Comparative Analysis of the Mitochondrial DNA of Wild Varieties and Domesticated Pleurotus citrinopileatus

The accumulation of somatic mutations during aging is not uniform across tissue types and, in addition, shows significant variability in the source of mutation that can be modified by small molecule interventions.

The accumulation of somatic mutations during aging is not uniform across tissue types and, in addition, shows significant variability in the source of mutation that can be modified by small molecule interventions.

The accumulation of somatic mutations during aging is not uniform across tissue types and, in addition, shows significant variability in the source of mutation that can be modified by small molecule interventions.

MITOCHONDRIAL DNA (mtDNA) contains genes for the ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) used in mitochondrial protein synthesis and for a limited number of proteins of the mitochondrial inner membrane1–4. By a combination of genetic and physical mapping, the location of most of these genes on yeast mtDNA has been determined3,4. There is a single gene for the RNA from the large subunit of yeast mitochondrial ribosomes5, but, nevertheless, this RNA hybridises to non-adjacent fragments on the physical map of mtDNA6. Although this suggested that the gene for this RNA is split, like some eukaryotic nuclear genes7, the presence of partial gene duplications complicated the interpretation of our hybridisation experiments6. By electron microscopy of RNA–DNA hybrids we now present direct evidence for an insertion in this rRNA gene.

With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity. Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes. This research constructed a circular mitochondrial map for D. hancockii, spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, "rpl16-ccmFn-rps3-rps19," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species.

Vanderbylia fraxinea (Bull.) D.A. Reid, 1973 is an important wood-inhabiting fungus that plays a significant role in nutrient recycling in most forest ecosystems. In this study, the complete mitochondrial genome of V. fraxinea was characterized through de novo assembly using Illumina sequencing data and genome annotation. The mitochondrial genome is a circular molecule of 115,473 bp with a GC content of 28.66%. It comprises a total of 62 genes. Among these, 36 are protein-coding genes including 21 free-standing open reading frames (ORFs), 24 transfer RNA genes, and two ribosomal RNA genes. Core gene set commonly found in fungal mitochondrial genomes is also present in this genome, such as the apocytochrome b (cob), three subunits of the cytochrome c oxidase (cox1, cox2, and cox3), seven subunits of the NADH dehydrogenase (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), and three subunits of the ATP synthase (atp6, atp8, and atp9), as well as ribosomal RNA subunits (rns and rnl) and a set of transfer RNA genes. Phylogenetic analysis of the protein-coding sequences from the mitochondrial genome revealed a close relationship between V. fraxinea and the Ganoderma species within the Polyporaceae family.

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA : A primitive form of plant mitochondrial genome

Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication

Human mitochondrial DNA (mtDNA) is 16,569 base pairs (bp) in length, coding for 37 genes. During the course of evolution, nearly all the genes expressing ribosomal proteins and ribosomal RNAs (rRNA) genes have been transferred from the mitochondria to the nucleus. However, mitochondrial DNA contains two ribosomal RNAs genes (12S and 16S), which have not yet transferred to the nucleus. These two, should, soon or later, end up in the nucleus. What does the future likely hold for these genes? In the nucleus everything has already been prepared, since all of the ribosomal protein genes are now chromosomally encoded, and nucleolar organizers, the nucleolus, and 45 rDNA are developed waiting for 12S rRNA and I6S rRNA genes to join them, thus enabling the formation of the third DNA-containing organelle, the ribosomal compartment. What could be the reason for this major event in the existence of life on Earth as it is currently understood? The advent of the ribosomal organelle will likely have an enormous impact on reproductive characteristics and on intellectual (thoughts, abstract and complex ideas, imagination, dreams, spirit) activity of the brain. Could this be the answer to the question: Are humans still evolving?

The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus

Functional cloning led to the isolation of a novel methotrexate (MTX) resistance gene in the protozoan parasite Leishmania. The gene corresponds to orfG, an open reading frame (ORF) of the LD1/CD1 genomic locus that is frequently amplified in several Leishmania stocks. A functional ORF G-green fluorescence protein fusion was localized to the plasma membrane. Transport studies indicated that ORF G is a high affinity biopterin transporter. ORF G also transports folic acid, with a lower affinity, but does not transport the drug analog MTX. Disruption of both alleles of orfG led to a mutant strain that became hypersensitive to MTX and had no measurable biopterin transport. Leishmania tarentolae MTX-resistant cells without their high affinity folate transporters have a rearranged orfG gene and increased orfG RNA levels. Overexpression of orfG leads to increased biopterin uptake and, in folate-rich medium, to increased folate uptake. MTX-resistant cells compensate for mutations in their high affinity folate/MTX transporter by overexpressing ORF G, which increases the uptake of pterins and selectively increases the uptake of folic acid, but not MTX.

The genetics and molecular biology of the ecologically important brown alga, Sargassum horneri (Turner) C. Agardh, are poorly known. In this investigation, the complete nucleotide sequence of the mitochondrial (mt) genome of S. horneri was determined using long PCR and primer walking techniques. The mt genome is 34,606 bp in length and contains 3 ribosomal RNA genes, 25 transfer RNA genes, 35 protein-coding genes, and 2 open reading frames (ORFs). The overall AT content of the genome is 63.84 %, and the intergenic spacers constitute only 4.29 %. The genome organization of S. horneri mitochondrial DNA (mtDNA) is very similar to Fucus vesiculosus except that the counterparts of one putative tRNATyr gene and ORF379 in Fucus were missing from S. horneri mtDNA. Phylogenetic analyses based on 3 ribosomal RNA genes and 35 protein-coding genes suggest that S. horneri has a closer relationship with F. vesiculosus than other analyzed brown algae. Sargassum horneri is the first species of Sargassaceae to have its mitochondrial genome sequenced. This will provide useful information on both population genetics and molecular evolution of the related species.

Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification

Vigna reflexo-pilosa can be found in both wild and cultivated forms. It is the only tetraploid species in the genus Vigna in Fabaceae, occurring through hybridization between Vigna hirtella and Vigna trinervia, with the chromosome number of 2n = 4x = 44. V. reflexo-pilosa provides an invaluable gene pool for improving cultivated Vigna crop varieties. This study aimed to report the complete mitochondrial and chloroplast genomes of V. reflexo-pilosa. A total of 6,496,297 raw reads were generated from V. reflexo-pilosa using the long-read PacBio technology. The complete mitochondrial genome was assembled into a linear structure with a total length of 370,913 base pairs (bp) with 45.20% GC content. It contains 32 protein-coding genes, 18 transfer RNA genes, and 3 ribosomal RNA genes. A total of 520 RNA editing sites were detected in 30 protein-coding genes. The V. reflexo-pilosa mitochondrial genome shared large colinear blocks with Vigna radiata as compared to nine other mitochondrial genomes in Fabaceae. In addition, Vigna hirtella (male parent) and Vigna trinervia (female parent) were sequenced using the MGI sequencing technology. The complete chloroplast genome of V. reflexo-pilosa, V. hirtella, and V. trinervia was assembled into a circular structure with a total length of 150,967, 151,915 and 151,226 bp, respectively. All three chloroplast genomes consist of 128 genes. We found no evidence of shared genes between the mitochondrial and chloroplast genomes of V. reflexo-pilosa. Comparison of the three Vigna chloroplast genomes showed high levels of similarity between V. reflexo-pilosa and V. trinervia, revealing maternal inheritance of the chloroplast genomes. Based on both mitochondrial and chloroplast genes, phylogenetic trees showed that V. reflexo-pilosa is closely related to V. radiata. These genomes enhance our understanding of mitochondrial and chloroplast evolution of V. reflexo-pilosa and are valuable genetic resources in legumes.

The first complete mitochondrial genome of a sunbird was determined for Gould’s sunbird Aethopyga gouldiae. The identity of the sample was verified by conducting nucleotide blast for each mitochondrial ribosomal RNA and protein-coding gene, and by estimating its phylogenetic position using five genes (12S, ND2, ATP6, ND3, CYTb) and 52 passerines (including 17 sunbirds and allies). The mitogenomic length of A. gouldiae was 16,893 bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. The nucleotide composition of the genome shows a bias toward A + T. Since the sunbirds and allies form a large bird group that feeds on nectar, along with the hummingbirds and honeyeaters, the mitogenome of A. gouldiae could contribute to understand the evolution of feeding behavior in birds and the phylogenetic position of the sunbirds.