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Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel

https://doi.org/10.1101/466771
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/1873-3468.12652openalex-snapshot
Promiscuity in post‐transcriptional control of gene expression: Drosophila sex‐lethal and its regulatory partnerships
inferredcites →https://doi.org/10.1002/wdev.289openalex-snapshot
Charting the genotype–phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel
inferredcites →https://doi.org/10.1007/s00335-017-9722-7openalex-snapshot
The road less traveled: from genotype to phenotype in flies and humans
inferredcites →https://doi.org/10.1016/j.abb.2014.10.008openalex-snapshot
Mitochondrial maintenance failure in aging and role of sexual dimorphism
inferredcites →https://doi.org/10.1016/j.cell.2012.09.004openalex-snapshot
Heteroplasmy of Mouse mtDNA Is Genetically Unstable and Results in Altered Behavior and Cognition
inferredcites →https://doi.org/10.1016/j.devcel.2015.03.013openalex-snapshot
REPTOR and REPTOR-BP Regulate Organismal Metabolism and Transcription Downstream of TORC1
inferredcites →https://doi.org/10.1016/j.mito.2009.03.003openalex-snapshot
DNA extraction procedures meaningfully influence qPCR-based mtDNA copy number determination
inferredcites →https://doi.org/10.1016/j.mito.2017.02.001openalex-snapshot
Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila
inferredcites →https://doi.org/10.1016/j.tem.2012.06.008openalex-snapshot
Mitochondrial oxidative stress and the metabolic syndrome
inferredcites →https://doi.org/10.1016/j.tree.2004.10.003openalex-snapshot
Cytonuclear coevolution: the genomics of cooperation
inferredcites →https://doi.org/10.1016/s0891-5849(98)00153-1openalex-snapshot
Oxidative stress and aging reduce COX I RNA and cytochrome oxidase activity in Drosophila
inferredcites →https://doi.org/10.1017/s0016672300031360openalex-snapshot
Evolution of the mitochondrial ATPase 6 gene in Drosophila: unusually high level of polymorphism in D. melanogaster
inferredcites →https://doi.org/10.1038/embor.2012.57openalex-snapshot
The neglected genome
inferredcites →https://doi.org/10.1038/nature10811openalex-snapshot
The Drosophila melanogaster Genetic Reference Panel
inferredcites →https://doi.org/10.1038/nature12678openalex-snapshot
Genetic incompatibilities are widespread within species
inferredcites →https://doi.org/10.1038/nature18618openalex-snapshot
Mitochondrial and nuclear DNA matching shapes metabolism and healthy ageing
inferredcites →https://doi.org/10.1038/nrg2344openalex-snapshot
Genome-wide association studies for complex traits: consensus, uncertainty and challenges
inferredcites →https://doi.org/10.1038/nrm.2017.66openalex-snapshot
Mitochondrial diseases: the contribution of organelle stress responses to pathology
inferredcites →https://doi.org/10.1038/srep08026openalex-snapshot
Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway
inferredcites →https://doi.org/10.1038/srep12049openalex-snapshot
MitoRCA-seq reveals unbalanced cytocine to thymine transition in Polg mutant mice
inferredcites →https://doi.org/10.1046/j.1365-294x.2000.01020.xopenalex-snapshot
TCS: a computer program to estimate gene genealogies
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btt730openalex-snapshot
CrossMap: a versatile tool for coordinate conversion between genome assemblies
inferredcites →https://doi.org/10.1093/genetics/132.2.619openalex-snapshot
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
inferredcites →https://doi.org/10.1093/genetics/138.3.757openalex-snapshot
Unraveling selection in the mitochondrial genome of Drosophila.
inferredcites →https://doi.org/10.1093/molbev/msw054openalex-snapshot
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
inferredcites →https://doi.org/10.1093/nar/gki198openalex-snapshot
MAFFT version 5: improvement in accuracy of multiple sequence alignment
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025634openalex-snapshot
Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans
inferredcites →https://doi.org/10.1101/313759openalex-snapshot
Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.171546.113openalex-snapshot
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
inferredcites →https://doi.org/10.1101/gr.177881.114openalex-snapshot
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
inferredcites →https://doi.org/10.1111/acel.12232openalex-snapshot
Diacylglycerol lipase regulates lifespan and oxidative stress response by inversely modulating TOR signaling in D rosophila and C . elegans
inferredcites →https://doi.org/10.1111/rssb.12028openalex-snapshot
Selective Inference on Multiple Families of Hypotheses
inferredcites →https://doi.org/10.1186/1471-2156-5-1openalex-snapshot
Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays
inferredcites →https://doi.org/10.1186/1471-2156-5-7openalex-snapshot
A new set of BXD recombinant inbred lines from advanced intercross populations in mice
inferredcites →https://doi.org/10.1186/1471-2164-14-281openalex-snapshot
Genome-wide association study of sleep in Drosophila melanogaster
inferredcites →https://doi.org/10.1186/s12864-015-2294-6openalex-snapshot
Locating rearrangement events in a phylogeny based on highly fragmented assemblies
inferredcites →https://doi.org/10.1186/s12864-016-3137-9openalex-snapshot
Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila
inferredcites →https://doi.org/10.1186/s13059-016-0996-yopenalex-snapshot
Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
inferredcites →https://doi.org/10.1212/wnl.0000000000001744openalex-snapshot
Mitochondrial DNA sequence variation in multiple sclerosis
inferredcites →https://doi.org/10.1371/journal.pbio.0060204openalex-snapshot
Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1003129openalex-snapshot
Population Genomics of the Wolbachia Endosymbiont in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1004354openalex-snapshot
G×G×E for Lifespan in Drosophila: Mitochondrial, Nuclear, and Dietary Interactions that Modify Longevity
inferredcites →https://doi.org/10.1371/journal.pgen.1004369openalex-snapshot
Recent Mitochondrial DNA Mutations Increase the Risk of Developing Common Late-Onset Human Diseases
inferredcites →https://doi.org/10.1371/journal.pone.0034745openalex-snapshot
Genome-Wide Association Analysis of Oxidative Stress Resistance in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
inferredcites →https://doi.org/10.1371/journal.pone.0138129openalex-snapshot
Quantitative Genetics of Food Intake in Drosophila melanogaster
inferredcites →https://doi.org/10.1523/jneurosci.5306-07.2008openalex-snapshot
Reduced Odor Responses from Antennal Neurons of G q α, Phospholipase Cβ, and rdgA Mutants in Drosophila Support a Role for a Phospholipid Intermediate in Insect Olfactory Transduction
inferredcites →https://doi.org/10.1534/g3.114.016477openalex-snapshot
A Genome-Wide Association Study for Nutritional Indices in Drosophila
inferredcites →https://doi.org/10.1534/g3.114.016493openalex-snapshot
Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens
inferredcites →https://doi.org/10.1534/genetics.116.187286openalex-snapshot
Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-020-76088-0openalex-snapshot
Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts
inferred← citeshttps://doi.org/10.1101/2021.03.30.437685openalex-snapshot
Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA
inferred← citeshttps://doi.org/10.31274/etd-20210609-54openalex-snapshot
Investigating monarch butterfly (Danaus plexippus) movement ecology to inform conservation strategies
inferred← citeshttps://doi.org/10.70675/fc10f9dcz6aefz4895zb683z6e871ef1ce68openalex-snapshot
Unraveling the genetic architecture of traits in natural yeast populations
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