Secondary follicles enable efficient germline mtDNA base editing at hard-to-edit site

Efficient germline mtDNA editing is required to construct disease-related animal models and future gene therapy. Recently, the DddA-derived cytosine base editors (DdCBEs) have made mitochondrial genome (mtDNA) precise editing possible. However, there still exist challenges for editing some mtDNA sites in germline via zygote injection, probably due to the suspended mtDNA replication during preimplantation development. Here, we introduce a germline mtDNA base editing strategy: injecting DdCBEs into oocytes of secondary follicles, at which stage mtDNA replicates actively. With this method, we successfully observed efficient G-to-A conversion at a hard-to-edit site and also obtained live animal models. In addition, for those editable sites, this strategy can greatly improve the base editing efficiency up to 3-fold, which is more than that in zygotes. More important, editing in secondary follicles did not increase more the risk of off-target effects than that in zygotes. This strategy provides an option to efficiently manipulate mtDNA sites in germline, especially for hard-to-edit sites.

The role of lysine acetylation in the function of mitochondrial ribosomal protein L12

Mitochondria play a central role in energy production and cellular metabolism. Mitochondria contain their own small genome (mitochondrial DNA, mtDNA) that carries the genetic instructions for proteins required for ATP synthesis. The mitochondrial proteome, including the mitochondrial transcriptional machinery, is subject to post-translational modifications (PTMs), including acetylation and phosphorylation. We set out to determine whether PTMs of proteins associated with mtDNA may provide a potential mechanism for the regulation of mitochondrial gene expression. Here, we focus on mitochondrial ribosomal protein L12 (MRPL12), which is thought to stabilize mitochondrial RNA polymerase (POLRMT) and promote transcription. Numerous acetylation sites of MRPL12 were identified by mass spectrometry. We employed amino acid mimics of the acetylated (lysine to glutamine mutants) and deacetylated (lysine to arginine mutants) versions of MRPL12 to interrogate the role of lysine acetylation in transcription initiation in vitro and mitochondrial gene expression in HeLa cells. MRPL12 acetyl and deacetyl protein mimics were purified and assessed for their ability to impact mtDNA promoter binding of POLRMT. We analyzed mtDNA content and mitochondrial transcript levels in HeLa cells upon overexpression of acetyl and deacetyl mimics of MRPL12. Our results suggest that MRPL12 single-site acetyl mimics do not change the mtDNA promoter binding ability of POLRMT or mtDNA content in HeLa cells. Individual acetyl mimics may have modest effects on mitochondrial transcript levels. We found that the mitochondrial deacetylase, Sirtuin 3, is capable of deacetylating MRPL12 in vitro, suggesting a potential role for dynamic acetylation controlling MRPL12 function in a role outside of the regulation of gene expression.

Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia

The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.

Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Characterization of the complete mitochondrial genome of the Libelloides sibiricus (Neuroptera, Ascalaphidae)

Libelloides sibiricus (Eversmann, 1850) is widely distributed in China, Korea and eastern Russia. To date, few studies have been conducted on this species, with the exception of morphological taxonomy studies. In this study, we sequenced the complete mitochondrial genome (mitogenome) of Libelloides sibiricus, which is 15,811 bp in length, with an overall A + T content of 74.8%, encoding 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region. The gene arrangement and components of L. sibiricus are identical to those of most other Neuropteran species. TAA is utilized as the termination codon for most PCGs and TAG for nd1, however, nd6 and atp6 used the incomplete termination codon TA- and cox1, cox2, nd5, cytb had termination codons consisting of only T-. In addition, we selected all known 59 species of Neuroptera from NCBI, and used Sialis hamata, Sialis melania, Sialis longidens and Sialis jiyuni (Megaloptera: Sialidae) as the outgroup. Phylogenetic analysis suggested that the mitogenome of L. sibiricus was the most closely related to L. macaronius and all the owlflies formed the monophyletic group within the superfamily Myrmeleontoidea.

The complete mitochondrial genome of the ice krill Euphausia crystallorophias Holt & Tattersall, 1906 (Euphausiacea, Euphausiidae), from the Ross Sea, Antarctica

The mitogenome of Euphausia crystallorophias collected from the Ross Sea Region Marine Protected Area (RSR MPA) is described for the first time. The assembled mitogenome was 17,291 bp in length and consisted of two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and noncoding regions, all of which were identical to those of other euphausiid species. The most common start codon for the 13 PCGs was ATG, and the most common termination codon was TAA. The overall G + C content was 33.2% in the heavy strand. Euphausia crystallorophias was sister to E. superba in the phylogenetic analysis. The mitogenome of E. crystallorophias provided significant DNA molecular data for further identification and phylogenetic analysis within the euphausiids.

Mitochondrial genome variation and intergenomic sequence transfers in Hevea species

Among the Hevea species, rubber tree (Hevea brasiliensis) is the most important source of natural rubber. In previous studies, we sequenced the complete nuclear and chloroplast genomes of Hevea species, providing an invaluable resource for studying their phylogeny, disease resistance, and breeding. However, given that plant mitochondrial genomes are more complex and more difficult to assemble than that of the other organelles, little is known about their mitochondrial genome, which limits the comprehensive understanding of Hevea genomic evolution. In this study, we sequenced and assembled the mitochondrial genomes of four Hevea species. The four mitochondrial genomes had consistent GC contents, codon usages and AT skews. However, there were significant differences in the genome lengths and sequence repeats. Specifically, the circular mitochondrial genomes of the four Hevea species ranged from 935,732 to 1,402,206 bp, with 34-35 unique protein-coding genes, 35-38 tRNA genes, and 6-13 rRNA genes. In addition, there were 17,294-46,552 bp intergenomic transfer fragments between the chloroplast and mitochondrial genomes, consisting of eight intact genes (psaA, rrn16S, tRNA-Val, rrn5S, rrn4.5S, tRNA-Arg, tRNA-Asp, and tRNA-Asn), intergenic spacer regions and partial gene sequences. The evolutionary position of Hevea species, crucial for understanding its adaptive strategies and relation to other species, was verified by phylogenetic analysis based on the protein-coding genes in the mitochondrial genomes of 21 Malpighiales species. The findings from this study not only provide valuable insights into the structure and evolution of the Hevea mitochondrial genome but also lay the foundation for further molecular, evolutionary studies, and genomic breeding studies on rubber tree and other Hevea species, thereby potentially informing conservation and utilization strategies.

Harnessing accurate mitochondrial DNA base editing mediated by DdCBEs in a predictable manner

Introduction: Mitochondrial diseases caused by mtDNA have no effective cures. Recently developed DddA-derived cytosine base editors (DdCBEs) have potential therapeutic implications in rescuing the mtDNA mutations. However, the performance of DdCBEs relies on designing different targets or improving combinations of split-DddA halves and orientations, lacking knowledge of predicting the results before its application. Methods: A series of DdCBE pairs for wide ranges of aC or tC targets was constructed, and transfected into Neuro-2a cells. The mutation rate of targets was compared to figure out the potential editing rules. Results: It is found that DdCBEs mediated mtDNA editing is predictable: 1) aC targets have a concentrated editing window for mtDNA editing in comparison with tC targets, which at 5'C8-11 (G1333) and 5'C10-13 (G1397) for aC target, while 5'C4-13 (G1333) and 5'C5-14 (G1397) for tC target with 16bp spacer. 2) G1333 mediated C>T conversion at aC targets in DddA-half-specific manner, while G1333 and G1397 mediated C>T conversion are DddA-half-prefer separately for tC and aC targets. 3) The nucleotide adjacent to the 3' end of aC motif affects mtDNA editing. Finally, by the guidance of these rules, a cell model harboring a pathogenic mtDNA mutation was constructed with high efficiency and no bystander effects. Discussion: In summary, this discovery helps us conceive the optimal strategy for accurate mtDNA editing, avoiding time- and effort-consuming optimized screening jobs.

The complete mitochondrial genome of Meller's mongoose (Rhynchogale melleri)

Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.

Characteristics of the complete mitochondrial genome of Gerres limbatus (Cuvier, 1830) (Perciformes: Gerreidae)

The saddleback silver-biddy Gerres limbatus (Cuvier 1830) is distributed in Indo-West Pacific Oceans and associated with shallow coastal marine waters and estuaries. In this study, the complete mitochondrial genome of G. limbatus was firstly documented, which is 16,730 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of the mitochondrial genome is 26.42% A, 28.68% C, 27.32% T, and 17.58% G. The Maximum Likelihood phylogenetic tree was constructed based on COI gene of the 31 species from the family Gerreidae, with Heteroclinus puellarum and Hypopterus macropterus as outgroups. It revealed that G. erythrourus was placed as the sister group to G. limbatus.

Genetic differentiation and phylogeography of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) in the southwestern karst area of China

Erythroneurini is the largest tribe of the microleafhopper subfamily Typhlocybinae. Most prior research on this tribe has focused on traditional classification, phylogeny, and control of agricultural pests, and the phylogeography of the group remains poorly understood. In this study, the mitochondrial genomes of 10 erythroneurine species were sequenced, and sequences of four genes were obtained for 12 geographical populations of Seriana bacilla. The new sequence data were combined with previously available mitochondrial DNA sequence data and analyzed using Bayesian and Maximum-Likelihood-based phylogenetic methods to elucidate relationships among genera and species and estimate divergence times. Seriana was shown to be derived from within Empoascanara. Phylogeographic and population genetic analysis of the endemic Chinese species Seriana bacilla suggest that the species diverged about 54.85 Mya (95% HPD: 20.76-66.23 million years) in the Paleogene period and that population divergence occurred within the last 14 million years. Ancestral area reconstruction indicates that Seriana bacilla may have originated in the central region of Guizhou, and geographical barriers are the main factors affecting gene flow among populations. Ecological niche modeling using the MaxEnt model suggests that the distribution of the species was more restricted in the past but is likely to expand in the future years 2050 and 2070.

Six complete mitochondrial genomes of ground beetles from the Harpalinae and Carabinae (Coleoptera, Carabidae) with phylogenetic analysis based on mitogenomic data

In this study, we employed high-throughput sequencing technology to determine the complete mitochondrial genomes of six ground beetles, encompassing five Harpalinae species and one Carabinae species. The sizes of mitochondrial genomes ranged from 15,334 to 16,972 bp, encompassing 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Furthermore, each species was found to possess a putative control region. Combining with 65 published mitochondrial genome sequences of Carabidae as ingroups and four species from Trachypachidae, Gyrinidae and Dytiscidae as outgroups, we conducted phylogenetic analyses utilizing Maximum likelihood and Bayesian inference methods. Moreover, we reconstructed a species tree of Carabidae based on mitochondrial genome data using the coalescent-based species tree method (ASTRAL). The results revealed that the family Carabidae was not a monophyletic group. The subfamily Harpalinae was supported to be a monophyletic group in Maximum likelihood analysis. Although the subfamily Carabinae was found to be nonmonophyletic in the concatenation analyses under both Maximum likelihood and Bayesian inference criteria, it was identified as a monophyletic group in the species tree analysis.

Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

Abies koreana E.H.Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history. Using the Illumina NovaSeq 6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A. koreana. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking conserved gene clusters. In the plastome, the ONT reads revealed two structural conformations of A. koreana. The short inverted repeats (1186 bp) of the A. koreana plastome are associated with different structural types. Transcriptomic sequencing revealed 1356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using A. koreana as a reference, we additionally produced nuclear and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (Balsamea, Momi, and Pseudopicea) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization. The obtained data illustrate that phylogenomic analyses based on sequences from differently inherited organelle genomes have resulted in conflicting trees. Organelle capture, organelle genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within Abies and new insights into the phylogenomic complexity of this genus.

Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals

The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.

The complete mitochondrial genome of Tauraco livingstonii (Musophagidae: Tauraco)

Livingstone's turaco, Tauraco livingstonii, belongs to the family Musophagidae. In this study, we obtained the complete mitochondrial genome sequence of Livingstone's turaco by high-throughput sequencing technology and constructed a phylogenetic tree. It was found that the mitochondria of this species are 19,015 bp in length and contain a total of 37 genes, comprising 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The base composition of the mitochondrial genome is 31.61% A, 24.22% T, 30.64% C, and 13.52% G, with a GC content of 44%. Notably, an intriguing phenomenon of mitochondrial genome rearrangements was observed, characterized by the duplication of the tRNA Glu-L-CR gene order. In addition, the results of the phylogenetic tree analysis shed light on the taxonomic position of Livingstone's turaco and supported the taxonomy of Otidimorphae. The study provides a basis for future phylogenetic and taxonomic investigations of Musophagiformes.

Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis

The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.

Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths

The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.

Complete mitochondrial genome of Basilepta melanopus Lefèvre, 1893 (coleoptera: chrysomelidae: eumolpinae), a tea pest from Southern China

The tea pest, Basilepta melanopus Lefèvre 1893 (Chrysomelidae), belongs to the subfamily Eumolpinae. In this study, the complete mitochondrial genome sequence of B. melanopus from southern China was sequenced using the next-generation sequencing technique, assembled, and annotated using bioinformatics tools. The complete mitochondrial genome was 15,905 bp in length. The overall GC content was 22.51%, in which the percentages for the bases A, T, C, and G were 41.23%, 36.26%, 8.92%, and 13.59%, respectively. Thirty-seven genes were predicted, including 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes. Phylogenetic analysis based on the complete mitochondrial genome sequences of 18 Chrysomelidae taxa revealed that B. melanopus was closely related to Basilepta fulvipes.

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, Emmelichthys)

We describe a new species of redbait in the genus Emmelichthys collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to E.struhsakeri but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs. 34-41). Additionally, mitochondrial DNA differentiates this taxon from other species of Emmelichthys. We generate mitochondrial genomes for two of the three type specimens and several other emmelichthyids to place the new taxon in a phylogenetic context. Analysis of the protein-coding mitochondrial loci calls into question the monophyly of two emmelichthyid genera (Emmelichthys and Erythrocles) and highlights the need for subsequent analyses targeting the intrarelationships of the Emmelichthyidae.

The complete mitochondrial genome of Hericium erinaceus (Bull.:Fr.) Pers., 1797 (Russulales, Basidiomycota): an edible and medicinal fungus

Hericium erinaceus (Bull.:Fr.) Pers., 1797, is an edible and medicinal fungus found in China. In this study, specimens of H. erinaceus HE0021 were collected from southeastern China (Yunhe County, Lishui City, Zhejiang Province, 28°7'12″N, 119°34'12″E). The whole mitochondrial genome of H. erinaceus HE0021 was sequenced using next-generation sequencing (NGS) technology, which comprised 15 protein-coding genes (PCGs), 27 transfer RNAs (tRNAs), two ribosomal RNAs, with a total length of 83,518 base pairs (bp). The results of the phylogenetic analysis show that H. erinaceus and H. coralloides were clustered in the same clade. The complete mitogenome sequence provides essential data for the subsequent investigation of Hericium and Russulales.

The Roles of CircRNAs in Mitochondria

Mitochondria participate in varieties of cellular events. It is widely accepted that human mitochondrial genome encodes 13 proteins, 2 rRNAs, and 22 tRNAs. Gene variation derived from human nuclear genome cannot completely explain mitochondrial diseases. The advent of high-throughput sequencing coupled with novel bioinformatic analyses decode the complexity of mitochondria-derived transcripts. Recently, circular RNAs (circRNAs) from both human mitochondrial genome and nuclear genome have been found to be located at mitochondria. Studies about the roles and molecular mechanisms underlying trafficking of the nucleus encoded circRNAs to mitochondria and mitochondria encoded circRNAs to the nucleus or cytoplasm in mammals are only beginning to emerge. These circRNAs have been associated with a variety of diseases, especially cancers. Here, we discuss the emerging field of mitochondria-located circRNAs by reviewing their identification, expression patterns, regulatory roles, and functional mechanisms. Mitochondria-located circRNAs have regulatory roles in cellular physiology and pathology. We also highlight future perspectives and challenges in studying mitochondria-located circRNAs, as well as their potential biomedical applications.

First mitogenomic characterization of Macromotettixoides (Orthoptera, Tetrigidae), with the descriptions of two new species

Classification of species is commonly based on morphological, molecular, and distribution depending on the taxa. Macromotettixoides Zheng, Wei & Jiang, 2005 and Formosatettix Tinkham, 1937 are both wingless types of Tetrigidae with extremely similar morphological characteristics, and in the current taxonomic system they are placed in two different subfamilies, Metrodorinae and Tetriginae, respectively. It is difficult to clearly identify the species of these two genera by morphological characteristics, and molecular data is often needed to assist identification. Here, the complete mitogenomes of two new species were sequenced and assembled, with that of Macromotettixoidesorthomargina. Molecular data of species of Formosatettix were used to test the monophyly of Macromotettixoides and to re-assess the generic characters, and also to test whether Macromotettixoides belongs to the Asian Metrodorinae or Tetriginae. Furthermore, mitochondrial characteristics were analyzed and the phylogeny of the Tetrigidae reconstructed based on mitochondrial protein-coding genes (PCGs). The results indicated that the two new species were clustered with Macromotettixoides rather than Formosatettix, and the anterior margin of the fastigium and pronotum of the two new species usually had the humeral angle different from that of Formosatettix. Therefore, after integrating morphological and molecular data, the two new species were placed in the genus Macromotettixoides, M.maoershanensissp. nov. and M.brachycornasp. nov. Finally, a phylogenetic reconstruction supported Macromotettixoides being assigned to Tetriginae rather than Metrodorinae, in contrast to the previous classification of this genus.

The complete mitochondrial genome and phylogenetic position of Schizothorax argentatus (Cyprinomorpha: Crypriniformes: Cyprinidae)

We investigated the vulnerable fish species Schizothorax argentatus Kessler, 1874, using low-coverage whole genome sequencing data. The assembled 16,587 bp mitochondrial genome has a nucleotide composition of A = 29.8%, T = 25.3%, G = 17.9%, and C = 27.0%, containing 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes with a gene arrangement identical to other cofamilial species. Phylogenetic analyses of 71 schizothoracine fishes suggest a close relationship between S. argentatus and Schizothorax eurystomus, sharing a common ancestor with Schizothorax pseudoaksaiensis. Our study supports dividing extant schizothoracine fishes into two tribes, Schizothoracini and Schizopygopsini. The estimated time to most recent common ancestor (tMRCA) and their distribution imply geological and climatic events during the Miocene around the Qinghai-Tibet Plateau as significant evolutionary drivers explaining the diversification of main clades in schizothoracine fishes.

Genomic insights into the clonal reproductive Opuntia cochenillifera: mitochondrial and chloroplast genomes of the cochineal cactus for enhanced understanding of structural dynamics and evolutionary implications

Background

The cochineal cactus (Opuntia cochenillifera), notable for its substantial agricultural and industrial applications, predominantly undergoes clonal reproduction, which presents significant challenges in breeding and germplasm innovation. Recent developments in mitochondrial genome engineering offer promising avenues for introducing heritable mutations, potentially facilitating selective sexual reproduction through the creation of cytoplasmic male sterile genotypes. However, the lack of comprehensive mitochondrial genome information for Opuntia species hinders these efforts. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.

Results

We sequenced the total DNA of the O. cochenillifera using DNBSEQ and Nanopore platforms. The mitochondrial genome was then assembled using a hybrid assembly strategy using Unicycler software. We found that the mitochondrial genome of O. cochenillifera has a length of 1,156,235 bp, a GC content of 43.06%, and contains 54 unique protein-coding genes and 346 simple repeats. Comparative genomic analysis revealed 48 homologous fragments shared between mitochondrial and chloroplast genomes, with a total length of 47,935 bp. Additionally, the comparison of mitochondrial genomes from four Cactaceae species highlighted their dynamic nature and frequent mitogenomic reorganizations.

Conclusion

Our study provides a new perspective on the evolution of the organelle genome and its potential application in genetic breeding. These findings offer valuable insights into the mitochondrial genetics of Cactaceae, potentially facilitating future research and breeding programs aimed at enhancing the genetic diversity and adaptability of O. cochenillifera by leveraging its unique mitochondrial genome characteristics.

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites

Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.

Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes

Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of D. filamentosa and P. nigrofasciata measure 16,598 and 16,948 bp, respectively. Both D. filamentosa and P. nigrofasciata exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that D. filamentosa is closely related to the sister group comprising Dawkinsia denisonii and Sahyadria chalakkudiensis. Similarly, P. nigrofasciata forms a sister group with Pethia ticto and Pethia stoliczkana.

Comparative Analysis of the Mitochondrial Genomes of Chloropidae and Their Implications for the Phylogeny of the Family

Chloropidae, commonly known as grass flies, represent the most taxonomically diverse family of Diptera Carnoidea, comprising over 3000 described species worldwide. Previous phylogenetic studies of this family have predominantly relied on morphological characters, with mitochondrial genomes being reported in a few species. This study presents 11 newly sequenced mitochondrial genomes (10 Chloropidae and 1 Milichiidae) and provides the first comprehensive comparative analysis of mitochondrial genomes for Chloropidae. Apart from 37 standard genes and the control region, three conserved intergenic sequences across Diptera Cyclorrhapha were identified in all available chloropid mitochondrial genomes. Evolutionary rates within Chloropidae exhibit significant variation across subfamilies, with Chloropinae displaying higher rates than the other three subfamilies. Phylogenetic relationships based on mitochondrial genomes were inferred using maximum likelihood and Bayesian methods. The monophyly of Chloropidae and all four subfamilies is consistently strongly supported, while subfamily relationships within Chloropidae remain poorly resolved, possibly due to rapid evolution.

Mitogenomics reveals extremely low genetic diversity in the endangered Jilin clawed salamander: Implications for its conservation

The Jilin clawed salamander (Onychodactylus zhangyapingi) is an endemic, endangered, and level-two protected amphibian species of China. In the context of serious threats to amphibians worldwide, conservation studies of this endangered species are urgently needed. In this study, mitogenomic conservation genetics and species distribution modeling analyses were performed for O. zhangyapingi. Sixty-three samples were collected from nine different locations, and the complete mitochondrial genome was sequenced. Population genetic analyses revealed that O. zhangyapingi exhibits only one genetic structure with extremely low nucleotide diversity. Late Pleistocene climate cooling may have led to a reduction in effective population size and extremely low mitogenomic nucleotide diversity in this salamander, and the subsequent temperature increase (~20 kya to present) provided the opportunity for rapid population growth. The continuous highly suitable region for O. zhangyapingi is only approximately 3000 km2 on the southeastern boundary of Jilin Province, China. Fortunately, there are three large forested national nature reserves within the distribution of O. zhangyapingi that can effectively protect endangered species. Our findings suggest that O. zhangyapingi is a vulnerable species with a narrow distribution and extremely low genetic diversity, and we should pay more attention to the conservation management of this species.

Mitochondrial genome sequence comparisons indicate that the elephant louse Haematomyzus elephantis (Piaget, 1869) contains cryptic species

The parvorder Rhynchopthirina contains three currently recognised species of lice that parasitize elephants (both African savanna elephant Loxodonta africana and Asian elephant Elephas maximus), desert warthogs (Phacochoerus aethiopicus) and Red River hogs (Potamochoerus porcus), respectively. The Asian elephant lice and the African savanna elephant lice are currently treated as the same species, Haematomyzus elephantis (Piaget, 1869), based on morphology despite the fact that their hosts diverged 8.4 million years ago. In the current study, we sequenced 23 mitochondrial (mt) genes of African savanna elephant lice collected in South Africa and analysed the sequence divergence between African savanna elephant lice and previously sequenced Asian elephant lice. Sequence comparisons revealed >23% divergence for the 23 mt genes as a whole and ~17% divergence for cox1 gene between African savanna and Asian elephant lice, which were far higher than the divergence expected within a species. Furthermore, the mt gene sequence divergences between these lice are 3.76-4.6 times higher than that between their hosts, the African savanna and Asian elephants, which are expected for the co-divergence and co-evolution between lice and their elephant hosts. We conclude that (1) H. elephantis (Piaget, 1869) contains cryptic species and (2) African savanna and Asian elephant lice are different species genetically that may have co-diverged and co-evolved with their hosts.

Mitochondrial genomes of Nemourinae species (Plecoptera: Nemouridae) and the phylogenetic implications

Currently, the classification system of 2 subfamilies within Nemouridae has been widely accepted. However, monophyly of 2 subfamilies has not been well supported by molecular evidence. To date, only mitogenomes from genus Nemoura of the subfamily Nemourinae were used in previous phylogenetic studies and produced conflicting results with morphological studies. Herein, we analyzed mitogenomes of 3 Nemourinae species to reveal their mitogenomic characteristics and to examine genus-level classification among Nemouridae. In this study, the genome organization of 3 mitogenomes is highly conserved in gene order, nucleotide composition, codon usage, and amino acid composition. In 3 Nemourinae species, there is a high variation in nucleotide diversity among the 13 protein-coding genes (PCGs). The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. The phylogenetic analyses highly support Nemurella as the sister group to Ostrocerca. Meanwhile, Nemoura is recovered as the sister group of Malenka; they are grouped with other Amphinemurinae and emerged from a paraphyletic Nemourinae. More molecular data from different taxonomic groups are needed to understand stoneflies phylogeny and evolution.

Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory

Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.

Characterization of the Complete Mitochondrial Genome of Schizothorax kozlovi (Cypriniformes, Cyprinidae, Schizothorax) and Insights into the Phylogenetic Relationships of Schizothorax

Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (-0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax.

Complete mitochondrial genome of the diving beetle, Cybister brevis Aubé, 1838 (Coleoptera, Dytiscidae) from Jeju Island

The mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history.

The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda

This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.

The complete mitochondrial genome of the bait worm, Marphysa victori (Annelida; Polychaeta; Eunicida; Eunicidae)

The complete mitochondrial genome of Marphysa victori Lavesque, Daffe, Bonifácio & Hutchings, 2017, was 15,891 bp in length with a GC content of 41%, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The maximum-likelihood tree showed the closest relationship between M. victori and M. sanguinea.

RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.

Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mitogenomes of nine other Pseudogastromyzon fish on GenBank to conduct a detailed comparative analysis of their phylogenetic relationships and evolutionary history. The findings revealed a conservation in both gene composition and gene order. Except for the trnS1 gene lacking dihydrouracil arms, the other 21 tRNAs showed the typical clover-leaf secondary structure. According to the ΔRSCU method, we identified the seven most abundant optimal codons: CUA, GUA, CCA, CAA, GAA, AGC, and GGC. The construction of maximum parsimony, maximum likelihood, and Bayes trees yielded congruent topologies, and the 11 Pseudogastromyzon species were clustered into two major clusters. Among them, one of which was composed of P. fangi, P. changtingensis changtingensis, and P. changtingensis tungpeiensis, while the remaining eight species formed another cluster, further subdivided into five smaller clusters. Distinct clusters formed between P. fasciatus jiulongjiangensis and P. meihuashanensis, P. cheni and P. peristictus, and P. laticeps and P. lianjiangensis, and the remaining two species were clustered separately, thereby enhancing our understanding of them. Furthermore, our analysis results of divergence times revealed that these 11 Pseudogasteromyzon species underwent rapid differentiation in the Pleistocene epochs. Overall, our study sheds light on the phylogenetic relationship and evolutionary history of Pseudogasteromyzon species, providing a necessary knowledge foundation for further understanding the intricacies of an ecosystem health assessment.

The overview of methods for assembling complex mitochondrial genomes in land plants

The large size and complex structural rearrangements inherent in mitochondrial genomes of land plants pose challenges for their sequencing. Originally, the assembly of these genomes required the cloning of mitochondrial DNA fragments, followed by Sanger sequencing. Subsequently, the advent of next-generation sequencing significantly expedited the process. This review highlights instances of plant mitochondrial genome assembly employing various technologies, including 454 sequencing, Illumina short sequencing reads, and Pacific Biosciences or Oxford Nanopore Technology long sequencing reads. The combination of short and long reads in hybrid assembly has proven to be the most efficient approach for achieving reliable assemblies of land plant mitochondrial genomes.

Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav

Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and phylogenetic relationships. Furthermore, we compared it with other plant mt genomes. The data we obtained will provide valuable information for studying evolutionary processes in the Capsicum genus and will assist in the functional analysis of Capsicum mitogenomes.

Complete mitochondrial genome of an oleaginous microalga Vischeria punctata (Eustigmatophyceae: Chlorobotryaceae) and phylogenetic analysis

Vischeria punctata, as first described by Vischer in 1945, is a member of the family Chlorobotryaceae, within the order Eustigmatales. This species is recognized for its potential as a source of biofuels and other high-value products. In the present investigation, the whole genome of V. punctata was sequenced utilizing the Illumina HiSeq 4000 platform, enabling the assembly and annotation of its complete mitochondrial genome. The resulting circular genome spans 41,528 base pairs (bp) with a guanine-cytosine (GC) content of 27.3%. This genome encompasses 36 protein-coding genes, alongside 28 transfer RNA (tRNA), and three ribosomal RNA (rRNA) genes. The evolutionary trajectory of V. punctata was further explored by constructing a phylogenetic tree derived from the mitochondrial 33 gene dataset of 16 Ochrophyta species. Comparative analysis reveals that V. punctata bears closer ties to Vischeria sp. CAUP Q202 than to Vischeria stellata strain SAG 33.83, suggesting shared evolutionary pathways and phenotypic traits. This investigation constitutes the inaugural study into the mitochondrial evolution and phylogenetic patterning of the mitogenome in V. punctata. The outcomes from this research bolster our understanding of the genetic diversity and evolutionary processes within the class Eustigmatophyceae. In particular, the mitochondrial genome of V. punctata serves as a valuable resource in elucidating these aspects.

The complete mitochondrial genome of Bauhinia variegata (Leguminosae)

The mitogenome of Bauhinia variegate was assembled and characterized in this study. The mitogenome size was 437,271 bp, and its GC content was 45.5%. 36 protein-coding genes, 17 tRNAs and 3 rRNAs were annotated in the mitogenome. A total of 12 MTPTs, ranging from 71 bp to 3562 bp, were identified in the mitogenome and covered 1.46% (6373 bp) of the mitogenome. Phylogenetic analysis of 15 species of Leguminosae based on 23 core protein-coding genes showed that B. variegata was sister to Tylosema esculentum, another member from the subfamily Cercidoideae. The mitogenome of B. variegata provides a valuable genetic resource for further phylogenetic studies of this family.

The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae

Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.

Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond (Prunus tenella)

Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.

Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications

Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.

The first complete mitochondrial genome of the agricultural pest Micromelalopha sieversi (Staudinger, 1892) (Lepidoptera: Notodontidae)

Micromelalopha sieversi (Staudinger, 1892) is a significant pest of Poplar trees in China. In this study, we used high-throughput sequencing to sequence the whole mitochondrial genome of M. sieversi. The length of the genome was 15,373 base pairs. The nucleotide composition was 39.8%, 11.5%, 8.0%, and 40.7% for A, C, G, and T, respectively. We used the maximum-likelihood method to construct a molecular phylogenetic tree based on complete mitogenome sequences of 19 Noctuoidea species as ingroups and five Geometroidea species as outgroups. The results indicate that the genus Micromelalopha is closely related to the genus Clostera in family Notodontidae.

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Butyriboletus hainanensis, a macrofungus belonging to the Boletaceae family, is named after its collection location on Hainan Island, China. However, little is known about its mitochondrial genome and its phylogenetic relationship with other boletes. In this study, we utilized next-generation sequencing technology to sequence the mitochondrial genome of Bu. hainanensis. Our findings revealed that the mitochondrial genome of this species is presumably a circular DNA molecule spanning 36,592 bp. It consists of 15 protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitochondrial genome is as follows: A (36.64%), C (12.22%), G (11.73%), and T (39.41%), with a GC content of 23.95%. Additionally, a phylogenetic tree was constructed based on 22 mitochondrial genomes, which provided valuable insights into the phylogenetic relationships of Bu. hainanensis with other boletes for the first time.

The Mitochondrial Genomes of Siboglinum plumosum and Oligobrachia dogieli (Annelida: Siboglinidae) and Their Phylogenetic Analysis

Frenulates are a group of sedentary Annelida within the family Siboglinidae that inhabit the ocean floor and present a unique challenge for comprehensive molecular and phylogenetic investigations. In this study, we focused on the frenulates, specifically assembling the mitochondrial genomes of Siboglinum plumosum and Oligobrachia dogieli. The phylogenetic reconstruction placed S. plumosum as a sister taxon to S. ekmani, and O. dogieli as a sister taxon to S. fiordicum, supporting the non-monophyletic nature of the genus Siboglinum. Overall, this study supports the phylogeny of the family Siboglinidae while highlighting the need for additional molecular data within frenulates.

An Overview of Aquatica Fu et al., a Phylogeny of Aquatic Fireflies Using Mitochondrial Genomes, a Description of Two New Species, and a New Record of Aquatic Fireflies in China (Coleoptera: Lampyridae: Luciolinae)

There are now seven species in the genus Aquatica Fu & Ballantyne, with all but one known from the characteristics of males, females, and larvae. Molecular information is combined with morphological taxonomy for the delimitation of both genus and species. The monophyly of the genus Aquatica is strongly supported in six trees, and its position as sister to the genus Nipponoluciola Ballantyne Kawashima Jusoh et Suzuki is stable across maximum likelihood and Bayesian inference results. Two new species of Aquatica Fu & Ballantyne, A. qingshen sp. nov. and A. xianning sp. nov., described from the features of males, females, and larvae, are closely related within a single clade within the genus Aquatica. Females have distinctively shaped median oviduct plates. A Chinese population identified as A. lateralis was found to be morphologically similar to the Japanese population, but genetic distances suggest that it is a distinctive species. No larvae are associated with this species. Definitions of the aquatic status of Luciolinae fireflies are expanded.

Complete mitochondrial genome sequence of Aureoboletus raphanaceus (Boletales, Basidiomycota)

Aureoboletus raphanaceus is a member of boletoid mushroom, which is named after its distinctive radish smell. The mitochondrial genome and phylogenetic relationships with other boletes need to be investigated to gain a comprehensive understanding of it. In this study, we sequenced the mitochondrial genome of A. raphanaceus using next-generation sequencing technology and found that its mitochondrial genome is a circular DNA molecule measuring 42,157 bp. It consists of 15 core protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The mitochondrial genome had a base composition of A (39.89%), C (11.06%), G (11.67%), and T (37.38%), with a GC content of 22.73%. A phylogenetic tree based on 22 mitochondrial genomes was constructed, which provided the first insights into the phylogenetic relationships of this species with related boletes.