Search Results (725)

Background: Velvet worms (Onychophora) occupy a pivotal phylogenetic position for deciphering the evolution of Panarthropoda, yet their exact placement within this clade remains debated. Furthermore, early studies in some onychophoran species revealed extensive gene rearrangements and the truncation or even loss of canonical transfer RNAs (tRNAs), features uncommon in other panarthropods. However, due to sparse representation, the pervasiveness and evolutionary significance of these genomic peculiarities across the phylum remain poorly understood. Methods: We sequenced and assembled three novel mitogenomes representing both extant onychophoran families (Epiperipatus barbadensis [Peripatidae]; Euperipatoides rowelli and Phallocephale tallagandensis [Peripatopsidae]) and conducted comparative analyses with five published species. Results: Onychophoran mitogenomes displayed high A+T content (mean 77.32%) but revealed a family-level divergence in GC skew. All genomes contained the standard 13 protein-coding genes (PCGs) and two ribosomal RNAs, yet tRNA counts varied significantly (ranging from 13 to 22), reflecting lineage-specific tRNA loss. Ancestral state reconstruction uncovered deep architectural divergence: Peripatopsidae retains the ancestral onychophoran gene arrangement, whereas Peripatidae exhibits a stable but derived gene order. Despite this architectural plasticity, synonymous codon usage patterns remained strictly conserved across the phylum, with all but one PCG evolving under strong purifying selection. Maximum likelihood phylogenetic reconstruction based on PCGs strongly supported Onychophora as the sister group to Arthropoda within Panarthropoda. Conclusions: Our findings provide robust molecular evidence supporting the Antennopoda hypothesis over the Tactopoda hypothesis for Panarthropoda phylogeny. Furthermore, we demonstrate extensive mitogenomic remodeling between the two extant onychophoran families, including divergent GC-skew patterns, tRNA contents, and gene arrangements. Full article

Liverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In this study, we assembled four new plastid and four new mitochondrial Pellidae genomes using Oxford Nanopore sequencing, supplementing 86 plastomes and 82 mitogenomes from databases. We assessed nucleotide diversity and codon usage, and inferred phylogenies using IQ-TREE with fossil-calibrated dating. Plastomes ranged 120.6–126.5 kb, and mitogenomes 109–180 kb, with Apopellia endiviifolia featuring an exceptionally reduced mitogenome (~109 kb). Native RNA sequencing enabled a revised annotation of the mitochondrial atp1 gene in Apopellia, revealing two introns (previously thought absent) and reducing the intergenic region share to 36.26%, the lowest known among liverworts. Comparative analyses revealed contrasting evolutionary dynamics between organelles: Plastomes displayed higher nucleotide diversity and phylogenetically inconsistent codon usage patterns, likely influenced by compositional bias, whereas mitogenomes were more conserved and largely consistent with established phylogenetic relationships among the orders. Phylogenomic analyses yielded discordant topologies: Chloroplast data recovered Pellidae as a monophyletic clade, whereas mitochondrial data placed Pelliales (Pellia/Apopellia) as basal Jungermanniopsida, rendering Pellidae paraphyletic. Within Pellidae-relevant clades, several major divergences were dated to the Carboniferous–Permian, but with systematic chloroplast–mitochondrial offsets. These results highlight recurrent organellar incongruence and the dynamic evolutionary history of Pellidae organellar genomes. Full article

Riptortus pedestris (Hemiptera, Alydidae) is widely distributed across East Asia, where significant genetic differentiation may occur among geographic populations. To understand the genetic structure, historical dynamics, and formation of geographic distribution patterns in China, we conducted a phylogeographic analysis using three mitochondrial genes (COI, COII, Cytb) from 35 populations. After PCR amplification, we performed genetic diversity analysis, Fst/Nm estimation, phylogenetic reconstruction (ML, BI, NJ), haplotype network, AMOVA, neutrality tests, mismatch distribution, and molecular dating. Results revealed high genetic diversity (Hd > 0.81, π > 0.011), an AT-rich base composition, and faster evolution at the first codon position. Genetic and geographic distances were significantly correlated, with high Fst values indicating strong differentiation, especially between southwestern/southern and other populations. Two main clades were identified: Clade 1 (mainly southern and southwestern China) and Clade 2 (central, northern, northwestern, and northeastern China). A star-like haplotype network and neutrality tests suggested a rapid expansion around 0.019–0.022 Ma (Last Glacial Maximum), and molecular dating estimated the main split at ~0.029 Ma. AMOVA and Gst/Nst confirmed significant phylogeographic structure with most variation among populations. This study provides initial evidence for the genetic differentiation and evolutionary history of R. pedestris in China, demonstrating that its population structure was shaped by climatic changes and geographical isolation, providing key insights into its adaptive evolution and dispersal. Full article

Puccinia striiformis f. sp. elymi (Pse) is a specialized forma specialis of stripe rust infecting Elymus dahuricus, yet its mitochondrial evolution remains poorly understood. In this study, we assembled the complete mitogenome of Pse using PacBio HiFi sequencing, yielding a circular mitogenome of 72,952 bp. This reveals a striking asymmetric evolutionary pattern with a 28.34% genomic contraction compared to the wheat stripe rust P. striiformis f. sp. tritici (Pst-CYR32). Our analysis demonstrates that this streamlining is strictly driven by a massive and systematic loss of mitochondrial introns. The Pse mitogenome exhibits negative GC-skew (−0.0184) consistent with strand-asymmetric mutational pressure, while maintaining a strictly conserved and syntenic complement of all 14 core protein-coding genes (PCGs), alongside 24 tRNAs and 2 rRNAs. Phylogenomic analysis positions Pse as sister to the Pst clade with strong support (100% bootstrap). A 748-bp SNP cluster within nad4 (14.2% sequence divergence versus 3.1% genome-wide average) provides a candidate molecular marker for lineage differentiation, pending population-level validation. This study establishes a genomic foundation for investigating mitochondrial reductive evolution in host-specialized rust lineages, highlighting the dynamic role of introns in driving organellar genome size variation. Full article

Fungi of the Phallales order are globally distributed and are important in forest ecosystems, and many species have medicinal and edible value. However, despite the rich diversity, the information on this order is limited, and its taxonomic classification remains contentious. In this study, the mitogenomes of five species from the Phallales order were sequenced, assembled, annotated, and compared. All five assembled mitogenomes were circular, ranging in size from 41,465 bp to 99,150 bp. Introns and intergenic regions were the key factors for mitogenome size variation in the Phallales order. The arrangement of 15 protein-coding genes, 2 rRNA genes, and 24 tRNA genes was highly conserved among the Phallales species. The only variation observed was the presence of an additional copy of trnI, trnT, trnD, and trnF in some mitogenomes. Specifically, the mitogenomes of P. rugulosus, P. hadriani, P. rigidiindusiatus, and P. dongsun had an additional copy of trnI, trnT, trnD, and trnF, respectively. A phylogenetic analysis produced well-supported phylogenetic tree, indicating that the mitogenome was an effective molecular marker for inferring evolutionary relationships. The phylogenetic analysis showed that the Phallales and Gomphales species share a closer evolutionary relationship. Our results contribute to a better understanding of the evolutionary dynamics, genetic constitution, and systematic classification of this important fungal community. Full article

Ustilago maydis is an economically significant biotrophic smut fungus, capable of infecting maize. This is a localized infection where tumors are formed, potentially in any of the aboveground parts of the plant. In extreme cases, maize plants may die. It is also dimorphic, i.e., it is capable of switching from yeast-like to filamentous forms. The switch can be induced by nitrogen sources, pH, and some lipids/oils. The active infectious form is the filamentous form which is capable of penetrating plant cells using the appressorium. This study focuses on understanding the mitochondrial genome diversity in U. maydis, the selection pressure on the genes encoded in the mitochondrial genome, and the phylogeny of the strains investigated. The results suggest that the strains maintained high consistency in genome architecture and synteny. The cox1 and cob genes in the genomes possessed different intron numbers, with the presence or absence of homing endonuclease genes (HEGs), which overall contributed to the differences in the genome sizes. Among the genes in the mitogenome, nad6 was the only gene that has a non-synonymous nucleotide change, but the overall changes within the mitogenomes suggest purifying selection. The study helped identify the different mitotypes using PCR, although further markers or whole-genome sequencing may be required to fully distinguish mitotypes. Full article

Leptobotia rotundilobus is a newly described species in the subfamily Leptobotinae (Teleostei: Cypriniformes), which is endemic to China. Research on this recently discovered species is preliminary, characterized by limited baseline data and the absence of a fully sequenced mitochondrial genome. To elucidate the structural features of the mitochondrial genome of L. rotundilobus, we performed whole-genome sequencing using next-generation sequencing technology and analyzed its genomic composition, gene content, and structural variation through genome assembly and bioinformatics. The complete circular sequence, spanning 16,593 bp, comprises 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (D-loop), all arranged in the canonical order. The overall base composition of the genome was determined to be 30.8% adenine (A), 24.4% thymine (T), 28.6% cytosine (C), and 16.2% guanine (G). This A+T bias (55.2%) is consistent with the mitochondrial genomes of other Leptobotia, which may affect secondary structure. The ratio of non-synonymous (Ka) to synonymous substitutions (Ks) of 13 PCGs of 16 Leptobotinae species is far less than 1 (0.012–0.063), indicating strong negative or purifying selection on the mitogenome in these species. Moreover, to investigate the phylogenetic relationships within the subfamily Leptobotinae, particularly within the genus Leptobotia, we constructed multiple phylogenetic trees of the mitogenome and concatenated 13 PCGs of 39 sequences with Sinibotia superciliaris as an outgroup. The phylogentic trees using the maximum likelihood (ML) and Bayesian inference (BI) methods consistently indicate that: (1) after correcting the species identification error, L. rotundilobus is closely related to L. micra; and (2) the species of Leptobotia and Parabotia each form a monophyletic group. This study provides new insights into the taxonomy and phylogenetic relationships of Leptobotinae, with a particular focus on the genus Leptobotia, thereby contributing to the clarification of the systematics, origin, and evolution of Botiidae. Full article

Intraspecific variation in mitogenomes has provided the resolution to distinguish between morphologically indistinguishable species and highlight cryptic speciation. This level of variation is underexplored in introduced marine algae. This study evaluated the mitogenomic variability of Gracilaria vermiculophylla, one of the most invasive red algae in the Northern Hemisphere. Nine mitogenomes, comprising seven newly generated complete mitogenomes from Korea, Japan, and Morocco, plus two publicly available mitogenomes, were included in our analysis. The mitogenomes were highly conserved, ranged from 26,064 to 26,178 bp in length, and contained 52 genes comprising 25 protein-coding genes, three rRNAs, and 24 tRNAs. Nucleotide composition showed a strong AT bias (71.6%), with AT skew and GC skew values of 0.050 and 0.014–0.021, respectively. Pairwise divergences of cox2, rnl and rns rRNA were remarkably low, in a range of 0–0.06%, suggesting alternate markers for determining recent introductions. The phylogenetic relationship based on protein-coding genes revealed three shallow groups in G. vermiculophylla, which were correlated with distribution: two C groups from warm temperate sites and one T group from cold temperate sites. This result highlights mitogenomics as a new tool for the deeper understanding of phylogeography and invasion genetics of marine red algae. Full article

Background/Objectives: A comprehensive analysis of the mitochondrial genomes of Japetella diaphana and Amphitretus pelagicus was conducted to investigate their genomic composition, gene size, sequence characteristics, and phylogenetic positioning within the Amphitretidae family. Methods: A rigorous phylogenetic analysis was performed utilizing a dataset comprising 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs derived from 26 cephalopod mitochondrial genomes, representing 25 species across seven families, Vampyroteuthidae, Tremoctopodidae, Octopodidae, Enteroctopodidae, Bolitaenidae, Argonautidae, and Amphitretidae, along with outgroup Nautilus macromphalus. Results: Notably, both focal species demonstrated a pronounced adenine–thymine bias in their mitochondrial genomes, with A. pelagicus exhibiting gene rearrangements and two extensive non-coding regions. The analysis, employing both the maximum likelihood and Bayesian inference methodologies, revealed a monophyletic relationship between Bolitaenidae and Vitreledonellidae, as well as a sister taxon relationship between Amphitretidae and Tremoctopodidae. The majority of species were classified into the Amphitretidae and Bolitaenidae clades, with numerous species exhibiting close phylogenetic relationships. Conclusions: This study provides novel insights into the evolutionary relationships within Octopodiformes, underscoring the significance of mitochondrial genome data in resolving phylogenetic relationships among cephalopods. The findings contribute to our understanding of the evolutionary history of octopi and pose implications for their classification and conservation. Furthermore, the results underscore the necessity for continued research into the evolutionary relationships among cephalopod taxa. Full article

Corydalis impatiens (Papaveraceae) is a traditional Tibetan medicinal plant (“Pa Xia Ga”) whose mitochondrial genome evolution remains unexplored, particularly in the context of high-altitude adaptation. This study presents the first complete mitochondrial genome sequence of an alpine Corydalis species to establish a comparative framework with the lowland congener C. pauciovulata for investigating environment-associated mitochondrial evolution. Using Illumina sequencing and reference-guided assembly, we characterized a 688,959 bp circular genome containing 74 genes, with GC content variations reflecting functional compartmentalization—elevated in structural RNA genes (tRNAs: 51.24%; rRNAs: 52.79%) versus protein-coding genes (44.19%). We identified 719 RNA editing sites concentrated in NADH dehydrogenase genes, suggesting post-transcriptional optimization of respiratory complex I under hypoxic conditions. The genome harbors 50 dispersed repeats (7.50%) and 67 SSRs with A-rich predominance, providing species-specific markers for authenticating “Pa Xia Ga” in Tibetan medicine quality control. Phylogenomic analysis confirms close affinity with C. pauciovulata while resolving intrageneral relationships within Ranunculales. These findings establish a dual-reference system for distinguishing conserved genus-level features from altitude-associated adaptations, enabling future comparative mitogenomics across the 465-species genus and supporting DNA-based medicinal plant identification. Full article

Correct species identification is essential for understanding biodiversity and managing ecosystems. The bisexual Brine Shrimp Artemia tibetiana and Artemia sorgeloosi represent two regional endemic taxa on the Tibetan Plateau, yet the taxonomic status of several populations remains unresolved. In particular, the Artemia population from Kyêbxang Co (Tibet, China) has been inconsistently assigned to either A. tibetiana or A. sorgeloosi in recent ecological and genomic studies, lacking formal taxonomic evaluation. To resolve this ambiguity, we conducted a precise biosystematic assessment based on DNA analyses: In this study, we performed a taxonomic reassessment of the Kyêbxang Co Artemia population, based on complete mitochondrial genome sequences and mitochondrial gene COI haplotype analyses. Phylogenetic analysis consistently positioned the Kyêbxang Co population within the A. sorgeloosi clade, clearly separated from the polyphyletic A. tibetiana lineage. Genetic distance values corroborated this placement, revealing minimal divergence from A. sorgeloosi (0.31%) but substantial divergence from A. tibetiana (9.07%). The COI haplotype network further indicated an exclusive maternal gene pool shared with topotypic A. sorgeloosi. Collectively, these results provide conclusive molecular evidence that the Brine Shrimp population of Kyêbxang Co belongs to A. sorgeloosi, not A. tibetiana. Full article

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

There is accumulating evidence that distinct mitochondrial DNA (mtDNA) methylation and hydroxymethylation patterns exist in Parkinson’s disease (PD). However, most studies have been limited to the investigation of specific target regions, rather than the entire mtDNA, and have been further hindered by other methodological discrepancies and the lack of non-CpG context investigation. Here, we provide a comprehensive profile of methylation and hydroxymethylation levels across the mitochondrial genome, at global and single-base resolution, in CpG and non-CpG (CHG, CHH) contexts in blood samples from early-onset PD (EOPD) patients (n = 39) and age- and sex-matched controls (n = 63). Bisulfite (BS) and oxidative-bisulfite (oxBS) conversions in parallel workflows followed by next-generation sequencing (NGS) using Illumina’s Novaseq 6000 sequencing system identified mitochondrial 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in all contexts. Global mtDNA methylation was significantly higher in EOPD patients vs. matched controls in the CpG context (p = 5.63 × 10⁻³) in the BS status, and in all contexts [CpG (p = 2.67 × 10⁻⁴), CHG (p = 0.015), CHH (p = 0.012)] in the oxBS status, i.e., “true methylation”. At single-base resolution, the most statistically significant sites across the mitogenome, in the D-loop region, and CpG context, were primarily hypomethylated in EOPD patients compared to matched controls. Upon further validation, both global and base resolution mtDNA (hydroxy)methylation results could act as blood-based biomarkers for EOPD. Full article

Background: Skipper butterflies (Hesperiidae) are a morphologically distinctive lineage within Papilionoidea, yet relationships among many groups remain difficult to resolve, and mitochondrial genomic resources remain limited for some tribes, including Celaenorrhinini. Methods: We sequenced and characterized the complete mitochondrial genome of Celaenorrhinus victor using Illumina short-read sequencing. Gene content and organization were annotated, codon-usage patterns were assessed across Celaenorrhinus using relative synonymous codon usage and multiple compositional/selection tests (ENC–GC3s, neutrality, and PR2 analyses), selective constraints were evaluated using Ka/Ks for 13 protein-coding genes, and phylogenetic relationships were inferred with a partitioned maximum-likelihood analysis of 66 complete hesperiid mitogenomes. Results: The circular mitogenome of C. victor is 15,180 bp and contains the typical 37 genes (13 protein-coding genes, 22 tRNAs, and two rRNAs) plus an A + T-rich control region, with an overall A + T content of 79.64%. Gene order and orientation match those of other Celaenorrhinus and hesperiid mitogenomes. All protein-coding genes use standard invertebrate mitochondrial start codons (with cox1 initiating with TTG) and terminate with complete TAA stop codons. Codon usage is strongly biased toward A/U-ending codons and is broadly similar among five sampled Celaenorrhinus mitogenomes; ENC–GC3s, neutrality, and PR2 analyses indicate a predominant influence of A + T-directed mutational pressure with additional effects beyond base composition. Ka/Ks values for all 13 protein-coding genes were <1, consistent with pervasive purifying selection; cox genes were the most conserved, whereas several NADH dehydrogenase subunit genes evolved comparatively faster. The phylogeny recovered monophyletic Celaenorrhinini and a well-supported Celaenorrhinus clade, placing C. victor as sister to Celaenorrhinus consanguineus, while deeper nodes among major hesperiid lineages showed only moderate support in parts of the tree. Conclusions: This study provides a new mitogenomic resource for Celaenorrhinini and a comparative reference for codon usage and selective constraints within Celaenorrhinus, supporting the placement of C. victor within Hesperiidae while highlighting remaining uncertainty at deeper hesperiid divergences. Full article

The Sharpchin Slickhead, Bajacalifornia burragei, is a rarely collected bathypelagic fish endemic to the eastern tropical Pacific Ocean, and its genetic diversity remains undocumented. This study characterizes mitochondrial diversity in a localized deep-basin collection from the Carmen Basin of the Gulf of California by sequencing complete mitochondrial genomes from four individuals collected simultaneously at 1300 m in a single Tucker trawl. A high-quality reference mitogenome was assembled using PacBio HiFi long reads, and three additional mitogenomes were generated from Illumina PE150 libraries mapped to this reference. The mitogenome of B. burragei exhibits the canonical 37 gene architecture and conserved gene order typical of teleost mitogenomes. Overall mitogenome divergence was low (Range: 0.21–0.29%), with most protein-coding and rRNA genes exceeding 99.5% identity. Slightly elevated variation occurred in atp8, nad6, and several tRNA genes. This study provides the first genetic characterization of B. burragei and establishes a baseline for evaluating mitochondrial diversity within a localized collection of individuals and provides a point of comparison for future studies assessing connectivity among deep basins. Full article