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Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.

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We report the complete mitochondrial genome of a causal agent of banana fusarium wilt isolated in Mexico. The whole set of genes encoding proteins related to respiration and ATP synthesis, rRNAs, tRNAs are enlisted. Two open reading frames of unknown function conserved in Fusarium oxysporum were also identified.

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BACKGROUND: As an important forage in arid and semi-arid regions, Agropyron cristatum provides livestock with exceptionally high nutritional value. Additionally, A. cristatum exhibits outstanding genetic characteristics to endure drought and disease. Therefore, rich genetic diversity serves as a cornerstone for the improvement of major food crops. The purposes of this study were to systematically describe mitogenome of A.cristatum and preliminarily analyze its internal variations. RESULT: The A. cristatum mitogenome was a single-ring molecular structure of 381,065 bp that comprised 52 genes, including 35 protein-coding, 3 rRNA and 14 tRNA genes. Among these, two pseudoprotein-coding genes and multiple copies of tRNA genes were observed. A total of 320 repetitive sequences was found to cover more than 10% of the mitogenome (105 simple sequences, 185 dispersed and 30 tandem repeats), which led to a large number of fragment rearrangements in the mitogenome of A. cristatum. Leucine was the most frequent amino acid (n = 1087,10.8%) in the protein-coding genes of A. cristatum mitogenome, and the highest usage codon was ATG (initiation codon). The number of A/T changes at the third base of the codon was much higher than that of G/C. Among 23 PCGs, the range of Pi values is from 0.0021 to 0.0539, with an average of 0.013. Additionally, 81 RNA editing sites were predicted, which were considerably fewer than those reported in other plant mitogenomes. Most of the RNA editing site base positions were concentrated at the first and second codon bases, which were C to T transitions. Moreover, we identified 95 sequence fragments (total length of 34, 343 bp) that were transferred from the chloroplast to mitochondria genes, introns, and intergenic regions. The stability of the tRNA genes was maintained during this process. Selection pressure analysis of 23 protein-coding genes shared by 15 Poaceae plants, showed that most genes were subjected to purifying selection during evolution, whereas rps4, cob, mttB, and ccmB underwent positive selection in different plants. Finally, a phylogenetic tree was constructed based on 22 plant mitogenomes, which showed that Agropyron plants have a high degree of independent heritability in Triticeae. CONCLUSION: The findings of this study provide new data for a better understanding of A. cristatum genes, and demonstrate that mitogenomes are suitable for the study of plant classifications, such as those of Agropyron. Moreover, it provides a reference for further exploration of the phylogenetic relationships within Agropyron species, and establishes a theoretical basis for the subsequent development and utilization of A. cristatum plant germplasm resources.

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Triplophysa grahami Regan 1906 is a member of the family Nemacheilidae, Cypriniformes, and native loach in Yunnan. In this study, the complete mitochondrial genome (mitogenome) of T. grahami Regan 1906 was firstly reported and analyzed. The mitogenome of T. grahami Regan 1906 is 16,566 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (D-loop). The arrangement and orientation of protein coding genes and RNAs in T. grahami Regan 1906 are identical to other species of Nemacheilidae. The base composition of T. grahami Regan 1906 mitogenome was 29.25% A, 28.55% T, 25.03% C, and 17.17% G. The phylogenetic analysis based on the mitogenome showed that T. grahami Regan 1906 belongs to the clade of genus Triplophysa and the monophyly of Triplophysa is identified. This study contributed valuable genetic data for T. grahami Regan 1906 and explored the phylogenetic relationships in Nemacheilidae.

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Monogeneans of the genus Dactylogyrus Diesing, 1850, the largest genus in the family Dactylogyridae, mostly parasitize the gills of cyprinoid hosts; however, only 3 Dactylogyrus' mitochondrial genomes (mitogenomes) are studied so far. The aim of this research is to extend our understanding of the mitogenomes of Dactylogyrus. We sequenced the mitogenomes of D. crucifer and D. zandti isolated from Rutilus rutilus and Abramis brama orientalis in northwest China, and then we compared these mitogenomes with other monogeneans. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of D. crucifer and D. zandti and characterized the mitogenomes to understand the gene structure, gene identity, the secondary structures of the 22 tRNA genes, and relative synonymous codon usage. We used the analytic Bayesian Information and Maximum Likelihood methods to determine their associated phylogenetic trees. The mitogenomes of D. crucifer and D. zandti were 14,403 and 18,584 bp, respectively. Organization and positioning of these genes were in accordance with Dactylogyrus lamellatus and Dactylogyrus tuba. The nucleotide composition of Dactylogyridae was different from other families of Monogenea, and the A+T count of genus Dactylogyrus (54 - 58.4 %) was lower than other genus species of the family Dactylogyridea (63.9 - 78.4 %) in protein-coding genes. Dactylogyrus members displayed a codon usage bias. The relative synonymous codon used by Dactylogyrus was not conserved and was lower than other monogeneans. The codon use patterns of closely-related species isolated from closely-related hosts were identical. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrus isolated from host subfamily Leuciscinae formed a sister-group. Our results contributed significantly to an increased database of mitogenomes, more than 50 %, for Dactylogyrus that may help future studies of mitochondrial genes and codon uses for the analysis of monogenean phylogenetics.

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A genomic investigation of the potentially invasive firefly Photinus signaticollis Blanchard1845 has been performed and led to the obtention of its complete 16,411 bp long mitochondrial genome. The mitogenome encodes 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. With other species of the Photinus complex it shares several premature terminations of some protein-coding genes and also an overlap between cox1 and tRNA-Tyr. By data-mining, the complete luciferase and luciferin-regenerating genes were also identified from the contigs file and compared with existing data, in addition to WG and CAD, two genes used in pioneering phylogenetic studies on fireflies. Three maximum likelihood phylogenies were derived from all these data. The multigene phylogeny based on all mitochondrial protein-coding genes strongly associates P. signaticollis with Photinus pyralis Linnaeus, 1758 and the lantern-less daily "winter firefly", Photinus corruscus Linnaeus, 1767. A second phylogeny based on concatenated sequences of the cox1, WG and CAD genes positions P. signaticollis as a sister clade to a large cluster of species containing the 7 sub-groups previously evidenced among the North American species of the Photinus complex. A third phylogeny based on the amino-acid sequence of the luciferase protein associates P. signaticollis to Photinus scintillans. The analysis presented here will most certainly help to come to a better understanding of the very complex inter-relationships in the very large Photinus genus.

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Ticks are important medical and veterinary parasites that represent a substantial health threat to humans, companion animals, and livestock. Ixodiphagus wasps (Hymenoptera; Encyrtidae) are known endoparasitoids of ixodid (hard) and argasid (soft) ticks, with potential utility as natural biocontrol agents. Two species, Ixodiphagus brunneus and Ixodiphagus mysorensis, are previously recorded from Australia, however, the genus lacks formal revisionary work in Australia, and the validity and host ranges of these species remain uncertain. This work aimed to investigate the diversity of Ixodiphagus in Australasia and provide a molecular data resource for future work on these understudied endoparasitoids. We extracted DNA from archival Ixodiphagus specimens from Australian and New Zealand insect collections and performed high-throughput sequencing which resulted in complete or mostly complete mitochondrial genome sequences from 11 specimens, including I. brunneus, Ixodiphagus taiaroaensis, and a novel Ixodiphagus sp. reared from Rhipicephalus linnaei from Townsville, Australia. In addition, approximately 70% of the genome of the Wolbachia endosymbiont of I. brunneus was recovered. Finally, we screened 178 recently collected pooled tick samples from southern New South Wales, Australia, for Ixodiphagus spp. using 28S rRNA and cytochrome c oxidase subunit 1(COI) gene PCR, and recovered 14 positive samples. Phylogenetic analysis of Australasian Ixodiphagus spp. based on 28S rRNA and complete mitochondrial genome sequences determined that members of the Australasian fauna are distinct from Ixodiphagus hookeri (the only other Ixodiphagus species for which genetic data exists), and that at least two distinct species are present in Australia; I. brunneus identified from Ixodes holocyclus and Haemaphysalis bancrofti ticks, and an uncharacterised Ixodiphagus sp. found in Rhipicephalus linnaei ticks from northern Queensland. Furthermore, there was substantial genetic diversity at the 28S rRNA loci among I. brunneus samples, which may represent normal genetic variability or a secondary cryptic species. The molecular data generated here represents the first known for the genus Ixodiphagus in Australasia, doubling that of the world fauna, and provides the first known complete mitochondrial genomes for these important tick parasitoids.

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Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.

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The marine red alga, Gracilaria eucheumatoides, is economically significant for its agar production and pharmacologically active compounds. This study reveals its complete mitochondrial genome (mitogenome), sequenced using Illumina's next-generation technology. The mitogenome is a 25,909 bp circular molecule with a G + C content of 27.21%, comprising 24 protein-coding genes, two ribosomal RNA genes, 24 transfer RNA genes, and one open reading frame (ORF) with an unidentified function. Both gene structure and composition are highly conserved within Gracilaria. The phylogenetic analyses fully support a close relationship of G. eucheumatoides with other Gracilaria species, as well as its sister relationship with G. urvillei. This mitogenome sequencing effort of G. eucheumatoides provides crucial data for future phylogenetic research on marine red algae.

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Argania spinosa (L.) Skeels, an endemic Moroccan plant species from the Sapotaceae family, holds significant ecological, pharmaceutical, and socioeconomic value in the arid mid-western region. However, it is facing rapid degradation. Therefore, understanding its genetic diversity is critical for preserving this national heritage. We sequenced, assembled, and annotated the mitochondrial genome of A. spinosa and compared it to other plants in the Ericales order. Mitochondrial-like sequences from the A. spinosa genome were assembled using GetOrganelle, resulting in a 707,441 base pair mitochondrial genome with 45.75 % GC content. Annotation identified 32 protein-coding genes, 16 transfer RNAs, and 2 ribosomal RNA genes. Phylogenetic analysis of 15 Ericales species affirms that A. spinosa is closely related to the Theaceae family, which is in accordance with results from the chloroplast genome.

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Rhopalosiphum maidis Fitch, 1856 is widespread in tropical and temperate regions. R. maidis can spread viral diseases in maize and harm various important crops. In the present study, we report the first complete mitochondrial genome of R. maidis. The circular genome is found to be 17,021 bp in length, includes a standard set of 22 transfer RNAs, two ribosomal RNAs, 13 protein-coding genes, and two non-coding control regions. The base composition is 84.32% AT and 15.79% GC. The phylogenetic tree of the 17 Aphidini families constructed based on the nucleotide sequences of complete mitochondrial genomes strongly supports the conclusion that R. maidis is closely related to R. rufiabdominalis.

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Lycophytes and ferns represent one of the earliest-diverging lineages of vascular plants, with the Lycopodiaceae family constituting the basal clade among lycophytes. In this research, we successfully assembled and annotated the complete Lycopodium japonicum Thunb. (L. japonicum) mitochondrial genome (mitogenome) utilizing PacBio HiFi sequencing data, resulting in a single circular molecule with a size of 454,458 bp. 64 unique genes were annotated altogether, including 34 protein-coding genes, 27 tRNAs and 3 rRNAs. It also contains 32 group II introns, all of which undergo cis-splicing. We identified 195 simple sequence repeats, 1,948 dispersed repeats, and 92 tandem repeats in the L. japonicum mitogenome. Collinear analysis indicated that the mitogenomes of Lycopodiaceae are remarkably conserved compared to those of other vascular plants. We totally identified 326 RNA editing sites in 31 unique protein-coding genes with 299 sites converting cytosine to uracil and 27 sites the reverse. Notably, the L. japonicum mitogenome has small amounts foreign DNA from plastid or nuclear origin, accounting for only 2.81% of the mitogenome. The maximum likelihood phylogenetic analysis based on 23 diverse land plant mitogenomes and plastid genomes supports the basal position of lycophytes within vascular plants and they form a sister clade to all other vascular lineages, which is consistent with the PPG I classification system. As the first reported mitogenome of Lycopodioideae subfamily, this study enriches our understanding of Lycopodium mitogenomes, and sets the stage for future research on mitochondrial diversity and evolution within the lycophytes and ferns.

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Colias sifanica Grum-Grshimailo, 1891, is a typical montane butterfly species which occurs on the Qinghai-Tibet Plateau (QTP) and adjacent regions in China. In this study, the complete mitochondrial genome of this species was assembled from data generated by next-generation sequencing. The mitogenome was 15,151 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The base composition of the C. sifanica mitogenome was 39.7% A, 41.3% T, 11.3% C and 7.7% G, significantly AT biased as commonly found in other Pieridae mitogenomes. Phylogenetic analyses based on all PCGs using both the maximum likelihood and Bayesian inference methods indicated that C. sifanica is closely related to C. fieldii with high support values, and the phylogenetic relationship of (Dercas + ((Gandaca + Gonepteryx) + (Phoebis + (Anteos + (Catopsilia + (Zerene + Colias))))))) was shown for the tribe Coliadini. Though both the mitogenomic gene order and overall base composition were found to be conserved, different Ka/Ks ratios for several mitogenomic PCGs were detected between Colias and other species in the tribe Coliadini.

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Clarias meladerma Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of C. meladerma from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of C. meladerma exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that C. meladerma has the same clade with C. macrocephalus, C. batrachus, and C. fucus. In essence, the findings of this study lay down a genetic foundation for future investigations into C. meladerma.

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The Chinese horned toads, Boulenophrys boettgeri (Boulenger, 1899) and Boulenophrys kuatunensis (Pope, 1929), are two captivating species within the family Megophryidae, which inhabit the mountainous streams in the Eastern of China. In this study, two new complete mitochondrial genomes of B. boettgeri and B. kuatunensis were sequenced, assembled, and annotated using next-generation sequencing. The length of mitochondrial genomes of B. boettgeri and B. kuatunensis was 16,597 and 17,921 bp, respectively, with both containing 13 protein coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Phylogenetic relationships based on protein-coding mitochondrial genes showed that the two Boulenophrys species formed a cluster with other Boulenophrys species. The two new sequences provide valuable insights into the mitochondrial genomes of these two species, offering important data for understanding the phylogenetic relationships of the genus Boulenophrys.

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Homoderus mellyi belongs to the Lucanidae family of Coleoptera. The first complete mitogenome of Homoderus is reported in this paper. The genome is 16,807 bp in length and contains the typical 37 genes with 22 transfer RNA genes, 13 protein coding genes, and 2 ribosomal RNA genes. The gene order is conserved across the lineage. The average base composition of the mitogenome is 36.6% for A, 20.8% for C, 11.6% for G, and 31.1% for T. The percentage of GC is 32.3%. The genome organization, nucleotide composition, and codon usage are similar to other beetles. Phylogenetic analysis shows that Lucanidae is monophyletic, and all subfamilies are monophyletic, respectively. The phylogenetic position of H. mellyi is consistent with other research.

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Cyanopterus ninghais is an important gregarious ectoparasitoid during the larval stage of Monochamus alternatus, a key vector for pine wilt disease in Asia. In this study, the complete mitochondrial genome of C. ninghais was sequenced and analyzed. The mitochondrial genome of C. ninghais is 15,386 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The nucleotide composition is 41.32% A, 8.29% G, 6.06% C, and 44.33% T. Phylogenetic trees of Braconidae were constructed using 13 PCG sequences via Bayesian inference (BI) and maximum likelihood (ML) analyses to determine their phylogenetic position. Both ML and BI analyses revealed that C. ninghais is closely related to Euurobracon yokahamae, Virgulibracon endoxylaphagus, and Habrobracon hebetor.

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Freshwater crabs play essential roles in the well-functioning of the inland aquatic ecosystems. However, due to the lack of sufficient molecular resources, the study of freshwater crabs has been greatly hindered. In this study, the mitochondrial genome of Huananpotamon koatenense, a freshwater crab endemic to China, was sequenced for the first time. This mitogenome sequence is 15,528 bp long, and contains 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. Phylogenetic analyses based on 25 mitogenomes showed that H. koatenense was clustered with the known congeneric species of H. lichuanense.

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The complete mitochondrial genome of Locastra muscosalis (Walker, 1866) was sequenced and characterized in this study, which was the first reported complete mitogenome of the genus Locastra. The mitogenome of L. muscosalis has a total length of 15,177 bp, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A-T rich region. Phylogenetic analysis revealed that L. muscosalis is closely associated with Orthaga euadrusalis. These data will serve as a valuable foundation for future investigations into the Epipaschiinae and Pyralidae evolutionary history.

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Fleas are the most important insect vectors that parasitize warm-blooded animals and are known vectors of zoonotic pathogens. A recent study showed that Stenoponia polyspina parasitizing Eospalax baileyi in Zoige County have carried Bartonella spp. and Spotted fever group Rickettsia (SFGR). Accurate identification and differentiation of fleas are essential for prevention and control of zoonotic pathogens. To understand phylogenetic relationship of the subfamily Stenoponiinae, we described morphological characteristics of S. polyspina and sequenced its mitogenome with 14,933 bp in size and high A + T content (~ 79%). The S. polyspina mitogenome retained the ancestral pattern of mitochondrial gene arrangement of arthropods without rearrangement. The start codons of 13 protein-coding genes (PCGs) are traditional ATN and the stop codons are TAA or TAG. Anticodon loops of all tRNA genes were 7 bp except for trnL2 and trnD had anticodon loops with 9 bp and the abnormal anticodon loops may be associated with frameshifting mutation. Genetic distance and Ka/Ks ratios indicated that all 13 PCGs of S. polyspina were subjected to purifying selection, with cox1 at the slowest rate and atp8 at the fastest rate. The mitogenomes of 24 species representing 7 families in the order Siphonaptera were selected to reconstruct phylogenetic tree based on concatenated nucleotide sequences of two datasets (PCGRNA matrix and PCG12RNA matrix) using Bayesian inference (BI) and Maximum likelihood (ML) methods. Phylogenetic tree supported that the superfamilies Ceratophylloidea, Vermipsylloidea, Pulicoidea were monophyletic and the superfamily Hystrichopsylloidea was paraphyletic. The family Ctenophthalmidae was monophyletic in PCGRNA-ML (codon partition) and paraphyletic in the remain trees. S. polyspina belongs to the subfamily Stenoponiinae was closely more related to the subfamily Rhadinopsyllinae. This paper explored phylogenetic position of diverse clades within the order Siphonaptera based on morphological and mitogenome data of S. polyspina. Our research enriched NCBI database of the order Siphonaptera.

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