Mitochondrial Genome Structure Research Articles

The first complete mitochondrial genome of Sumatran striped rabbit Nesolagus netscheri (Schlegel, 1880), and its phylogenetic relationship with other Leporidae

Nesolagus netscheri, a Sumatran striped rabbit, is one of the rarest rabbits in the Leporidae family, and its genetic information is still limited. This study provides the first mitochondrial genome and molecular systematic characterization of the Sumatran striped rabbit, Nesolagus netscheri, Indonesia’s rarest rabbit. It consists of a circular double-stranded DNA of 16,709 bp. It showed that the mitochondrial genome structure of N. netscheri is similar to that of N. timminsi. The mitochondrial genome of N. netscheri contained 22 transfer RNA (tRNA) genes, and all tRNA except for trnS1 showed a characteristic cloverleaf secondary structure. Evidence was found that the atp8 gene of N. netscheri is under positive selection pressure. The phylogenetic analysis shows Leporidae was monophyletic, with Nesolagus at the basal. The study indicates a split between N. netscheri and N. timminsi in the Late Pleistocene around 0.43 million years ago. This research is a fundamental reference for the conservation of the rarest lagomorph species and provides important information for future evolutionary studies in the Leporidae family.

Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane

BackgroundSugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular “energy factories”, provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS).ResultsWe performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species.ConclusionIn this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.

Description of the mitochondrial genomes of Sichuan Tetrastes sewerzowi (Galliformes: Tetraonidae) and phylogenetic relationship.

The Chinese Grouse (Tetrastes sewerzowi), a rare endemic bird in China, belongs to the Galliformes order and Tetraonidae family. Despite extensive research, subspecies classification remains inadequate, especially in Pingwu, Sichuan. This study sequenced the mitochondrial genome of T. sewerzowi in Wanglang Nature Reserve, Sichuan, analyzed its structural features, and reconstructed phylogenetic relationships within Tetraonidae. The results indicate that the high conservation in mitochondrial genome structure and sequence between the T. sewerzowi from Wanglang, Sichuan and Lianhuashan, Gansu indicates that they may belong to the same subspecies. Furthermore, we observed significant differences in the length of the mitochondrial control region between T. sewerzowi and Tetrastes bonasia. Based on the phylogenetic tree constructed using a comprehensive mitochondrial dataset, we propose the reclassification of the Hazel Grouse genus into two independent genera: Tetrastes and Bonasa. This study is the first to sequence the mitochondrial genome of T. sewerzowi from Sichuan and compare it with populations from Gansu, providing important insights into the distribution pattern of T. sewerzowi subspecies and facilitating the formulation of effective conservation strategies.

Assembly and comparative analysis of the multichromosomal mitochondrial genome of globally endangered seagrass Halophila beccarii

BackgroundHalophila beccarii is one of the oldest two generations of seagrass plants and one of the 10 species of seagrass currently at risk of extinction worldwide. Therefore, how to effectively protect the H. beccarii resources from extinction is a huge challenge. Molecular biology research can provide a scientific basis for species conservation. So far, there has been no detailed analysis of the mitochondrial genome of the genus Halophila.ResultsThe mitochondrial genome of H. beccarii was assembled into 28 circular chromosomes, ranging in length from 41,738 bp to 104,744 bp, with a total length of 1,964,072 bp and a GC content of 46.71%. It contains 39 genes, including 26 protein coding genes, 10 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 850 dispersed repeats, 1,205 simple repeats, 61 tandem repeats, and 120 RNA editing sites. Analysis of codon usage indicates that codons ending in A/U are preferred. Gene migration between the mitochondrial genome and the chloroplast genome was observed through homologous fragment detection. In addition, Ka/Ks analysis showed that most protein coding genes in the mitochondrial genome experienced negative selection, while only the nad3 gene experienced potential positive selection in most Alismatales. Nucleotide polymorphism analysis revealed variations in each gene, with rpl10 being the most significant. In addition, comparative analysis shows that the GC content is conserved, but there are significant differences in the size and structure of mitochondrial genomes among different species of Alismatales. The phylogenetic analysis based on the mitochondrial genome reflects the exact evolutionary and taxonomic status of H. beccarii.ConclusionIn this study, we sequenced and annotated the mitochondrial genome of H. beccarii, and compared it with the mitochondrial genomes of other plants in Alismatales. Our findings enrich the mitogenome database of seagrass plants and highlight the potential for mitochondrial genes to help decipher plant evolutionary history.

Mitochondrial genome of the Indian spot-billed duck and its phylogenetic and conservation implications.

The Indian spot-billed duck, Anas poecilorhyncha is a large dabbling and non-migratory breeding bird. The identification and phylogenetic relationship of A. poecilorhyncha remain uncertain due to the presence of overlapping meristic characters and hybridization with closely related species. Molecular data aids when there are challenges in morphological identification. However, genetic characterization of A. poecilorhyncha has been paid less attention. Apart from their functional and physiological role, mitochondrial genome can also be used for various purposes, including species identification, phylogenetic analysis, understanding the domestication history of species etc. Therefore, the present study aimed to sequence the mitochondrial genome of A. poecilorhyncha and its closely related domestic species A. platyrhynchos (mallard duck) to understand their mitochondrial genome structure and phylogenetic relationships. The length of mitochondrial genome of A. poecilorhyncha and A. platyrhynchos was 16,608 and 16,604bp respectively. Mitochondrial genome contained 37 genes and a non-coding control region. Overall, the characteristics of mitochondrial genome of both species were found to be conserved. The phylogenetic tree exhibited seven major clades (A to G) with a high bootstrap support. Notably, the Indian A. poecilorhyncha population formed a distinct clade (C) whereas the A. poecilorhyncha that were probably sampled from China grouped along with A. zonorhyncha (clade B). Besides, one of the A. poecilorhyncha probably sampled from China was placed in the clade A, which predominantly consisted of A. platyrhynchos. It suggests that Indian A. poecilorhyncha population is genetically different from Chinese A. poecilorhyncha population. Further, it sheds light on the importance of conducting a comprehensive phylogenetic study on these species. The newly sequenced mitochondrial genome of A. poecilorhyncha and A. platyrhynchos would be useful not only to have a better understanding of the phylogeny and evolution of Anas species but also to help in the conservation of A. poecilorhyncha which is under constant threat from rapid urbanization, interspecific hybridization and other human activities.

Identification of Haemoproteus infection in an imported grey crowned crane (Balearica regulorum) in China

Blood parasites from the order Haemosporida infect many vertebrates and cause malaria-like diseases. In this study, a haemosporidian infection was detected in a sick grey crowned crane imported into China using a combination of morphological and molecular approaches. Blood samples were collected from the jugular vein and processed for morphological identification of infective parasites using stained blood smears and microscopy. No merogony occurs in the blood cells, and sporadic pigment granules were observed. Nested-PCR assays were employed for a molecular examination, which indicated that the cytb gene of this parasite had 94.1–94.9% identity to Haemoproteus antigonis. Subsequently, its mitochondrial genome structure was determined by high-throughput sequencing using the DNBSEQ-T7 platform. The determined structure was confirmed by the Sanger sequencing using amplicons. The mitochondrial genome obtained for this parasite exhibited a low CG content (32.0%) and possessed three protein-coding genes, encoding 1068 amino acids, which constituted 53.7% of the genome. Phylogenetic analysis indicated that this parasite clustered with Haemoproteus sp. is detected in grey crowned cranes from Africa. This parasite was likely acquired during importation of this animal; thus, strict quarantine of imported ornamental animals is required to prevent the entry of new pathogens.

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.

Comparative analysis of the mitochondrial genomes of four Dendrobium species (Orchidaceae) reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing.

The genus Dendrobium, part of the Orchidaceae family, encompasses species of significant medicinal, nutritional, and economic value. However, many Dendrobium species are threatened by environmental stresses, low seed germination rates, and overharvesting. Mitochondria generate the energy necessary for various plant life activities. Despite their importance, research on the mitochondrial genomes of Dendrobium species is currently limited. To address this gap, we performed a comprehensive genetic analysis of four Dendrobium species-D. flexicaule, D. nobile, D. officinale, and D. huoshanense-focusing on their mitochondrial and chloroplast genomes to elucidate their genetic architecture and support conservation efforts. We utilized advanced sequencing technologies, including Illumina for high-throughput sequencing and Nanopore for long-read sequencing capabilities. Our findings revealed the multichromosomal mitochondrial genome structures, with total lengths ranging from 596,506 bp to 772,523 bp. The mitochondrial genomes contained 265 functional genes, including 64-69 protein-coding genes, 23-28 tRNA genes, and 3 rRNA genes. We identified 647 simple sequence repeats (SSRs) and 352 tandem repeats, along with 440 instances of plastid-to-mitochondrial gene transfer. Additionally, we predicted 2,023 RNA editing sites within the mitochondrial protein-coding genes, predominantly characterized by cytosine-to-thymine transitions. Comparative analysis of mitochondrial DNA across the species highlighted 25 conserved genes, with evidence of positive selection in five genes: ccmFC, matR, mttB, rps2, and rps10. Phylogenetic assessments suggested a close sister relationship between D. nobile and D. huoshanense, and a similar proximity between D. officinale and D. flexicaule. This comprehensive genomic study provides a critical foundation for further exploration into the genetic mechanisms and biodiversity of Dendrobium species, contributing valuable insights for their conservation and sustainable utilization.

Insights into Fungal Mitochondrial Genomes and Inheritance Based on Current Findings from Yeast-like Fungi.

The primary functions of mitochondria are to produce energy and participate in the apoptosis of cells, with them being highly conserved among eukaryotes. However, the composition of mitochondrial genomes, mitochondrial DNA (mtDNA) replication, and mitochondrial inheritance varies significantly among animals, plants, and fungi. Especially in fungi, there exists a rich diversity of mitochondrial genomes, as well as various replication and inheritance mechanisms. Therefore, a comprehensive understanding of fungal mitochondria is crucial for unraveling the evolutionary history of mitochondria in eukaryotes. In this review, we have organized existing reports to systematically describe and summarize the composition of yeast-like fungal mitochondrial genomes from three perspectives: mitochondrial genome structure, encoded genes, and mobile elements. We have also provided a systematic overview of the mechanisms in mtDNA replication and mitochondrial inheritance during bisexual mating. Additionally, we have discussed and proposed open questions that require further investigation for clarification.

Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae)

Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salviamiltiorrhiza and Platostoma chinense. Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks <1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$<1$$\\end{document} for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.

The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis

Channidae (snakehead fish) is a family of medium-to-large freshwater carnivorous fish and contain the genus, Channa. Here, the complete mitogenomes of two Channa fish were determined and comparatively analyzed with the mitogenomes of 16 other Channidae fish species. The two newly sequenced complete mitogenomes were circular DNA molecules with sizes of 16,953 bp (Channa burmanica; OP954106) and 16,897 bp (Channa aurantimaculata; OQ134162). The mitogenomes were composed of 37 genes and one D-loop region. Positive AT skews and negative GC skews were found in the mitogenomes. Most protein-coding genes (PCGs) started with the conventional start codon, ATG; however, the sequence of the stop codon was variable. There was no obvious difference in relative synonymous codon usage among the two mitogenomes, and the two species shared a similar number of codon usage of mitogenomic PCGs, which was also similar to the mean values for the other 15 species of Channa. All Ka/Ks values were &lt;1; cox1 had the lowest value, and atp8 had the highest. All of the tRNAs were typical clover structures, except trnS1. Phylogenetic analysis showed that C. burmanica and C. aurantimaculata shared a close relationship and that they were also closely related to C. gachua. These findings enrich the gene database of Channidae species, clarify the mitochondrial genome structure of the two species, and provide basic data for invasive biological surveillance in the future.

The rearrangement features and phylogenetic signals of mitochondrial genomes of gall midge subfamily Cecidomyiinae (Diptera: Cecidomyiidae) with first complete mitogenome of an economically important mango gall midge pest, Procontarina fructiculi from Guangxi, China

ABSTRACT In this study, we obtained the first complete mitochondrial genome of Procontarina fructiculi, an important mango gall midge pest from Guangxi, China. The mitogenome of P. fructiculi was sequenced and annotated for the first time, and compared with all the published and annotated data of Cecidomyiidae species to summarise the gall midge organisation and rearrangement features of mitochondrial genomes with phylogenetic analysis. The comparison of gall midge mitochondrial genome structure shows that the rearrangement of the mitochondrial gene structure is very common, and most rearrangements are embodied in rearrangement in the order of tRNAs. The phylogenetic results based on the maximum likelihood (ML) and Bayesian inference (BI) methods both highly supported the monophyly of Cecidomyiinae. Cecidomyiinae can be divided into two distinct clades (except Cecidomyiidae sp. 3): A: (Mayetiola destructor + Rhopalomyia pomum) and B: (Asphondylia rosetta + ((Procontarinia fructiculi + Orseolia oryzae) + ((Cecidomyiidae sp. 1 + Aphidoletes aphidimyza) + Cecidomyiidae sp. 2))). Based on the above results, some phylogenetic signals in rearrangement have been found in the mitochondrial genome structure of Cecidomyiinae for the first time.

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny.

Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.

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.

Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

BackgroundPhylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae).ResultsCustom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit.ConclusionsTarget enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.

Analysis of the Rhodomyrtus tomentosa mitochondrial genome: Insights into repeat-mediated recombination and intra-cellular DNA transfer

Plant mitochondrial genomes participate in encoding proteins crucial to the major producers of ATP in the cell and replication and heredity of their own DNA. The sequences and structure of the plant mitochondrial genomes profoundly impact these fundamental processes, and studies of plant mitochondrial genomes are needed. We reported the complete sequences of the Rhodomyrtus tomentosa mitochondrial genome here, totaling 400,482 bp. Nanopore ONT reads and PCR amplification provided evidence for recombination mediated by the eight repeat pairs for the R. tomentosa mitochondrial genome. Thirty-eight genes were identified in the R. tomentosa mitochondrial genome. Comparative analyses of the mitochondrial genome and plastome and PCR amplification suggest that five fragments of mitochondrial plastid DNA were unfunctional sequences resulting from intracellular gene transfer. Phylogenetic analysis based on each and all of the 27 mitochondrial protein-coding genes of nine Myrtales species revealed that R. tomentosa always clustered with other species of Myrtaceae. This study uncovered the enormous complexity of the R. tomentosa mitochondrial genome, the active repeat-mediated recombinations, the presence of mitochondrial plastid DNAs, and the topological incongruence of Myrtales among the single-gene trees.

The Complete Mitochondrial Genomes of Aelia sibirica and A. fieberi (Hemiptera, Pentatomidae), and Phylogenetic Implications

Species of genus Aelia are important pests of wheat crops in arid areas. In this study, the mitogenomes of A. sibirica and A. fieberi were sequenced using high-throughput sequencing technology. The mitochondrial genome characteristics of both Aelia species were compared and analyzed, and the phylogenetic relationships of Pentatomidae were constructed based on protein-coding genes. In addition, the taxonomic status of the genus Aelia was confirmed. The results showed that the total length of the mitogenome sequences of A. sibirica and A. fieberi were 15,372 bp and 15,450 bp, respectively, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. By comparing the mitochondrial genome structure, base composition, codon usage, RNA secondary structure, and other characteristics, it was found that the mitochondrial genome characteristics of the two species were similar. Phylogenetic analysis showed that Phyllocephalinae and Asopinae both formed monophyletic groups, but the relationship between Podopinae and Pentatominae was not resolved. Within the subfamily Pentatominae, (Nezarini + Antestiini), (Aeliini + Carpocorini), and (Strachiini + Pentatoma) formed stable clades. Aelia sibirica and A. fieberi were found to be a stable sibling pair, and the clade was closely related to Dolycoris baccarum.

First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae).

Gastrodia elata Blume, a valuable traditional Chinese medicine with significant clinical and nutritional importance, is a fungal heterotrophic orchid. We present the first report of the mitochondrial genome structure and characteristics of 3 Scarabaeidae pests affecting G. elata: Sophrops peronosporus Gu & Zhang, Anomala rufiventris Kollar & Redtenbacher, and Callistethus plagiicollis Fairmaire. Each mitogenome contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region, with no gene rearrangements observed. All 21 tRNAs, except trnS1 that lacks a dihydrouridine, had a stable cloverleaf secondary structure. Maximum likelihood and Bayesian inference analyses based on the 13 PCGs produced 2 topologically similar phylogenetic trees, both of with high nodal support. Larvae of these Scarabaeidae pests cause substantial damage by gnawing on the tubers and roots of G. elata, leading to reduced yield and compromised quality. These findings contribute to phylogenetic studies of Scarabaeidae, expand knowledge of G. elata pests, and offer valuable reference materials for their identification and control.

Complete mitochondrial genome and phylogenetic analysis of the marine microalga Symbiochlorum hainanensis (Ulvophyceae, Chlorophyta)

Symbiochlorum hainanensis Gong et al. (2018). is a unicellular green alga belonging to Ulvophyceae, Chlorophyta, and considered as an important species in coral-algae symbiont areas. In this study, we revealed firstly the mitochondrial genome sequence of the S. hainanensis. This mitochondrial genome was a circular DNA molecule of 59,508 bp, including 24 transfer RNA genes, 3 ribosomal RNA genes, and 31 protein-coding genes. The GC content of the genome was 35.4%. The phylogenetic tree suggested that S. hainandiae was a sister to the OUU clade within the class Ulvophyceae. The mitochondrial genome structure and gene content of S. hainanensis supported that S. hainanensis was a new unidentified green alga in Ulvophyceae.

Characterization and phylogenetic analysis of the complete mitochondrial genome of a unique economic plant &lt;i&gt;Lycium barbarum&lt;/i&gt; L.

&lt;i&gt;Lycium barbarum&lt;/i&gt; L. (&lt;i&gt;L. barbarum&lt;/i&gt;), an important medicinal and food crop from the Solanaceae family, is known for excellent tolerance to saline–alkaline and drought stresses. Therefore, it has significant research and application value. The nuclear and chloroplast genomes of &lt;i&gt;L. barbarum&lt;/i&gt; have been previously reported; however, its mitochondrial genome is still unexplored. In this study, mitochondrial DNA sequencing and assembly in &lt;i&gt;L. barbarum&lt;/i&gt; were studied via second- and third-generation sequencing technologies using the anthers collected from the main cultivars “Ningqi No.1” (fertile line) and its male-sterile natural mutant “Ningqi No.5” from Ningxia, China. The results revealed that “Ningqi No.1” and “Ningqi No.5” have the same mitochondrial circular genome structure with a total length of 413,881 bp. In total, 61 genes were annotated, including 35 protein-coding genes, four rRNA genes, 22 tRNA genes, and 2,242 open reading frames with unknown functions. The repeat sequences in mtDNA were analyzed, in which short repeats (30–59 bp) exhibited the highest number. Overall, 23 protein-coding genes in “Ningqi No.1” and “Ningqi No.5” exhibited RNA-editing phenomenon, with different RNA-editing site number and distribution position. Phylogenetic analysis demonstrated that &lt;i&gt;L. barbarum&lt;/i&gt; has the closest relationship with &lt;i&gt;Hyoscyamus niger&lt;/i&gt;. These results provided a basis for a comprehensive understanding of the mitochondrial genome of &lt;i&gt;L. barbarum&lt;/i&gt; and the relevant data for omics studies on &lt;i&gt;L. barbarum&lt;/i&gt;.