Dihydrouridine Arm Research Articles

The first report of complete mitogenomes of two endangered species of genus Propomacrus (Coleoptera: Scarabaeidae: Euchirinae) and phylogenetic implications.

To understand the mitochondrial genome structure of two endangered and long-armed scarab beetles, Propomacrus davidi and Propomacrus bimucronatus, their complete mitogenomes were sequenced for the first time in this study. The complete mitogenomes of P. davidi and P. bimucronatus were 18, 042 bp and 18, 104 bp in length, respectively. The gene orders of their mitogenomes were highly consistent with other Coleopteran species, and the typical ATN was used as the start codon in most protein coding genes. The incomplete stop codon T was used in cox1, cox2, and nad5, and TAN was used as a complete stop codon in most protein coding genes. All predicted tRNAs could form a typical cloverleaf secondary structure, except that trnS1 lacked the dihydrouridine arm. Based on the maximum likelihood and the Bayesian inference methods, phylogenetic trees of 50 species were reconstructed. The results showed that P. davidi, P. bimucronatus, Cheirotonus jansoni and Cheirotonus gestroi clustered in the same branch, and were the most closely related. The results supported that subfamily Euchirinae is a monophyletic group of Scarabaeidae, which was consistent with the morphological classification. These molecular data enriched the complete mitogenome database of Euchirinae, and improved our understanding of the phylogenetic relationship and evolutionary characteristics of these two endangered species.

The complete mitochondrial genome of the leopard shark Triakis semifasciata (Triakidae)

ABSTRACT The leopard shark Triakis semifasciata (family Triakidae) is threatened by habitat loss and targeted by recreational and commercial fishermen in the Eastern Pacific Ocean, from Oregon, USA, to the Gulf of California, Mexico. Despite environmental issues, there are few genetic and genomic resources available for this species. This study assembled the complete mitochondrial genome of T. semifasciata from a skin metagenomic sample and described it in detail. The phylogenetic position of T. semifasciata amongst closely related species was also examined using mitochondrial protein-coding genes (PCGs). The mitochondrial genome of T. semifasciata is 16,613 bp in length and consists of 13 PCGs, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. A 30 bp long region was identified as the origin of replication for the light strand (OL) between the trnN and trnC genes, and a 974 bp long putative control region (CR) contains the origin of replication for the heavy strand (OH). The gene order in T. semifasciata is identical to that of cofamilial species. An analysis of Ka/Ks ratios for all PCGs yielded values < 1, indicating that all PCGs experience strong purifying selection. All tRNAs exhibit a canonical ‘cloverleaf’ secondary structure except for tRNA-Ser1 which lacks the stem of the dihydrouridine (DHU) arm and in place possesses a simple loop. A phylomitogenomic maximum likelihood (ML) analysis did not support the monophyly of the family Trakidae and placed T. semifasciata in a sister position to Hemitriakis japanica. However, the aforementioned sister position was poorly supported by ML bootstrap values. This study represents a new genomic resource for this commercially and recreationally important species and confirms that mitochondrial genomes can be assembled from skin metagenomic samples as shown before in an unrelated shark species.

The complete mitochondrial genome of the imperiled Bullnose ray Myliobatis freminvillei (Myliobatiformes: Myliobatidae) with comments on its phylogenetic position and claims of diversifying selection affecting protein coding genes in a closely related species

The Bullnose ray Myliobatis freminvillei is a bentho-pelagic eagle ray that inhabits the north Gulf of Mexico and the Western Atlantic Ocean Coast, discontinuously, from Massachusetts, USA to Buenos Aires, Argentina. Myliobatis freminvillei is currently listed as vulnerable by the 2019 IUCN Red List of Threatened Species given that it is often captured as bycatch by artisanal and commercial fisheries, along the coasts of Argentina, Brazil, and Venezuela. This study, for the first time, assembled and characterized the mitochondrial genome of M. fremnvillei. The A+T rich mitochondrial genome of M. fremnvillei is 18,356 bp long and encodes 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (12S ribosomal RNA and 16S ribosomal RNA), 13 protein coding genes (PCGs), and also contains a non coding control region 2,617 bp long. Nonsynonomous codon usage with a preference for A+T rich codons was observed in all 13 PCGs. Leu (CTA), Ile (ATC), Phe (TTC), Thr (ACA), and Ala (GCC) were the most frequently used codons. Ka/Ks ratios estimated for all 13 PCGs exhibited values < 1, indicating strong purifying selection affecting all these genes. In contrast to the results of a previous study that claimed diversifying selective pressure in two mitochondrial PCGs of Mobula tarapacana, reanalysis of the Ka/Ks values for the same species indicated purifying selection in all 13 PCGs. Of the 22 tRNA genes, all have a cloverleaf secondary structure except tRNA-Ser1 which has a truncated dihydrouridine arm. In the control region, A+T rich microsatellites (n = 42) and short tandem repeats (n = 6) were identified, and the secondary structure of the same region contained numerous hairpin loops. Phylomitogenomic analyses supported the monophyletic status of the order Myliobatiformes and family Myliobatidae. The assembled mitochondrial genome will assist with conservation efforts in Myliobatis fremnvillei.

The Characterization of the Mitochondrial Genome of Fulgoraria rupestris and Phylogenetic Considerations within the Neogastropoda.

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.

Characterization of the mitochondrial genomes of the Mexican endemic bats Corynorhinus mexicanus and Corynorhinus leonpaniaguae (Chiroptera: Vespertilionidae).

The genus Corynorhinus is composed of four recognized species: C. rafinesquii, C. townsendii, C. mexicanus, and C. leonpaniaguae, the latter two being endemic to Mexico. According to the IUCN, C. mexicanus is considered "Near Threatened", as its populations are dwindling and habitats are affected by anthropogenic disturbance. Corynorhinus leonpaniaguae has not been assigned to an IUCN Red List risk category due to its recent description. In this study, the mitochondrial genomes of C. mexicanus and C. leonpaniaguae were assembled and characterized in detail. The mitochondrial genomes (mtDNA) of C. mexicanus and C. leonpaniaguae have lengths of 16,470 and 16,581bp respectively, with a predominant nucleotide usage of adenine (31.670% and 31.729%, respectively) and thymine (26.15% and 26.18%, respectively). The mtDNA of C. mexicanus and C. leonpaniaguae is composed of 37 coding and non-coding elements: 22 transfer RNAs (tRNA), 13 protein-coding genes (PCGs), two ribosomal RNAs and a non-coding region, the control region, which has a length of 933bp and 1,149bp, respectively. All tRNAs exhibited a cloverleaf secondary structure, with the exception of trn-Ser1 which showed a deletion of the dihydrouridine arm in the two species. All PCGs are subjected to purifying selection, with atp8 being the gene showing the highest Ka/Ks value. These are the first whole mitogenomic resources developed for C. mexicanus and C. leonpaniaguae and enhance our knowledge of the ecology of these species and aid in their conservation.

Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae

BackgroundThe order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops.ResultsThe mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae.ConclusionsOur results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.

Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications.

Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.

Comparative mitochondrial genome analysis of three leafhopper species of the genus Abrus Dai & Zhang (Hemiptera: Cicadellidae: Deltocephalinae) from China with phylogenetic implication

BackgroundThe phylogenetic position and classification of Athysanini are poorly defined, as it includes a large group of polyphyletic genera that have historically been assigned to it mainly because they still exhibit the most typical deltocephaline genitalic and external body characters but lack the distinctive characteristics that other tribes possess. The bamboo-feeding leafhopper genus Abrus belong to the tribe Athysanini of subfamily Deltocephalinae, which currently comprises 19 valid described species, and are limited to the Oriental and Palaearctic regions in China. Although the taxonomy of Abrus are well updated, the references on comparative mitogenomic analyses of Abrus species are only known for a single species. In this study, we sequenced and analyzed the complete mitochondrial genomes (mitogenomes) of Abrus daozhenensis Chen, Yang & Li, 2012 (16,391bp) and A. yunshanensis Chen, Yang & Li, 2012 (15,768bp) (Athysanini), and compared with published mitogenome sequence of A. expansivus Xing & Li, 2014 (15,904bp).ResultsThese Abrus species shared highly conserved mitogenomes with similar gene order to that of the putative ancestral insect with 37 typical genes and a non-coding A + T-rich region. The nucleotide composition of these genomes is highly biased toward A + T nucleotides (76.2%, 76.3%, and 74.7%), AT-skews (0.091 to 0.095, and 0.095), negative GC-skews (− 0.138, − 0.161, and − 0.138), and codon usage. All 22 tRNA genes had typical cloverleaf secondary structures, except for trnS1 (AGN) which lacks the dihydrouridine arm, and distinctively trnG in the mitogenome of A. expansivus lacks the TψC arm. Phylogenetic analyses based on 13 PCGs, 2 rRNA genes, and 22 tRNA genes consistently recovered the monophyletic Opsiini, Penthimiini, Selenocephalini, Scaphoideini, and Athysanini (except Watanabella graminea, previously sequenced species as Chlorotettix nigromaculatus) based on limited available mitogenome sequence data of 37 species.ConclusionAt present, Abrus belongs to the tribe Athysanini based on both morphological and molecular datasets, which is strongly supported in present phylogenetic analyses in both BI and ML methods using the six concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Phylogenetic trees reconstructed herein based on the BI and ML analyses consistently recovered monophylitic Athysanini, except Watanabella graminea (Athysanini) in Opsiini with high support values.

Comparative mitogenomic analysis of three bugs of the genus Hygia Uhler, 1861 (Hemiptera, Coreidae) and their phylogenetic position.

Hygia Uhler, 1861 is the largest genus in the bug family Coreidae. Even though many species of this genus are economically important, the complete mitogenomes of Hygia species have not yet been reported. Therefore, in the present study, the complete mitogenomes of three Hygia species, H.lativentris (Motschulsky, 1866), H.bidentata Ren, 1987, and H.opaca (Uhler, 1860), are sequenced and characterized, and submitted in a phylogenetic analysis of the Coreidae. The results show that mitogenomes of the three species are highly conserved, typically with 37 genes plus its control region. The lengths are 16,313 bp, 17,023 bp, and 17,022 bp, respectively. Most protein-coding genes (PCGs) in all species start with the standard codon ATN and terminate with one of three stop codons: TAA, TAG, or T. The tRNAs secondary structures of all species have a typical clover structure, except for the trnS1 (AGC) in H.bidentata, which lacks dihydrouridine (DHU) arm that forms a simple loop. Variation in the length of the control region led to differences in mitochondrial genome sizes. The maximum-likelihood (ML) and Bayesian-inference (BI) phylogenetic analyses strongly supported the monophyly of Hygia and its position within Coreidae, and the relationships are ((H.bidentata + (H.opaca + (H.lativentris + Hygia sp.))). The results provide further understanding for future phylogenetic studies of Coreidae.

First mitochondrial genomes of the crane fly tribe Elephantomyiini (Diptera, Tipuloidea, Limoniidae): comparative analysis and phylogenetic implications

Limoniidae, the most speciose family in the superfamily Tipuloidea, consists of four subfamilies and more than 11,000 species. However, mitochondrial (mt) genome sequences, which have been widely used for phylogenetic study, are available for only 11 species across three subfamilies. Thus, a larger variety of mt genome sequences in Limoniidae are required to improve our understanding of tipuloid phylogeny and genomic evolution. Here we present mt genomes of Elephantomyia (Elephantomyia) inulta Alexander, 1938 and Helius (Helius) pluto Alexander, 1932, representing the first mt genomes of the tribe Elephantomyiini (Limoniidae). The two mt genomes are typical circular DNA molecules and show similar gene order, nucleotide composition and codon usage. Standard ATN start and TAR stop codons are present in most protein-coding genes. All transfer RNA (tRNA) genes exhibited the cloverleaf secondary structure typical for metazoans except in tRNASer(AGN), which lacks the dihydrouridine arm. Phylogenetic analyses were performed based on four nucleotide matrixes for the currently sequenced species of Tipuloidea using Bayesian inference and maximum likelihood methods. Four-cluster likelihood mapping was used to study incongruent signals between different topologies. Pediciidae is supported as the earliest lineage in Tipuloidea, and the sister-group relationship between Cylindrotomidae and Tipulidae is also supported, but the monophyly of Limoniidae is not supported. Our study also supports the monophyly of Elephantomyiini (Elephantomyia + Helius), as one of origins of flower-visiting in Limoniidae. Although Elephantomyiini is sister to Limoniinae + Epiphragma (Limnophilinae) in our study, a more precise understanding of its phylogenetic position in Tipuloidea will require additional studies that include a broader species sample.

The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants.

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.

Genetic structural variation in mitochondrial genomes of four species of Gomphidae and their phylogenetic implications

The Gomphids are the most diverse and important group in the (sub)tropics. Currently, research on Gomphids is mainly focused on fieldwork and morphological classification, however, the molecular-based study is still insufficient. Here, complete mitogenomes of Nihonogomphus semanticus (15,368 bp), Nihonogomphus lieftincki (15,342 bp), Asiagomphus septimus (15,334 bp), and Davidius fruhstorferi (15,682 bp) were obtained by high-throughput sequencing. Of the 37 genes conserved in order and orientation, 9 protein-coding genes (PCGs) and 14 tRNA genes were encoded by heavy strand, while the rest were encoded by light strand. The secondary structures of the protein encoded by 13 PCGs showed a general trend of proportion: α helix > random coil > extended strand > β turn. The trnS1 gene lacked a dihydrouridine arm and was thus reduced to a loop. The 3D structures of the protein encoded by 13 PCGs showed moderate to high levels of consistency among species. Phylogenetic analysis showed that Gomphids were well-supported monophyletic group, both BI and ML tree showed clear phylogenetic relationships in known Gomphidae: ((((D. lunatus + D. fruhstorferi) + A. septimus) + ((N. semanticus + N. lieftincki) + Ophiogomphus cecilia)) + Ictinogomphus sp MT 2014). Our study provides insight into the gene or their protein structure features of the family Gomphidae mitogenomes and lays the foundation for further phylogenetic studies.

The mitochondrial genome of the endemic and endangered trumpet-nosed bat Musonycteris harrisoni (Chiroptera: Phyllostomidae)

ABSTRACT The trumpet-nosed bat Musonycteris harrisoni (family Phyllostomidae) is endemic to the western Pacific slope of Mexico, and is considered endangered given prolonged and continuous population decline. This study, for the first time, assembled and characterised in detail the mitochondrial genome of this species that is in need of genomic resources. The mitogenome of Musonycteris harrisoni is 16,668 bp in length and encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a relatively long non-coding putative control region (CR) 1229 bp in length. Mitochondrial synteny is identical to that reported before in the family Phyllostomidae. As reported before in all phyllostomids, most mitochondrial genes are encoded on the heavy strand (H-strand), except for nad6 and eight tRNA genes that are encoded on the light strand (L-strand). All the tRNAs exhibit a ‘cloverleaf’ secondary structure, except tRNA Serine-1 that is missing the dihydrouridine (DHU) arm. All 13 mitochondrial PCGs are evolving under purifying selection, with atp8, nad4l and nad6 experiencing relaxed purifying selection in comparison to the other PCGs. Tandem repeats, microsatellites, and hairpin structures are observed in the CR of Musonycteris harrisoni, in agreement with what has been reported before in other cofamilial bats. The CR contains three functional domains: extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain. The mitochondrial genome sequence herein characterised completely and in detail represents a new genomic resource for M. harrisoni that will further the understanding of genetic diversity in this endangered species.

The Complete Mitochondrial Genome of the Freshwater Fish Onychostoma ovale (Cypriniformes, Cyprinidae): Genome Characterization and Phylogenetic Analysis.

In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Onychostoma ovale. The mitogenome of O. ovale was 16,602 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The nucleotide composition of the O. ovale mitogenome was 31.47% A, 24.07% T, 15.92% G, and 28.54% C, with a higher A + T content (55.54%) than G + C content (44.46%). All PCGs began with the standard ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene and the NADH dehydrogenase 3 (ND3) gene with GTG, while six PCGs ended with incomplete termination codons (TA or T). The Ka/Ks ratios of 13 PCGs were all less than one, indicating that they were under purifying selection. All tRNA genes were folded into the typical cloverleaf secondary structures with the exception of tRNASer(AGY), whose dihydrouridine (DHU) arm was absent. The phylogenetic trees showed that Onychostoma and Acrossocheilus were classified into three clades. There was a mosaic relationship between Onychostoma and Acrossocheilus. Moreover, the phylogenetic tree analysis showed that O. rarum was the closest species to O. ovale. This study can provide a useful resource for further phylogeny and population genetic analyses of Onychostoma and Acrossocheilus.

The complete mitochondrial genome of Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae) and its phylogenetic implications.

Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae, Pentatominae) are mainly distributed in southern China, India, Myanmar, and Sri Lanka. Both species are also common agricultural pests. However, only the morphology of the genus Aeschrocoris has previously been studied, and molecular data have been lacking. In this study, the whole mitochondrial genomes of A.tuberculatus and A.ceylonicus are and annotated. The lengths of the complete mitochondrial genomes of the two species are 16,134 bp and 16,142 bp, respectively, and both contain 37 typical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. The mitochondrial genome structure, gene order, nucleotide composition, and codon usage of A.tuberculatus and A.ceylonicus are consistent with those of typical Pentatomidae. Most PCGs of both species use ATN as the start codon, except atp8, nad1, and cox1, which use TTG as the start codon. cox1, cox2, and atp6 use a single T, and nad1 use TAG as the stop codon; the remaining PCGs have TAA as the stop codon. The A+T contents of the two species are 73.86% and 74.08%, respectively. All tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. The phylogenetic tree is reconstructed using the maximum-likelihood method based on the newly obtained mitochondrial genome sequences and 87 existing mitochondrial genomes of Pentatomoidea from the NCBI database and two species of Lygaeoidea as outgroups. The phylogenetic trees strongly support the following relationships: (Urostylididae + ((Acanthosomatidae + ((Cydnidae + (Dinidoridae + Tessaratomidae)) + (Scutelleridae + Plataspidae))) + Pentatomidae). This study enriches the mitochondrial genome database of Pentatomoidea and provides a reference for further phylogenetic studies.

The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea.

Capniidae are a family of stoneflies, also known as snow flies, who emerge in winter. The phylogeny of Capniidae is widely accepted to be based on morphological analysis. Until now, only five Capniidae mitochondrial genomes have been sequenced so far. In addition, sampling is required to determine an accurate phylogenetic association because the generic classification of this family is still controversial and needs to be investigated further. In this study, the first mitogenome of genus Isocapnia was sequenced with a length of 16,200 bp and contained 37 genes, including a control region, two rRNAs, 22 tRNAs, and 13 PCGs, respectively. Twelve PCGs originated with the common start codon ATN (ATG, ATA, or ATT), while nad5 used GTG. Eleven PCGs had TAN (TAA or TAG) as their last codon; however, cox1 and nad5 had T as their final codon due to a shortened termination codon. All tRNA genes demonstrated the cloverleaf structure, which is distinctive for metazoans excluding the tRNASer1 (AGN) that missed the dihydrouridine arm. A Phylogenetic analysis of the superfamily Nemouroidea was constructed using thirteen PCGs from 32 formerly sequenced Plecoptera species. The Bayesian inference and maximum likelihood phylogeny tree structures derived similar results across the thirteen PCGs. Our findings strongly supported Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). Ultimately, the best well-supported generic phylogenetic relationship within Capniidae is as follows; (Isocapnia + (Capnia + Zwicknia) + (Apteroperla + Mesocapnia)). These findings will enable us to better understand the evolutionary relationships within the superfamily Nemouroidea and the generic classification and mitogenome structure of the family Capniidae.

Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation.

Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.

Mitogenome of the Doleschallia bisaltide and Phylogenetic Analysis of Nymphalinae (Lepidoptera, Nymphalidae)

The complete mitogenome of Doleschallia bisaltide was sequenced with a size of 16,389 bp. Gene orientation and arrangement in the newly sequenced mitogenome are the same as other mitogenomes in Lepidoptera. Except for trnS1(AGN), which lacks the dihydrouridine (DHC) arm, the other 21 tRNA genes all contain a typical cloverleaf structure. Ka/Ks ratio analysis of 13 protein-coding genes (PCGs) from 23 Nymphalinae species indicates that the evolutionary rate of COX1 was slowest, while that of ATP8, ND5, and ND6 was substantially high. Phylogenetic analysis revealed that Nymphalinae and Kallimini were nonmonophyletic. Trees constructed only from the nuclear DNA (nDNA) dataset had lower support than mitochondrial or combined datasets. The addition of RNA genes did not improve the phylogenetic signal, and nodal support decreased. These data provide important information for future studies into the phylogeny of Nymphalinae.

Characterization of the Complete Mitochondrial Genome of a Flea Beetle Luperomorpha xanthodera (Coleoptera: Chrysomelidae: Galerucinae) and Phylogenetic Analysis.

In this study, the mitochondrial genome of Luperomorpha xanthodera was assembled and annotated, which is a circular DNA molecule including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), and 1388 bp non-coding regions (A + T rich region), measuring 16,021 bp in length. The nucleotide composition of the mitochondrial genome is 41.3% adenine (A), 38.7% thymine (T), 8.4% guanine (G), and 11.6% cytosine (C). Most of the protein-coding genes presented a typical ATN start codon (ATA, ATT, ATC, ATG), except for ND1, which showed the start codon TTG. Three-quarters of the protein-coding genes showed the complete stop codon TAR (TAA, TAG), except the genes COI, COII, ND4, and ND5, which showed incomplete stop codons (T- or TA-). All the tRNA genes have the typical clover-leaf structure, except tRNASer1 (AGN), which has a missing dihydrouridine arm (DHU). The phylogenetic results determined by both maximum likelihood and Bayesian inference methods consistently supported the monophyly of the subfamily Galerucinae and revealed that the subtribe Luperina and genus Monolepta are polyphyletic groups. Meanwhile, the classification status of the genus Luperomorpha is controversial.

The Complete Mitochondrial Genome of Torix tukubana (Annelida: Hirudinea: Glossiphoniidae).

Torix tukubana is a poorly understood proboscidate leech species, generally an ectoparasite on amphibian species. In this study, the complete mitochondrial genome (mitogenome) of T. tukubana was sequenced using next-generation sequencing (NGS), and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the T. tukubana mitogenome was 14,814 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (CR). The mitogenome composition presented a strong A + T bias (73.6%). All tRNAs had the typical clover structure except the trnS1 (TCT), whose dihydrouridine (DHU) arm was short, having only one complementary base pair. Additionally, 8 gene order patterns were identified among 25 known Hirudinea species, and T. tukubana was identical to the Hirudinea ground pattern. A phylogenetic analysis based on 13 PCGs indicated that all the studied species clustered into three main clades. The relationships among Hirudinea species were basically consistent with their gene arrangement results, but different from their morphological taxonomy. T. tukubana was in the monophyletic group of Glossiphoniidae, a finding consistent with previous research. Our results provided the essential characteristics of the T. tukubana mitogenome. As the first complete mitogenome of Torix, it could offer valuable information for a systematic understanding of the Hirudinea species.