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30 results for “heteroplasmy”
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - MiSeq - U5-H1-M1-M2-M3-M4-M5 - FASTQ
<p>mtDNA mixture model of 2 mtDNA sequences belonging to haplogroups U5 and H1. Run on Illumina MiSeq with 3 different polymerases (Clontech, Herculase, NEB Taq), and different DNA extraction protocols - Paired-end Fastq files</p> <p>M1 = Mixture 1:2 i.e. 50%</p> <p>M2 = Mixture 1:10 i.e. 10%</p> <p>M3 = Mixture 1:50 i.e. 2%</p> <p>M4 = Mixture 1:100 i.e. 1%</p> <p>M5 = Mixture 1:200 i.e. 0.5%</p>
Figure S1 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S1. Map of the Gigantometra gigas mitogenome using Sanger method (GenBank accession number: MF177288). Genes in the outer circle indicate the direction of transcription of the majority strand (J-strand), and those in the inner circle indicate that of the minority strand (N-strand). The GC content, GC skew+, and GC skew- are separately shown in the circle.
Figure 6 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 6. Two examples of the heteroplasmic sites in Sanger sequencing which correspond to the differently sequenced sites. Panels A and B indicate the sites at which the second-peak is obviously higher than the third-peak and fourth-peak, and the base state of the second-peak can be obtained by at least one result of HTS. The different fluorescence densities of base situated at np 1923 in the cox1 are shown in the panel A, and the panel B shows the nucleotides with amino acids at np 1923 in the results of Sanger and HTS methods. The nucleotides are C in the results of HTS sequencing, while the corresponding nucleotides are T in the results of Sanger method in both positions, and the different nucleotides lead not to the amino acids changed. Panels C and D indicate the site at the unobvious second-peak, which is slightly higher than the third-peak and fourth-peak, and the base state of the second-peak can also be obtained by at least one result of HTS. Panel C shows the unobvious second-peak at np 7125, and the nucleotide and amino acid of the site in the results of Sanger and HTS methods are shown in panel D. The amino acids are listed using single-letter amino acid abbreviations.
Figure 4. Intraspecific pairwise K2P in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 4. Intraspecific pairwise K2P distance of G. gigas based on barcode fragment size of cox1 (Sanger). The red boxplot shows the genetic distances of individuals in all three collecting sites, and the boxplots (blue, green, and yellow) separately show the distances of individuals within each place (HNYG, HNDL, and VIET). The pink boxplot shows the distances of the corresponding cox1 sequences obtained by the two sequencing methods. Abbreviation: HNYG—Yinggeling Nature Reserve, Hainan; HNDL— Diaoluoshan Nature Reserve, Hainan; VIET—northern Vietnam.
Figure S5 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure S5. The coverage of short fragments at each position in the assembly results of HTS. The three results of HTS method were separately used as reference sequences to be mapped back onto the corresponding HTS scaffolds, and the mitochondrial genes were shown below the corresponding coverage. The scale bar had an indicator at the mean coverage level and the coverage for each nucleotide position was indicated by the height of the blue line.
Figure 3 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 3. The different nucleotides in the ITS-1 and ITS-2 regions are shown. The result shows the different nucleotides at nucleotide position np 1897 (G nucleotide and T nucleotide) and np 2790 (C nucleotide and T nucleotide) obtained by Sanger and HTS methods.
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 1. Gigantometra gigas. A. Female, dorsal view. B. Male, dorsal view. C. The narrow distribution of G. gigas.
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - MiSeq - U5-H1-M1-M2-M3-M4-M5 - BAM
<p>mtDNA mixture model of 2 mtDNA sequences belonging to haplogroups U5 and H1. Run on Illumina MiSeq with 3 different polymerases (Clontech, Herculase, NEB Taq), and different DNA extraction protocols - <strong>BAM FILES </strong></p> <p>M1 = Mixture 1:2 i.e. 50%</p> <p>M2 = Mixture 1:10 i.e. 10%</p> <p>M3 = Mixture 1:50 i.e. 2%</p> <p>M4 = Mixture 1:100 i.e. 1%</p> <p>M5 = Mixture 1:200 i.e. 0.5%</p>
Data from: Evidence for hybridisation-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake
<p><span>Heteroplasmy, </span><span>the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual,</span><span> is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report </span><span>heteroplasmy in the ricefish species <em>Oryzias matanensis</em>, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the <span class="shorttext">mitochondrial NADH dehydrogenase subunit 2 (ND2) gene</span>. </span><span>In this study, </span><span>we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic <em>O. matanensis</em> individuals clustered with haplotypes of </span><em><span>O. marmoratus</span></em><span>, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridisation. </span><span>The extra haplotype was unique and contained </span><span>t</span><span>wo</span><span> nonsynonymous substitutions. </span><span>These findings demonstrate that this hybridisation-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.</span></p>
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
<p>Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.</p>
Heteroplasmy Benchmark Dataset - mitochondrial DNA mixture model - HiSeq - M1-M4 - BAM
<p>Illumina HiSeq data of mixtures M1 (50%), M2 (10%), M3 (2%) and M4 (1%) of haplotypes H1c6 and U5a2e (decreasing).</p> <p>See <a href="https://doi.org/10.1371/journal.pone.0135643">https://doi.org/10.1371/journal.pone.0135643</a> for technical/lab-related informations</p>
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
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Data from: Evidence for hybridisation-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake
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Pervasive heteroplasmy in an invasive ambrosia beetle (Scolytinae) in southern California
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Data from: Northern Bobwhite (Colinus virginianus) mitochondrial population genomics reveals structure, divergence, and evidence for heteroplasmy
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Figure 5. The polymorphism sites among the 25 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 5. The polymorphism sites among the 25 different cloning sequences of cox1. Weblogo 3.0 was used to show the nucleotide content of 25 cloning sequences of cox1 (Crooks et al., 2004). The abscissa stands for the number of the bases, while the ordinate stands for the proportion of nucleotide content provided by the 25 different cloning sequences in the same position. The sequence length between the two arrows stands for the barcode fragment size of cox1. The black triangles show the polymorphism positions in the 25 different cloning sequences, the red circles show the positions exhibited obvious second-peak in the results of direct Sanger sequencing without cloning, and the yellow stars show the different sites between the results of Sanger and HTS.
Figure 2 in Biased heteroplasmy within the mitogenomic sequences of Gigantometra gigas revealed by sanger and high-throughput methods
Figure 2. The different nucleotides of all 13 PCGs in mitogenomes obtained by Sanger and HTS sequencing. The different sequences of HTS sequencing are separately compared with the consequence of Sanger method. The horizontal axis stands for the nucleotide position, of which the sequences of 13 PCGs are ordered according to the circular mitochondrial DNA from nad2 to nad1 in the clockwise direction. The vertical axis stands for the number of the different sites in the sequences of 13 PCGs, and the different nucleotide in each site of all three HTS sequences compared with Sanger is shown in the corresponding panel.
Higher levels of heteroplasmy at OriL control mtDNA copy number, glucose metabolism and lifespan in mice
GEO Series GSE94315. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma
GEO Series GSE81178. Homo sapiens. 28 samples. Type: Other.
Somatic mtDNA mutations at intermediate levels of heteroplasmy are a source of functional heterogeneity among primary leukemic cells
GEO Series GSE207455. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
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