Tag: NUMTS

Andersen HF, Jordal BH, Kambestad M, Kirkendall LR (2012) Improbable but true: the invasive inbreeding ambrosia beetle Xylosandrus morigerus has generalist genotypes. Ecol Evol 2:247–257 Article  PubMed  PubMed Central  Google Scholar  Arif S, Gerth M, Hone‐Millard WG, Nunes MDS, Dapporto L, Shreeve TG (2021) Evidence for multiple colonisations and Wolbachia…

Hi Matthew and Robert,   HNY!  I have a question for the UCSC Genome Browser Help Desk I was wondering if you could advise us how to do this.  I downloaded the table information for the Track NumtS Sequence from the Group Variations and Repeats from the Mouse mm9 Assembly…

A single cat hair contains DNA which could link a suspect and a crime-scene, or a victim, according to a new study led by University of Leicester scientist Emily Patterson. While a human perpetrator may take pains not to leave their own DNA behind, transferred cat hair contains its own…

Mr Win, whose hair DNA identified his missing mother. Credit: Jane Elliot Cat hair could be the purr-fect way to catch criminals, according to researchers from the University of Leicester. They have shown that a single cat hair contains DNA which could link a suspect and a crime-scene, or a…

Plant material and growth conditions Nicotiana tabacum cultivar Petit Havana was used for all experiments. The TALEN design and the TALEN-expressing line Nt-JF1006-30 were described previously19. For plant growth under sterile conditions, surface-sterilized seeds were germinated on Murashige and Skoog (MS) medium52 consisting of premixed MS salts and modified vitamins…

doi: 10.1093/mutage/gead031. Online ahead of print. Affiliations Expand Affiliation 1 Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia. Item in Clipboard Tigran Harutyunyan. Mutagenesis. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/mutage/gead031. Online ahead of print. Affiliation 1 Department of Genetics…

Introduction: Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. Areas covered: In…

Our evaluation of synonymous codon bias has revealed that at least two MDPs, humanin and SHLP6, show evidence of natural selection, implying these peptides have biological roles that have been important during the course of vertebrate evolution. For humanin the synonymous codon bias analysis in vertebrates shows robust evidence of…

Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…

doi: 10.1186/s12864-023-09541-9. Affiliations Expand Affiliations 1 State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. shaozhenyu2017@sibcb.ac.cn. 2 Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical…

mtDNA variant number and heteroplasmy – rectal cancer patients The median coverage depth was 15 237 × . After processing the sequences with adequate quality scores (Q30, median of 89.9%), the proportions of aligned sequence reads for WB, PBMCs, EVs, and FFPE tumor tissue were 98.7%, 99.7%, 99.8%, and 99.8%, respectively. The…

Rojansky R, Cha M-Y, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. eLife 5:e17896. doi.org/10.7554/eLife.17896 CrossRef  CAS  PubMed  PubMed Central  Google Scholar  Wei W, Pagnamenta AT, Gleadall N et al (2020) Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA…

Introduction Osteoarthritis (OA) is a chronic musculoskeletal disease with a polygenic and heterogeneous nature that involves movable joints. The set of features that take place during the development of the disease lead to consider OA as a severe disease of the whole joint as an organ.1–3 The aetiology of knee…

Megalobrama is China’s most economically valuable fish genera. Four species make up this genus: M. amblycephala (MA), M. terminalis (MT), M. pellegrini (MP), and M. hoffmanni (MH). Many researchers have investigated the genetic relationship of Megalobrama based on mitochondrial DNA (mtDNA) and discovered that the branches of the phylogenetic tree…

Author Response Reviewer #1 (Public Review): The paper states that they observed a combined total of 77,017 single-nucleotide variants (SNVs) and 12,031 insertion/deletions (In/Dels) across all tissue, age, and intervention groups. Collectively, these data represent the largest collection of somatic mtDNA mutations obtained in a single study to date. However,…

Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three…

Detecting NUMTS (nuclear mitochondrial sequences) in the whole genome sequenced data 0 Hi All, I want to detect NUMTS (nuclear mitochondrial sequences) that have migrated from the mitochondrial to the nuclear genome using the whole genome sequence data. What could be the best Bioinformatic approach ?? Their presence, extent and…