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Genes Oct 2022(Motschulsky, 1854) and Gressitt & Rondon, 1970 are two commonly found longicorn beetles from China. However, the lack of sufficient molecular data hinders the...
(Motschulsky, 1854) and Gressitt & Rondon, 1970 are two commonly found longicorn beetles from China. However, the lack of sufficient molecular data hinders the understanding of their evolution and phylogenetic relationships with other species of Cerambycidae. This study sequenced and assembled the complete mitochondrial genomes of the two species using the next-generation sequencing method. The mitogenomes of and are 15,622 bp and 15,527 bp in length, respectively. The mitochondrial gene content and gene order of and are highly conserved with other sequenced longicorn beetles. The calculation of nonsynonymous (Ka) and synonymous (Ks) substitution rates in PCGs indicated the existence of purifying selection in the two longicorn beetles. The phylogenetic analysis was conducted using the protein-coding gene sequences from available mitogenomes of Cerambycidae. The two species sequenced in this study are, respectively, grouped with their relatives from the same subfamily. The monophyly of Cerambycinae, Dorcasominae, Lamiinae, and Necydalinae was well-supported, whereas Lepturinae, Prioninae, and Spondylidinae were recovered as paraphyletic.
Topics: Animals; Genome, Mitochondrial; Coleoptera; Phylogeny; Genes, Mitochondrial; China
PubMed: 36292766
DOI: 10.3390/genes13101881 -
Frontiers in Bioscience (Scholar... Mar 2024Disorders of mitochondrial function are responsible for many inherited neuromuscular and metabolic diseases. Their combination of high mortality, multi-systemic... (Review)
Review
Disorders of mitochondrial function are responsible for many inherited neuromuscular and metabolic diseases. Their combination of high mortality, multi-systemic involvement, and economic burden cause devastating effects on patients and their families. Molecular diagnostic tools are becoming increasingly important in providing earlier diagnoses and guiding more precise therapeutic treatments for patients suffering from mitochondrial disorders. This review addresses fundamental molecular concepts relating to the pathogenesis of mitochondrial dysfunction and disorders. A series of short cases highlights the various clinical presentations, inheritance patterns, and pathogenic mutations in nuclear and mitochondrial genes that cause mitochondrial diseases. Graphical and tabular representations of the results are presented to guide the understanding of the important concepts related to mitochondrial molecular genetics and pathology. Emerging technology is incorporating preimplantation genetic testing for mtDNA disorders, while mitochondrial replacement shows promise in significantly decreasing the transfer of diseased mitochondrial DNA (mtDNA) to embryos. Medical professionals must maintain an in-depth understanding of the gene mutations and molecular mechanisms underlying mitochondrial disorders. Continued diagnostic advances and comprehensive management of patients with mitochondrial disorders are essential to achieve robust clinical impacts from comprehensive genomic testing. This is especially true when supported by non-genetic tests such as biochemical analysis, histochemical stains, and imaging studies. Such a multi-pronged investigation should improve the management of mitochondrial disorders by providing accurate and timely diagnoses to reduce disease burden and improve the lives of patients and their families.
Topics: Humans; Mitochondrial Diseases; DNA, Mitochondrial; Mitochondria; Mutation; Genes, Mitochondrial
PubMed: 38538347
DOI: 10.31083/j.fbs1601007 -
Genome Nov 2016DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer... (Review)
Review
DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.
Topics: Animals; Biodiversity; Birds; DNA Barcoding, Taxonomic; Evolution, Molecular; Genes, Mitochondrial; Genetic Variation; Phylogeny; Phylogeography
PubMed: 27824508
DOI: 10.1139/gen-2016-0086 -
ENeuro 2021Mitochondrial composition varies by organ and their constituent cell types. This mitochondrial diversity likely determines variations in mitochondrial function. However,...
Mitochondrial composition varies by organ and their constituent cell types. This mitochondrial diversity likely determines variations in mitochondrial function. However, the heterogeneity of mitochondria in the brain remains underexplored despite the large diversity of cell types in neuronal tissue. Here, we used molecular systems biology tools to address whether mitochondrial composition varies by brain region and neuronal cell type in mice. We reasoned that proteomics and transcriptomics of microdissected brain regions combined with analysis of single-cell mRNA sequencing (scRNAseq) could reveal the extent of mitochondrial compositional diversity. We selected nuclear encoded gene products forming complexes of fixed stoichiometry, such as the respiratory chain complexes and the mitochondrial ribosome, as well as molecules likely to perform their function as monomers, such as the family of SLC25 transporters. We found that the proteome encompassing these nuclear-encoded mitochondrial genes and obtained from microdissected brain tissue segregated the hippocampus, striatum, and cortex from each other. Nuclear-encoded mitochondrial transcripts could only segregate cell types and brain regions when the analysis was performed at the single-cell level. In fact, single-cell mitochondrial transcriptomes were able to distinguish glutamatergic and distinct types of GABAergic neurons from one another. Within these cell categories, unique SLC25A transporters were able to identify distinct cell subpopulations. Our results demonstrate heterogeneous mitochondrial composition across brain regions and cell types. We postulate that mitochondrial heterogeneity influences regional and cell type-specific mechanisms in health and disease.
Topics: Animals; Cell Nucleus; Genes, Mitochondrial; Hippocampus; Mice; Mitochondria; Neurons
PubMed: 34312306
DOI: 10.1523/ENEURO.0232-21.2021 -
Proceedings. Biological Sciences Oct 2013The uniparental inheritance (UPI) of mitochondria is thought to explain the evolution of two mating types or even true sexes with anisogametes. However, the exact role...
The uniparental inheritance (UPI) of mitochondria is thought to explain the evolution of two mating types or even true sexes with anisogametes. However, the exact role of UPI is not clearly understood. Here, we develop a new model, which considers the spread of UPI mutants within a biparental inheritance (BPI) population. Our model explicitly considers mitochondrial mutation and selection in parallel with the spread of UPI mutants and self-incompatible mating types. In line with earlier work, we find that UPI improves fitness under mitochondrial mutation accumulation, selfish conflict and mitonuclear coadaptation. However, we find that as UPI increases in the population its relative fitness advantage diminishes in a frequency-dependent manner. The fitness benefits of UPI 'leak' into the biparentally reproducing part of the population through successive matings, limiting the spread of UPI. Critically, while this process favours some degree of UPI, it neither leads to the establishment of linked mating types nor the collapse of multiple mating types to two. Only when two mating types exist beforehand can associated UPI mutants spread to fixation under the pressure of high mitochondrial mutation rate, large mitochondrial population size and selfish mutants. Variation in these parameters could account for the range of UPI actually observed in nature, from strict UPI in some Chlamydomonas species to BPI in yeast. We conclude that UPI of mitochondria alone is unlikely to have driven the evolution of two mating types in unicellular eukaryotes.
Topics: Biological Evolution; Cell Nucleus; Eukaryota; Genes, Mitochondrial; Genetic Fitness; Heredity; Models, Genetic; Mutation; Reproduction; Selection, Genetic
PubMed: 23986113
DOI: 10.1098/rspb.2013.1920 -
American Journal of Transplantation :... Jun 2021
Topics: Allografts; Biomarkers; Calcium; Calcium Channels; Genes, Mitochondrial; Graft Rejection; Heart Transplantation; Transcriptome
PubMed: 33278854
DOI: 10.1111/ajt.16429 -
Frontiers in Bioscience (Landmark... Sep 2023(L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be...
BACKGROUND
(L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress.
METHODS
In this study, we sequenced the mitochondrial genome of using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of , which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more.
RESULTS
The mitochondrial genome of has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within . values estimated for mitochondrial genes of and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that and × are most closely related.
CONCLUSIONS
In this study, we obtained basic information on the mitochondrial genome of and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the ratio to estimate the selection pressure on mitochondrial genes of . We also discussed the systematic evolutionary position of based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of
Topics: Genome, Mitochondrial; Fallopia; Phylogeny; Genes, Mitochondrial
PubMed: 37919084
DOI: 10.31083/j.fbl2810233 -
Plant Physiology Apr 2023How mitochondria regulate the expression of their genes is poorly understood, partly because methods have not been developed for stably transforming mitochondrial...
How mitochondria regulate the expression of their genes is poorly understood, partly because methods have not been developed for stably transforming mitochondrial genomes. In recent years, the disruption of mitochondrial genes has been achieved in several plant species using mitochondria-localized TALEN (mitoTALEN). In this study, we attempted to disrupt the NADH dehydrogenase subunit7 (NAD7) gene, a subunit of respiratory chain complex I, in Arabidopsis (Arabidopsis thaliana) using the mitoTALEN method. In some of the transformants, disruption of NAD7 was accompanied by severe growth inhibition and lethality, suggesting that NAD7 has an essential function in Arabidopsis. In addition, the mitochondrial genome copy number and overall expression of genes encoding mitochondrial proteins were generally increased by nad7 knockout. Similar increases were also observed in mutants with decreased NAD7 transcripts and with dysfunctions of other mitochondrial respiratory complexes. In these mutants, the expression of nuclear genes involved in mitochondrial translation or protein transport was induced in sync with mitochondrial genes. Mitochondrial genome copy number was also partly regulated by the nuclear stress-responsive factors NAC domain containing protein 17 and Radical cell death 1. These findings suggest the existence of overall gene-expression control through mitochondrial genome copy number in Arabidopsis and that disruption of single mitochondrial genes can have additional broad consequences in both the nuclear and mitochondrial genomes.
Topics: Arabidopsis; Arabidopsis Proteins; Genes, Mitochondrial; DNA Copy Number Variations; NADH Dehydrogenase; Mitochondrial Proteins; Gene Expression Regulation, Plant
PubMed: 36703221
DOI: 10.1093/plphys/kiad024 -
Epigenetics and migraine; complex mitochondrial interactions contributing to disease susceptibility.Gene Jun 2014Migraine is a common neurological disorder classified by the World Health Organisation (WHO) as one of the top twenty most debilitating diseases in the developed world.... (Review)
Review
Migraine is a common neurological disorder classified by the World Health Organisation (WHO) as one of the top twenty most debilitating diseases in the developed world. Current therapies are only effective for a proportion of sufferers and new therapeutic targets are desperately needed to alleviate this burden. Recently the role of epigenetics in the development of many complex diseases including migraine has become an emerging topic. By understanding the importance of acetylation, methylation and other epigenetic modifications, it then follows that this modification process is a potential target to manipulate epigenetic status with the goal of treating disease. Bisulphite sequencing and methylated DNA immunoprecipitation have been used to demonstrate the presence of methylated cytosines in the human D-loop of mitochondrial DNA (mtDNA), proving that the mitochondrial genome is methylated. For the first time, it has been shown that there is a difference in mtDNA epigenetic status between healthy controls and those with disease, especially for neurodegenerative and age related conditions. Given co-morbidities with migraine and the suggestive link between mitochondrial dysfunction and the lowered threshold for triggering a migraine attack, mitochondrial methylation may be a new avenue to pursue. Creative thinking and new approaches are needed to solve complex problems and a systems biology approach, where multiple layers of information are integrated is becoming more important in complex disease modelling.
Topics: Epigenesis, Genetic; Epistasis, Genetic; Genes, Mitochondrial; Genetic Predisposition to Disease; Genetic Therapy; Humans; Inheritance Patterns; Migraine Disorders; Mitochondria
PubMed: 24704026
DOI: 10.1016/j.gene.2014.04.001 -
BMC Evolutionary Biology Apr 2019Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a...
BACKGROUND
Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss.
RESULTS
Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive.
CONCLUSIONS
We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales.
Topics: Analysis of Variance; Evolution, Molecular; Genes, Mitochondrial; Genes, Plant; Genome, Mitochondrial; Magnoliopsida; Phylogeny; Plants
PubMed: 30961535
DOI: 10.1186/s12862-019-1401-8