Mitochondrial DNA Research Articles

The genome sequence of the willow leaf beetle, Lochmaea capreae Linnaeus, 1758.

We present a genome assembly from an individual female Lochmaea capreae (the willow leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 534.7 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.85 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,254 protein coding genes.

The genome sequence of the common awl robberfly, Neoitamus cyanurus (Loew, 1849).

We present a genome assembly from an individual female Neoitamus cyanurus (the common awl robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 365.5 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,046 protein-coding genes.

The genome sequence of the Plain Wave moth, Idaea straminata (Borkhausen, 1794)

We present a genome assembly from an individual male Idaea straminata (the Plain Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence spans 411.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,493 protein-coding genes.

My Early Years of Yeast Mitochondrial Genetics.

There have been massive technological advances in molecular biology and genetics over the past five decades. I have personally experienced these advances and here I reflect on those origins, from my perspective, studying yeast mitochondrial genetics leading up to deciphering the functions of the mitochondrial genome. The yeast contributions commenced in the middle of the last century with pure genetics, correlating mutants with phenotypes, in order to discover genes, just like the early explorations to discover new lands. The quest was to explore the mitochondrial genome and find its genes and their products. It was most fortunate that DNA sequencing technologies became available in the late 1970s, and laboratories were restructured enormously to keep pace with the emerging technologies. There were considerable costs in equipping laboratories, purchasing ultracentrifuges and restriction endonucleases, and undertaking DNA sequencing; additionally, workers required special safety gear.

Hidden in the plains: Two new extra‐andean species of Euathlus (Mygalomorphae, Theraphosidae) from Argentina with comments on their sexual behaviour

AbstractTwo new species of Euathlus (Verhandlungen der Kaiserlich‐Königlichen Zoologisch‐Botanischen Gesellschaft in Wien, 1875, 25, 125) from Argentina are described. Euathlus ameghinoi sp. n. and Euathlus ventus sp. n. are the first records for the Patagonian Steppe. Here we used mitochondrial DNA (cox1) to perform the first molecular phylogeny of some representatives of the genus. In addition, we present the first description of the sexual behaviour of the genus. Both molecular and cladistic morphological analysis showed the genus Euathlus as monophyletic, and new species were recovered as sister groups. New species show new morphological variations of typical characters for the genus (e.g. tibial apophyses and palpal organs).

Characterization of mitochondrial metabolism related molecular subtypes and immune infiltration in colorectal adenocarcinoma

Colorectal adenocarcinoma (COAD) is the most common subtype of colorectal cancer. Due to the imperfect prognosis of COAD, related prognostic factors and possible mechanisms need to be further investigated. During tumor development, mitochondria help tumor cells survive in a variety of ways, so that further screening of mitochondrial metabolism related targets has positive implications for COAD. We screened the mitochondrial metabolism-related genes (MMRG) associated with the COAD prognosis and explored the MMRG-related molecular subtype characteristics of by unsupervised consensus clustering analysis. Using ESTIMATE and ssGSEA algorithms, we evaluated the immunoinfiltration characteristic landscape of different molecular subtypes defined by MMRG. Combining the expression profiles of differentially expressed genes associated with the MMRG subgroup and the survival characteristics of COAD, we constructed an MMRG prognostic model using LASSO-univariate Cox analysis and successfully validated its impact on independently predicting risk stratification of COAD. The potential clinical value of the MMRG score was subsequently evaluated by subgroup immunoinfiltration characteristics and drug susceptibility prediction analysis. We also offer SEC11A as a new potential target for COAD by single-cell sequencing analysis. The effect of SEC11A on the proliferation, invasion abilities and mitochondrial dysfunction of COAD cells was confirmed through in vitro experiments. Our study provides new insights into the role of MMRG and new target for COAD potential intervention.

Three Mitochondrial Genomes of Chrysochroinae (Coleoptera, Buprestidae) and Phylogenetic Analyses

Three mitochondrial genomes of Chrysochroinae (Buprestidae) were sequenced and analyzed. The mitogenomes of the genera Catoxantha and Nipponobuprestis are first reportedand Chrysochroa opulenta is a first record for China. The complete mitogenomes of Catoxantha luodiana, Nipponobuprestis guangxiensis and Chrysochroa opulenta exhibit striking similarities in their lengths and composition. Specifically, their lengths are 15,594 bp, 15,775 bp and 15,587 bp, respectively. Each of these genomes encodes 37 typical mitochondrial genes. The overwhelming majority of protein-coding genes (PCGs) have the typical ATN (ATT, ATA, ATG or ATC) as the start codon and terminate with TAR (TAA or TAG) as the stop codon or an incomplete stop codon T-. Among the three mitogenomes, Leu2, Ser2 and Phe were the most frequently encoded amino acids. In the PCGs, the Ka/Ks ratio of cox1 is the lowest, whereas atp6 has the highest value. This suggests that cox1 can be used as a molecular barcode for species delimitation and phylogeny in Chrysochroinae. The phylogenetic results showed that C. luodiana and two Chrysochroa species formed a clade. Based on the topology of the phylogenetic tree, the genus Catoxantha should be reassigned as a subgenus of Chrysochroa.

Repeat-mediated recombination results in Complex DNA structure of the mitochondrial genome of Trachelospermum jasminoides

BackgroundTrachelospermum jasminoides has medicinal and ornamental value and is widely distributed in China. Although the chloroplast genome has been documented, the mitochondrial genome has not yet been studied.ResultsThe mitochondrial genome of T. jasminoides was assembled and functionally annotated using Illumina and nanopore reads. The mitochondrial genome comprises a master circular molecular structure of 605,764 bp and encodes 65 genes: 39 protein-coding genes, 23 transfer RNA (tRNA) genes and 3 ribosomal RNA genes. In addition to the single circular conformation, we found many alternative conformations of the T. jasminoides mitochondrial genome mediated by 42 repetitive sequences. Six repetitive sequences (DRS01–DRS06) were supported by nanopore long reads, polymerase chain reaction (PCR) amplifications, and Sanger sequencing of the PCR products. Eleven homologous fragments were identified by comparing the mitochondrial and chloroplast genome sequences, including three complete tRNA genes. Moreover, 531 edited RNA sites were identified in the protein-coding sequences based on RNA sequencing data, with nad4 having the highest number of sites (54).ConclusionTo our knowledge, this is the first description of the mitochondrial genome of T. jasminoides. Our results demonstrate the existence of multiple conformations. These findings lay a foundation for understanding the genetics and evolutionary dynamics of Apocynaceae.

Mitochondrial DNA copy number and neurocognitive outcomes in children.

Low mitochondria DNA copy number (mtDNAcn) has been linked to cognitive decline. However, the role of mtDNAcn in healthy cognitive development is unclear. We hypothesized early-life mtDNAcn would be associated with children's learning and memory. We quantified mtDNAcn in umbilical cord blood and child blood at ages 5-7 from participants in a prospective birth cohort. We administered the Children's Memory Scale (CMS) at ages 9-14 (N = 342) and the Wechsler Intelligence Scale for Children (WISC-IV) at ages 7 and 9 (N = 457). Associations between mtDNAcn tertiles and CMS and WISC were evaluated with linear regression and linear mixed-effects models, respectively. We examined non-linear associations using generalized additive mixed models. Relative to the middle tertile of mtDNAcn, lower childhood mtDNAcn was associated with lower WISC Working Memory (β = -2.65, 95% CI [-5.24, -0.06]) and Full-Scale IQ (β = -3.71 [-6.42, -1.00]), and higher CMS Visual Memory (β = 4.70 [0.47, 8.93]). Higher childhood mtDNAcn was linked to higher CMS Verbal Memory (β = 7.75 [2.50, 13.01]). In non-linear models, higher childhood mtDNAcn was associated with lower WISC Verbal Comprehension. Our study provides novel evidence that mtDNAcn measured in childhood is associated with children's neurocognitive performance. mtDNAcn may be a marker of healthy child development. Mitochondrial DNA copy number (mtDNAcn) may serve as a biomarker for early-life neurocognitive performances in the children's population. Both low and high mtDNAcn may contribute to poorer neurocognition, reflected through learning and memory abilities. This research elucidated the importance of investigating mitochondrial biomarkers in healthy populations and facilitated advancements of future studies to better understand the associations between mitochondrial markers and adverse children's health outcomes.

Quantifying constraint in the human mitochondrial genome.

Mitochondrial DNA (mtDNA) has an important yet often overlooked role in health and disease. Constraint models quantify the removal of deleterious variation from the population by selection and represent powerful tools for identifying genetic variation that underlies human phenotypes1-4. However, nuclear constraint models are not applicable to mtDNA, owing to its distinct features. Here we describe the development of a mitochondrial genome constraint model and its application to the Genome Aggregation Database (gnomAD), a large-scale population dataset that reports mtDNA variation across 56,434 human participants5. Specifically, we analyse constraint by comparing the observed variation in gnomAD to that expected under neutrality, which was calculated using a mtDNA mutational model and observed maximum heteroplasmy-level data. Our results highlight strong depletion of expected variation, which suggests that many deleterious mtDNA variants remain undetected. To aid their discovery, we compute constraint metrics for every mitochondrial protein, tRNA and rRNA gene, which revealed a range of intolerance to variation. We further characterize the most constrained regions within genes through regional constraint and identify the most constrained sites within the entire mitochondrial genome through local constraint, which showed enrichment of pathogenic variation. Constraint also clustered in three-dimensional structures, which provided insight into functionally important domains and their disease relevance. Notably, we identify constraint at often overlooked sites, including in rRNA and noncoding regions. Last, we demonstrate that these metrics can improve the discovery of deleterious variation that underlies rare and common phenotypes.

Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini)

Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.

The genome sequence of an ant, Lasius platythorax Seifert, 1991

We present a genome assembly from an individual female ant, Lasius platythorax (Arthropoda; Insecta; Hymenoptera; Formicidae). The genome sequence has a total length of 288.70 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.73 kilobases in length.

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

The genome sequence of a cranefly, Tipula (Lunatipula) helvola Loew, 1873

We present a genome assembly from an individual female cranefly, Tipula helvola (Arthropoda; Insecta; Diptera; Tipulidae). The genome sequence has a total length of 1,204.70 megabases. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.48 kilobases in length.

The genome sequence of a fold-wing cranefly, Ptychoptera albimana (Fabricius, 1787)

We present a genome assembly from an individual male fold-wing cranefly, Ptychoptera albimana (Arthropoda; Insecta; Diptera; Ptychopteridae). The genome sequence has a total length of 197.90 megabases. Most of the assembly (97.54%) is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,210 protein-coding genes.

Maternal total sleep deprivation causes oxidative stress and mitochondrial dysfunction in oocytes associated with fertility decline in mice.

Previous studies have shown sleep deprivation is increasingly reported as one of the causes of female infertility. However, how and by what relevant mechanisms it affects female fertility remains unclear. In this study, female mice underwent 72 hours of total sleep deprivation (TSD) caused by rotating wheel or 2 different controls: a stationary wheel, or forced movement at night. Even though, there was no significant difference in the number of eggs ovulated by the TSD mice compared to the control groups. Overall levels of estrogen and FSH were lower throughout the estrus cycle. A total of 42 genes showed significant differential expression in GV oocytes after TSD by RNA sequencing (RNA-Seq). These included genes were enriched in gene ontology terms of mitochondrial protein complex, oxidoreductase activity, cell division, cell cycle G1/S phase transition, as well as others. The increased concentrations of reactive oxygen species (ROS) in germinal vesicle (GV) and metaphase II (MII) oocytes from TSD mice were observed, which might be induced by impaired mitochondrial function caused by TSD. The GV oocytes displayed increased mitochondrial DNA (mtDNA) copy number and a significant transient increase in inner mitochondrial membrane potential (Δψm) from the TSD mice probably due to compensatory effect. In contrast, MII oocytes in the TSD group showed a decrease in the mtDNA copy number and a lower Δψm compared with the controls. Furthermore, abnormal distribution of mitochondria in the GV and MII oocytes was also observed in TSD mice, suggesting mitochondrial dysfunction. In addition, abnormal spindle and abnormal arrangement of chromosomes in MII oocytes were markedly increased in the TSD mice compared with the control mice. In conclusion, our results suggest that TSD significantly alters the oocyte transcriptome, contributing to oxidative stress and disrupted mitochondrial function, which then resulted in oocyte defects and impaired early embryo development in female mice.

How Do ROS Induce NETosis? Oxidative DNA Damage, DNA Repair, and Chromatin Decondensation.

Neutrophil extracellular traps (NETs) are intricate, DNA-based, web-like structures adorned with cytotoxic proteins. They play a crucial role in antimicrobial defense but are also implicated in autoimmune diseases and tissue injury. The process of NET formation, known as NETosis, is a regulated cell death mechanism that involves the release of these structures and is unique to neutrophils. NETosis is heavily dependent on the production of reactive oxygen species (ROS), which can be generated either through NADPH oxidase (NOX) or mitochondrial pathways, leading to NOX-dependent or NOX-independent NETosis, respectively. Recent research has revealed an intricate interplay between ROS production, DNA repair, and NET formation in different contexts. UV radiation can trigger a combined process of NETosis and apoptosis, known as apoNETosis, driven by mitochondrial ROS and DNA repair. Similarly, in calcium ionophore-induced NETosis, both ROS and DNA repair are key components, but only play a partial role. In the case of bacterial infections, the early stages of DNA repair are pivotal. Interestingly, in serum-free conditions, spontaneous NETosis occurs through NOX-derived ROS, with early-stage DNA repair inhibition halting the process, while late-stage inhibition increases it. The intricate balance between DNA repair processes and ROS production appears to be a critical factor in regulating NET formation, with different pathways being activated depending on the nature of the stimulus. These findings not only deepen our understanding of the mechanisms behind NETosis but also suggest potential therapeutic targets for conditions where NETs contribute to disease pathology.

A chromosomal reference genome sequence for the malaria mosquito, Anopheles nili, Theobald, 1904

We present a genome assembly from an individual male Anopheles nili (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 195 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.

A new species of the Genus Margattea (Blattodea: Pseudophyllodromiidae) from Yonaguni-jima Island, the Ryukyus, Japan

A new species of the cockroach genus Margattea Shellford, 1911 (Blattodea: Pseudophyllodromiidae) is described from Yonaguni-jima Island, the Ryukyus, Japan. The new species M. ventrinigra sp. nov. was compared with three species of the same genus on the basis of morphology and mitochondrial DNA sequences (COI and COII): M. satsumana, M. ogatai and M. nimbata.

Metal-Phenolic Nanomaterial with Organelle-Level Precision Primes Antitumor Immunity via mtDNA-dependent cGAS-STING Activation.

New generation of nanomaterials with organelle-level precision provide significant promise for targeted attacks on mitochondria, exhibiting remarkable therapeutic potency. Here, we report a novel amphiphilic phenolic polymer (PF) for the mitochondria-targeted photodynamic therapy (PDT), which can trigger excessive mitochondrial DNA (mtDNA) damage by the synergistic action of oxidative stress and furan-mediated DNA cross-linking. Moreover, the phenolic units on PF enable further self-assembly with Mn2+ via metal-phenolic coordination to form metal-phenolic nanomaterial (PFM). We focus on the synergistic activation of the cGAS-STING pathway by Mn2+ and tumor-derived mtDNA in tumor-associated macrophages (TAMs), and subsequently repolarizing M2-like TAMs to M1 phenotype. We highlight that PFM facilitates the cGAS-STING-dependent immunity at the organelle level for potent antitumor efficacy.