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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 -
Tropical Biomedicine Mar 2020Spirometra larvae are etiological agents of human sparganosis. However, the systematics of spirometrid cestodes has long been controversial. In order to determine the...
Spirometra larvae are etiological agents of human sparganosis. However, the systematics of spirometrid cestodes has long been controversial. In order to determine the current knowledge on the evolution and genetic structure of Spirometra, an exhaustive population diversity analysis of spirometrid cestodes using the mitochondrial gene: cytochrome c oxidase subunit 1 (cox1) was performed. All publicly available cox1 sequences available in the GenBank and 127 new sequencing genes from China were used as the dataset. The haplotype identify, network, genetic differentiation and phylogenetic analysis were conducted successively. A total of 488 sequences from 20 host species, representing four spirometrid tapeworms (S. decipiens, S. ranarum, S. erinaceieuropaei and Sparganum proliferum) and several unclassified American and African isolates from 113 geographical locations in 17 countries, identified 45 haplotypes. The genetic analysis revealed that there are four clades of spirometrid cestodes: Clade 1 (Brazil + USA) and Clade 2 (Argentina + Venezuela) included isolates from America, Clade 3 contained African isolates and one Korean sample, and the remainders from Asia and Australia belonged to Clade 4; unclassified Spirometra from America and Africa should be considered the separate species within the genus; and the taxonomy of two Korea isolates (S. erinaceieuropaei KJ599680 and S. decipiens KJ599679) was still ambiguous and needs to be further identified. In addition, the demographical analyses supported population expansion for the total spirometrid population. In summary, four lineages were found in the spirometrid tapeworm, and further investigation with deeper sampling is needed to elucidate the population structure.
Topics: Animals; DNA, Helminth; DNA, Mitochondrial; Genes, Mitochondrial; Genetic Variation; Haplotypes; Phylogeny; Spirometra
PubMed: 33612735
DOI: No ID Found -
BMC Genomics Jan 2023Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial...
BACKGROUND
Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported.
RESULTS
In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates.
CONCLUSIONS
The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.
Topics: Animals; Hemiptera; Genome, Mitochondrial; Phylogeny; Genes, Mitochondrial; RNA, Transfer
PubMed: 36670383
DOI: 10.1186/s12864-023-09131-9 -
Parasitology Jun 2023is a gamasid mite that is of medical and veterinary significance as parasites and vectors of disease agents, which can carry pathogens of zoonosis such as , , , , and...
is a gamasid mite that is of medical and veterinary significance as parasites and vectors of disease agents, which can carry pathogens of zoonosis such as , , , , and . At present, only single mitochondrial genes have been analysed for in the world, and no complete mitochondrial genome has been reported. However, information carried by a single gene is limited. Therefore, the complete mitochondrial genome of was determined for the first time by Illumina Hiseq X-Ten platform in this study. The mitochondrial genome is 15 736 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region of 1561 bp in length. Codon analysis of 13 protein-coding genes revealed that UUU, UUA, AUU, AUA and AAU were the most frequently used, while had the fastest evolutionary rate and the slowest. Comparative analysis of genome structure and breakpoint distances of the mitochondrial genomes of 23 species in 17 genera from 10 families of Gamasida deposited in GenBank revealed a novel gene arrangement type of the mitochondrial genome, and different degrees of rearrangement among different taxa of Gamasida. Phylogenetic analyses of Gamasida were performed using the maximum likelihood and Bayesian inference methods. was clustered with Dermanyssoidea and formed a more supportive sister group with This study provides novel insights into rearrangement patterns and evolution of mitochondrial genomes of Gamasida.
Topics: Animals; Phylogeny; Genome, Mitochondrial; Bayes Theorem; Genes, Mitochondrial; Mites
PubMed: 37165885
DOI: 10.1017/S0031182023000367 -
Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea).PloS One 2023Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin...
Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.
Topics: Animals; Hymenoptera; Genes, Mitochondrial; Phylogeny; Bayes Theorem; Ecosystem; Ultraviolet Rays; Mitochondrial Proteins; Genome, Mitochondrial
PubMed: 37988339
DOI: 10.1371/journal.pone.0294687 -
Frontiers in Immunology 2022In addition to their role in cellular energy production, mitochondria are increasingly recognized as regulators of the innate immune response of phagocytes. Here, we...
In addition to their role in cellular energy production, mitochondria are increasingly recognized as regulators of the innate immune response of phagocytes. Here, we demonstrate that altering expression levels of the mitochondria-associated enzyme, cytidine monophosphate kinase 2 (CMPK2), disrupts mitochondrial physiology and significantly deregulates the resting immune homeostasis of macrophages. Both CMPK2 silenced and constitutively overexpressing macrophage lines portray mitochondrial stress with marked depolarization of their membrane potential, enhanced reactive oxygen species (ROS), and disturbed architecture culminating in the enhanced expression of the pro-inflammatory genes IL1β, TNFα, and IL8. Interestingly, the long-term modulation of CMPK2 expression resulted in an increased glycolytic flux of macrophages akin to the altered physiological state of activated M1 macrophages. While infection-induced inflammation for restricting pathogens is regulated, our observation of a total dysregulation of basal inflammation by bidirectional alteration of CMPK2 expression only highlights the critical role of this gene in mitochondria-mediated control of inflammation.
Topics: Humans; Genes, Mitochondrial; Homeostasis; Macrophages; Inflammation
PubMed: 36451821
DOI: 10.3389/fimmu.2022.935710 -
Biochimica Et Biophysica Acta Jun 2011Tumor microenvironment promotes mtDNA mutations. A number of these mutations will affect cell metabolism and increase cell survival. These mutations are positively... (Review)
Review
Tumor microenvironment promotes mtDNA mutations. A number of these mutations will affect cell metabolism and increase cell survival. These mutations are positively selected and contribute to other tumor features, such as extracellular matrix remodeling and angiogenic processes, thus favoring metastases. Like somatic mutations, although with less marked effects, some mtDNA population polymorphisms will affect OXPHOS function, cell metabolism, and homeostasis. Thus, they could behave as inherited susceptibility factors for cancer. However, in addition to epidemiological evidence, other more direct clues are required. The cybrid approach can help to clarify this issue.
Topics: Animals; Female; Genes, Mitochondrial; Genetic Predisposition to Disease; Humans; Inheritance Patterns; Maternal-Fetal Exchange; Models, Biological; Neoplasms; Oxidative Phosphorylation; Pregnancy
PubMed: 20732295
DOI: 10.1016/j.bbabio.2010.08.004 -
Investigative Ophthalmology & Visual... Oct 2020The coronavirus disease 2019 (COVID-19) pandemic severely challenges public health and necessitates the need for increasing our understanding of COVID-19 pathogenesis,...
PURPOSE
The coronavirus disease 2019 (COVID-19) pandemic severely challenges public health and necessitates the need for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and propagation. The aim of this study was to investigate key factors for cellular susceptibility to severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection in the ocular surface cells.
METHODS
We combined co-expression and SARS-CoV-2 interactome network to predict key genes at COVID-19 in ocular infection based on the premise that genes underlying a disease are often functionally related and functionally related genes are often co-expressed.
RESULTS
The co-expression network was constructed by mapping the well-known angiotensin converting enzyme (ACE2), TMPRSS2, and host susceptibility genes implicated in COVID-19 genomewide association study (GWAS) onto a cornea, retinal pigment epithelium, and lung. We found a significant co-expression module of these genes in the cornea, revealing that cornea is potential extra-respiratory entry portal of SARS-CoV-2. Strikingly, both co-expression and interaction networks show a significant enrichment in mitochondrial function, which are the hub of cellular oxidative homeostasis, inflammation, and innate immune response. We identified a corneal mitochondrial susceptibility module (CMSM) of 14 mitochondrial genes by integrating ACE2 co-expression cluster and SARS-CoV-2 interactome. The gene ECSIT, as a cytosolic adaptor protein involved in inflammatory responses, exhibits the strongest correlation with ACE2 in CMSM, which has shown to be an important risk factor for SARS-CoV-2 infection and prognosis.
CONCLUSIONS
Our co-expression and protein interaction network analysis uncover that the mitochondrial function related genes in cornea contribute to the dissection of COVID-19 susceptibility and potential therapeutic interventions.
Topics: Betacoronavirus; COVID-19; Cell Line; Cornea; Coronavirus Infections; Gene Expression Regulation; Genes, Mitochondrial; Humans; Pandemics; Peptidyl-Dipeptidase A; Pneumonia, Viral; RNA; SARS-CoV-2
PubMed: 33049061
DOI: 10.1167/iovs.61.12.13 -
Proceedings. Biological Sciences Jan 2018Strict maternal inheritance renders the mitochondrial genome susceptible to accumulating mutations that harm males, but are otherwise benign or beneficial for females....
Strict maternal inheritance renders the mitochondrial genome susceptible to accumulating mutations that harm males, but are otherwise benign or beneficial for females. This 'mother's curse' effect can degrade male survival and fertility if unopposed by counteracting evolutionary processes. Coadaptation between nuclear and mitochondrial genomes-with nuclear genes evolving to compensate for male-harming mitochondrial substitutions-may ultimately resolve mother's curse. However, males are still expected to incur a transient fitness cost during mito-nuclear coevolution, and it remains unclear how severe such costs should be. We present a population genetic analysis of mito-nuclear coadaptation to resolve mother's curse effects, and show that the magnitude of the 'male mitochondrial load'-the negative impact of mitochondrial substitutions on male fitness components-may be large, even when genetic variation for compensatory evolution is abundant. We also find that the male load is surprisingly sensitive to population size: male fitness costs of mito-nuclear coevolution are particularly pronounced in both small and large populations, and minimized in populations of intermediate size. Our results reveal complex interactions between demography and genetic constraints during the resolution of mother's curse, suggesting potentially widespread species differences in susceptibility to mother's curse effects.
Topics: Animals; Cell Nucleus; Female; Fertility; Genes, Mitochondrial; Genome; Genome, Mitochondrial; Longevity; Male; Models, Genetic
PubMed: 29343598
DOI: 10.1098/rspb.2017.2257 -
Communications Biology Jul 2022The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several...
The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.
Topics: Animals; Evolution, Molecular; Genes, Mitochondrial; Genome, Mitochondrial; Insecta; Phthiraptera
PubMed: 35804150
DOI: 10.1038/s42003-022-03625-0