteristics. tRNA rearrangements were detected in all three families. Eulophidae harbors conserved PCGs, while the inverse transposition of trnA and transposition of trnV are likely reported for the first time within this family. The two Neotrichoporoides species differ only in the arrangement of several tRNAs. Comparative analysis of PCGs revealed differences in molecular evolutionary rates among genes, with ATP8, ND2 and ND4 evolving faster than the others. Phylogenetic analysis based on mitochondrial genome sequences showed that species from two subfamilies formed a monophyletic group, and congeneric species clustered into a single clade. This study contributes to resolving phylogenetic relationships within Eulophidae and further deepens our understanding of this family.

Eulophidae↗
PubMed2026

Complete mitochondrial genomes and phylogenetic analysis of three species of Indo-Pacific freshwater gobies, Stiphodon (Gobiiformes,Oxudercidae).

Stiphodon is a genus of gobioid fishes found primarily in freshwater streams on islands throughout the Indo-Pacific region. It is the most speciose genus of Sicydiinae, with more than three dozen named species. Complete mitochondrial genome (mtDNA) sequences were determined for three species, namely Stapledon atropurpureus, Stapledon elegans, and Stapledon semoni. Maximum likelihood and Bayes inference inferences from 13 protein-coding genes (11,433 bp) or the COXI gene (1,551 bp) alone were made on these three together with four mitogenomes previously available. S. percnopterygionus and S. tuivi formed an outgroup to the other five Stiphodon species, meanwhile Stapledon atropurpureus and S. semoni were recovered as sister species. The ratios of the non-synonymous to the synonymous ubstitution rates for all PCGs were in the range 0\ (Ka/Ks) \1, which suggests they have been subject to purifying selection.

Animals↗
PubMed2026

First complete mitochondrial genome of Uzelothrips scabrosus (Thysanoptera: Uzelothripidae) provides insights into gene rearrangements and phylogenetic position within Terebrantia.

The family Uzelothripidae is represented by a single genus Uzelothrips and can be distinguished from others by the presence of whip-like antennae, a circular ventral sensorium on antennal segment III, a well-developed tentorium, and a membranous ovipositor. Here, we generated the first complete mitochondrial genome of Uzelothrips scabrosus (15,674 bp) using next-generation sequencing to explore the gene rearrangements and phylogenetic relationships. It consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two putative control regions. The genome exhibits strong AT bias (71.35%) with negative AT and GC skew. Codon usage analyses indicate a strong bias towards A/U-ending codons and influenced by both natural selection and mutation pressure. All PCGs were under purifying selection, with cox1 being the most conserved and nad4L the most variable. The gene order of the family Uzelothripidae is highly rearranged compared to the ancestral insect gene order. Comparative analysis revealed that gene block B was the most widely conserved, whereas the remaining gene blocks exhibited family or lineage-specific conservation patterns, reflecting extensive mitochondrial gene rearrangements during the evolution of the Thysanoptera. Moreover, 228 synapomorphic and 68 autapomorphic gene boundaries were identified across thysanopteran mitogenomes. Phylogenies indicated that the family Uzelothripidae is in a sister relationship with Stenurothripidae, and the Uzelothripidae + Stenurothripidae clade is sister to Thripidae. This study provides the first mitogenomic insights into Uzelothripidae and highlights the need for broader taxon sampling and nuclear genomic data to resolve deep evolutionary relationships within Thysanoptera.

Comparative analysis↗
PubMed2026

Assembly and characterization of the first complete mitochondrial genome of Epimedium sagittatum (Sieb. et Zucc.) Maxim (Berberidaceae):an invaluable traditional Chinese medicine.

BACKGROUND: Epimedium sagittatum (Sieb. et Zucc.) Maxim is an invaluable traditional Chinese medicine plant known for its properties of tonifying kidney yang, strengthening bones and muscles, and dispelling rheumatism. The chloroplast (cp) genome of E. sagittatum have been sequenced, offering critical insights for breeding and phylogenetic research. However, the mitochondrial (mt) genome of E. sagittatum remains uncharacterized, limiting comprehensive insights into its genomic evolution. RESULTS: In this study, we assembled the first complete mt genome of E. sagittatum employing Illumina and Nanopore sequencing technology and subsequently investigated comparative analysis with its closely related species. The mt genome of E. sagittatum was assembled as a multi-branched structure with a length of 339,191 bp, within a GC content of 46.91%. Our annotation results have shown 39 protein-coding genes (PCGs), 22 tRNA genes, three rRNA genes and four pseudogenes in the E. sagittatum mt genome. The analysis of sequence repeats has detected 79 simple sequence repeats (SSRs), 10 tandem repeats and 255 dispersed repeats in the E. sagittatum mt genome. A total of 720 C to U RNA editing sites of the 34 PCGs was predicted in E. sagittatum. The codons exhibited a strong preference for A or U bases in the E. sagittatum mt genome. The analysis of nucleotide diversity (Pi) highlighted differences in genetic variability across the tested genes, with atp9 gene exhibiting the highest genetic variation. Selection pressure analysis showed that most genes were affected by negative selection during evolution, whereas ccmB, rps10, and rps12 underwent positive selection in different plants. Additionally, a Bayesian phylogenetic tree showed that E. sagittatum was closely related to E. wushanense and E. pubescens. In total of 14 homologous fragments totaling 8,954 bp were identified between the cp and mt genomes of E. sagittatum. CONCLUSIONS: This study presents the first assembled and annotated mt genome of E. sagittatum, which provides a valuable genetic resource for the Epimedium genus and lays the foundation for investigating the phylogenetic relationship and genetic variation of this invaluable medicinal plant.

Epimedium↗
PubMed2026

Complete mitochondrial genomes of eight cyclophyllidean tapeworms: genome pattern and phylogenetic analysis.

Cyclophyllidean tapeworms are widespread parasites of significant medical and veterinary importance. However, mitochondrial (mt) genomic resources for cyclophyllideans from China, particularly those recovered from wildlife hosts, remain comparatively limited. In this study, we sequenced and characterized the complete mt genomes of eight cyclophyllidean isolates collected from diverse wild and domestic hosts in China, including two Hymenolepis sp. isolates and two Raillietina sp. isolates from China, and four additional isolates of previously sequenced Taenia species. The circular mt genomes ranged from 13,387 to 14,021 bp in length, encoding 36 typical genes with variable non-coding regions. Comparative analysis revealed highly conserved gene composition and mostly conserved mt architecture, with localized rearrangement patterns detected among the cyclophyllidean lineages examined. In particular, all sampled Taeniidae exhibited a consistent trnL1-trnS2 arrangement, whereas the examined non-Taeniidae families showed the trnS2-trnL1 arrangement, confirming and extending, across additional wildlife-associated isolates, a previously proposed family-associated gene-order marker within Cyclophyllidea. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes placed the eight isolates within their expected families, in topologies broadly consistent with previous mitogenomic studies. These data provide additional Chinese mitogenomic references, especially for underrepresented wildlife-associated isolates, and support family-associated gene-order patterns in Cyclophyllidea.

Animals↗
PubMed2026

Characterization and comparative analysis of the complete mitochondrial genome sequence of Aucklandia lappa Decne.

BACKGROUND: Aucklandia lappa Decne, a precious medicinal herb in China, utilises the dried rhizome as its medicinal part, which riches in volatile oils, sesquiterpene compounds and other active constituents. Although the mitogenome of A. lappa has been assembled, related research remains in its preliminary stages, far from achieving comprehensive and in-depth understanding. RESULTS: In this paper, the complete mitogenome of A. lappa was assembled by employing a hybrid strategy that combined Illumina short-read and Nanopore long-read sequencing. The assembled mitogenome is 436,648 bp in size with a GC content of 45.06%. The mitogenome has only one chromosomal structure, It contains 54 genes, including 31 protein-coding genes(PCG), 19 tRNA genes, and 4 rRNA genes. A total of 32 high-frequency codons exhibiting significant AT-bias, 431 RNA editing sites, and 26 homologous fragments were transferred from the chloroplast to mitochondria genes (7,337 bp, 1.68%). Furthermore, we conducted a phylogenetic analysis involving in A. lappa and 27 other taxa to clarify its evolutionary and taxonomic status. These findings provide a foundation for further understanding the evolutionary relationships within Asteraceae plant. CONCLUSION: Through the assembly and comprehensive analysis of A. lappa mitogenome, This study has for the first time fully elucidated its mitogenomic structural characteristics.These results not only provide high-quality genetic resources for research on the Asteraceae mitogenome but also lay a solid foundation for in-depth exploration of the evolution and functional genomics of medicinal plants in the Asteraceae family.

Genome, Mitochondrial↗
PubMed2026

The first complete mitochondrial genome of Strigea falconis (Digenea: Strigeidae) reveals six tandemly repeated trnE-containing units and provides mt evidence for the non-monophyly of the family Strigeidae.

BACKGROUND: Phylogenetic relationships among members in the order Diplostomida remain contentious, with mitochondrial (mt) and nuclear genomic data often yielding conflicting topologies. A major limitation is the availability of only a few mt genomes from the type genus Strigea, hindering a robust test of the monophyly of the family Strigeidae and the order Diplostomida. RESULTS: The mt genome of S. falconis was completely sequenced for the first time, which was a circular molecule of 16,872 bp in length, encoding the typical set of 36 mt genes and six duplicate tRNA-Glu genes. Notably, there were seven identical and consecutive tandem repeat units each consist of a 169 bp non-coding region followed by a trnE gene in the newly assembled genome. Phylogenomic analyses based on concatenated predicted amino acid sequences of 12 proteins robustly placed S. falconis in the same clade as Apharyngostrigea pipientis. Crucially, the family Strigeidae was not recovered as monophyletic. Instead, two species within Strigeidae, Cardiocephaloides medioconiger and Cotylurus marcogliesei, clustered with representatives of Diplostomidae, providing mt evidence for the paraphyly of Strigeidae under the current sampling. CONCLUSIONS: The newly sequenced mt genome of S. falconis reveals a previously unreported six-copy tandem repeat of trnE-containing units among currently available diplostomoid mt genomes. Phylogenetic analyses based on mt protein-coding genes provide additional mt evidence that the family Strigeidae was not recovered as monophyletic under the present taxon sampling. However, because mt genomes represent a single maternally inherited linkage group, broader taxon sampling, independent nuclear phylogenomic data, and explicit sensitivity analyses will be required to confirm these relationships and guide any formal systematic revision.

Animals↗
PubMed2026

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Mesenchytraeus (Annelida, Enchytraeidae).

The Changbai Mountain range is one of the key glacial refugia in Northeast Asia. Mesenchytraeus exhibits high species diversity, strong endemism, and widespread cryptic species in this region, for which mitogenomes provide useful molecular markers for exploring cryptic species complexes. This makes Mesenchytraeus an ideal model for studying mitogenome evolution among closely related lineages; however, no mitogenome data have been reported for this genus to date. In this study, we performed de novo assembly, annotation, and comparative analysis of the mitogenomes of 13 Mesenchytraeus species (14 individuals) from Changbai Mountain. All mitogenomes are typical circular molecules containing 37 genes, but putative control regions are rearranged and consistently located between ATP6 and trnR. All species exhibit annelid-specific strand nucleotide biases, characterized by negative GC skew and near-zero AT skew. Codon usage analysis reveals that codon families with wobble U are significantly biased toward mtDNA codons, whereas those with wobble C or G are biased toward non-mtDNA codons, suggesting a conserved mitochondrial codon usage pattern in annelids. All tRNAs form typical cloverleaf secondary structures except trnS2, which lacks the D-stem and the dihydrouridine (DHU) arm in some species. The putative control regions commonly contain complex palindromic repeats, hairpins, and repetitive elements, and may harbor dual replication origins. Phylogenetic analyses support the monophyly of Mesenchytraeus and reveal significant molecular divergence among morphologically cryptic species. This study provides the first mitogenome dataset for Mesenchytraeus and offers new insights into the evolution and replication mechanisms of mitogenomes in Clitellata and broader Annelida.

Mesenchytraeus↗
PubMed2026

Emergence of Babesia naoakii infection in Indonesian domestic cattle, a new host record in water buffaloes, and characterization of complete mitochondrial protein-coding genes.

Babesia (B.) naoakii, previously referred to as Babesia sp. Mymensingh, is a recently characterized tick-borne haemoprotozoan parasite of cattle. In Indonesia, we first reported its presence in 2022 from clinically affected cattle in Central Java. To investigate the wider epidemiology of this neglected ruminant-associated Babesia species, we surveyed apparently healthy cattle (Bos indicus) and water buffaloes (Bubalus bubalis) across three districts of Java, Indonesia. A PCR assay targeting the B. naoakii-specific apical membrane antigen 1 (ama1) gene detected the parasite occurrence in 34.39% of assessed cattle (87/253; 95% CI: 28.80-40.44%) and 30.77% of water buffaloes (12/39; 95% CI: 18.47-46.52%). These results represent the first record of B. naoakii infection in water buffaloes in the country and confirm that the parasite circulates in subclinically infected bovine hosts. To characterise this apicomplexan parasite further at the molecular level, we assembled in full length the three mitochondrial protein-coding genes (PCGs): cytochrome c oxidase subunits 1 (cox1) and 3 (cox3), as well as cytochrome b (cytb). These genes were reconstructed by next-generation sequencing of blood DNA collected during the acute haemolytic-phase of B. naoakii infection, from calves that subsequently succumbed to the disease in the endemic area. Phylogenetic analyses of the concatenated amino-acid sequences of cox1, cox3, and cytb placed the Indonesian isolates within a well-supported monophyletic clade, distinct from all previously characterised ruminant-associated Babesia species and sister to the Babesia bigemina/Babesia ovata lineage. This placement confirmed species identity and reinforced the genetic distinctiveness of B. naoakii in Indonesia. Notably, although B. naoakii circulates in peripheral blood and mirrors the diagnostic behaviour of the mild pathogen B. bigemina, its clinical impact more closely resembles that of the severe pathogenic B. bovis, particularly in young animals. This diagnostic-clinical discordance highlights the need for B. naoakii-specific molecular surveillance and species-level differentiation in regions of co-endemicity. Given the high prevalence in subclinically B. naoakii-infected adults, the documented severity of babesiosis in calves, and the potential for substantial economic losses, broader epidemiological investigations and species-specific control measures for B. naoakii are urgently performed. The same holds true for future epizootiological investigations of underdiagnosed B. naoakii-infections possibly circulating in Indonesian endemic ruminant bovids such as the banteng (Bos javanicus), the lowland anoa (Bubalus depressicornis) and the tamaraw (Bubalus mindorensis).

Animals↗