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Impacts of sex ratio meiotic drive on genome structure and defense in a stalk-eyed fly

https://doi.org/10.1101/2020.09.23.310227

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What this work says

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

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The Role of Host Factors in the Population Dynamics of Selfish Transposable Elements

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Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

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BUSCO: Assessing Genome Assembly and Annotation Completeness

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Molecular domestication of transposable elements: From detrimental parasites to useful host genes

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The relation of recombination to mutational advance

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Association between a satellite DNA sequence and the responder of segregation distorter in D. melanogaster

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Selfish genetic elements

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Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

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The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters

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UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery

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Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

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Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons

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Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery

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The hpRNA/RNAi Pathway Is Essential to Resolve Intragenomic Conflict in the Drosophila Male Germline

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Drosophila P75 safeguards oogenesis by preventing H3K9me2 spreading

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The Genetic Makeup of the Drosophila piRNA Pathway

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Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

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The Ecology and Evolutionary Dynamics of Meiotic Drive

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Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline

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The hitch-hiking effect of a favourable gene

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On the role of unequal exchange in the containment of transposable element copy number

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Artificial sexual selection alters allometry in the stalk-eyed flyCyrtodiopsis dalmanni(Diptera: Diopsidae)

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The hitch-hiking effect of a favourable gene

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Covariance in species diversity and facilitation among non-interactive parasite taxa: all against the host

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The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

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Molecular domestication of mobile elements

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Responder (Rsp) Alleles in the Segregation Distorter (SD) System of Meiotic Drive in Drosophila may Represent a Complex Family of Satellite Repeat Sequences

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Male eye span in stalk-eyed flies indicates genetic quality by meiotic drive suppression

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Initial sequencing and analysis of the human genome

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Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

inferredcites →https://doi.org/10.1038/hdy.2013.131openalex-snapshot

Male eyespan size is associated with meiotic drive in wild stalk-eyed flies (Teleopsis dalmanni)

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Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

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An endogenous small interfering RNA pathway in Drosophila

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Embryonic stem cells use ZFP809 to silence retroviral DNAs

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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

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Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

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Fast gapped-read alignment with Bowtie 2

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A unified classification system for eukaryotic transposable elements

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JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila

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Satellite DNA-mediated diversification of a sex-ratio meiotic drive gene family in Drosophila

inferredcites →https://doi.org/10.1038/s41559-021-01592-zopenalex-snapshot

Rapid evolutionary dynamics of an expanding family of meiotic drive factors and their hpRNA suppressors

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PIWI-interacting RNAs: small RNAs with big functions

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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

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Accurate detection of complex structural variations using single-molecule sequencing

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Chromosome-wide linkage disequilibrium as a consequence of meiotic drive

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Selfish genetic elements, genetic conflict, and evolutionary innovation

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Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

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APOBEC3 Proteins Inhibit Human LINE-1 Retrotransposition

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Population and clinical genetics of human transposable elements in the (post) genomic era

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Maintenance of Fertility in the Face of Meiotic Drive

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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GMAP: a genomic mapping and alignment program for mRNA and EST sequences

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Fast and accurate short read alignment with Burrows–Wheeler transform

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The Sequence Alignment/Map format and SAMtools

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BEDTools: a flexible suite of utilities for comparing genomic features

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

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NextGenMap: fast and accurate read mapping in highly polymorphic genomes

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The MaSuRCA genome assembler

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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SAMBLASTER : fast duplicate marking and structural variant read extraction

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An Analysis of Variance Test for Normality (Complete Samples)

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Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae)

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inferredcites →https://doi.org/10.1093/genetics/128.4.841openalex-snapshot

Causes of sex ratio bias may account for unisexual sterility in hybrids: a new explanation of Haldane's rule and related phenomena.

inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot

The effect of deleterious mutations on neutral molecular variation.

inferredcites →https://doi.org/10.1093/genetics/142.2.641openalex-snapshot

Further Evidence Consistent With Stellate's Involvement in Meiotic Drive

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Sex Chromosome Meiotic Drive in Stalk-Eyed Flies

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EXPERIMENTAL AND THEORETICAL ANALYSIS OF THE "SEX-RATIO" POLYMORPHISM IN DROSOPHILA PSEUDOOBSCURA

inferredcites →https://doi.org/10.1093/genetics/iyaa018openalex-snapshot

X-linked meiotic drive can boost population size and persistence

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Recurrent Adaptation in RNA Interference Genes Across the Drosophila Phylogeny

inferredcites →https://doi.org/10.1093/molbev/msw137openalex-snapshot

PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq

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Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera

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Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites

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The Dfam database of repetitive DNA families

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

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Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

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Rapid evolution and conserved function of the piRNA pathway

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Genetic linkage between a sexually selected trait and X chromosome meiotic drive

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Meiotic drive reduces egg-to-adult viability in stalk-eyed flies

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The evolution of RNAi as a defence against viruses and transposable elements

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The role of meiotic drive in hybrid male sterility

inferredcites →https://doi.org/10.1101/675108openalex-snapshot

Maintenance of fertility in the face of meiotic drive

inferredcites →https://doi.org/10.1101/gad.209841.112openalex-snapshot

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

inferredcites →https://doi.org/10.1101/gr.115402.110openalex-snapshot

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot

Direct determination of diploid genome sequences

inferredcites →https://doi.org/10.1101/gr.251546.119openalex-snapshot

Rapid evolution of piRNA-mediated silencing of an invading transposable element was driven by abundant de novo mutations

inferredcites →https://doi.org/10.1111/evo.12011openalex-snapshot

RECURRENT AND RECENT SELECTIVE SWEEPS IN THE piRNA PATHWAY

inferredcites →https://doi.org/10.1111/j.0014-3820.2001.tb01276.xopenalex-snapshot

SEX-LINKED EXPRESSION OF A SEXUALLY SELECTED TRAIT IN THE STALK-EYED FLY, CYRTODIOPSIS DALMANNI

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THE ECOLOGY AND GENETICS OF FITNESS IN CHLAMYDOMONAS. XII. REPEATED SEXUAL EPISODES INCREASE RATES OF ADAPTATION TO NOVEL ENVIRONMENTS

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MEIOTIC DRIVE AND SEX CHROMOSOME CYCLING

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Host immunization shapes interspecific associations in trematode parasites

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Genetic divergence does not predict change in ornament expression among populations of stalk‐eyed flies

inferredcites →https://doi.org/10.1111/j.1365-313x.1993.00739.xopenalex-snapshot

Construction of integrated genetic linkage maps by means of a new computer package: Join Map

inferredcites →https://doi.org/10.1111/j.1420-9101.2006.01169.xopenalex-snapshot

Fitness effects of X chromosome drive in the stalk-eyed fly, Cyrtodiopsis dalmanni

inferredcites →https://doi.org/10.1111/jeb.12411openalex-snapshot

Sex‐ratio meiotic drive and interspecific competition

inferredcites →https://doi.org/10.1111/jeb.13140openalex-snapshot

Contrasting patterns of X‐chromosome divergence underlie multiple sex‐ratio polymorphisms in stalk‐eyed flies

inferredcites →https://doi.org/10.1111/mec.14921openalex-snapshot

Pervasive gene conversion in chromosomal inversion heterozygotes

inferredcites →https://doi.org/10.1126/science.1129333openalex-snapshot

A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline

inferredcites →https://doi.org/10.1126/science.1133953openalex-snapshot

Two Dobzhansky-Muller Genes Interact to Cause Hybrid Lethality in Drosophila

inferredcites →https://doi.org/10.1126/science.1146484openalex-snapshot

The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race

inferredcites →https://doi.org/10.1126/science.1157396openalex-snapshot

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

inferredcites →https://doi.org/10.1126/science.156.3774.477openalex-snapshot

Extraordinary Sex Ratios

inferredcites →https://doi.org/10.1146/annurev.ecolsys.32.081501.113958openalex-snapshot

Sex Chromosome Meiotic Drive

inferredcites →https://doi.org/10.1146/annurev.ge.24.120190.003051openalex-snapshot

PREMEIOTIC INSTABILITY OF REPEATED SEQUENCES IN NEUROSPORA CRASSA

inferredcites →https://doi.org/10.1146/annurev.ge.25.120191.002455openalex-snapshot

SEGREGATION DISTORTERS

inferredcites →https://doi.org/10.1186/1759-8753-5-13openalex-snapshot

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

inferredcites →https://doi.org/10.1186/s12859-018-2485-7openalex-snapshot

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

inferredcites →https://doi.org/10.1186/s12862-014-0233-9openalex-snapshot

The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1242/dev.00310openalex-snapshot

Maelstrom , a Drosophila spindle -class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage

inferredcites →https://doi.org/10.1242/jeb.148148openalex-snapshot

Genetic conflicts: the usual suspects and beyond

inferredcites →https://doi.org/10.1261/rna.2270710openalex-snapshot

Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis

inferredcites →https://doi.org/10.12688/f1000research.23297.1openalex-snapshot

GFF Utilities: GffRead and GffCompare

inferredcites →https://doi.org/10.1371/journal.pbio.0050292openalex-snapshot

A sex-ratio Meiotic Drive System in Drosophila simulans. I: An Autosomal Suppressor

inferredcites →https://doi.org/10.1371/journal.pbio.0050293openalex-snapshot

A sex-ratio Meiotic Drive System in Drosophila simulans. II: An X-linked Distorter

inferredcites →https://doi.org/10.1371/journal.pbio.0050310openalex-snapshot

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

inferredcites →https://doi.org/10.1371/journal.pbio.1001428openalex-snapshot

Drosophila Interspecific Hybrids Phenocopy piRNA-Pathway Mutants

inferredcites →https://doi.org/10.1371/journal.pbio.1002078openalex-snapshot

Numerous Transitions of Sex Chromosomes in Diptera

inferredcites →https://doi.org/10.1371/journal.pgen.1001121openalex-snapshot

Comparative Genomic Hybridization (CGH) Reveals a Neo-X Chromosome and Biased Gene Movement in Stalk-Eyed Flies (Genus Teleopsis)

inferredcites →https://doi.org/10.1371/journal.pgen.1002900openalex-snapshot

A Genetic Basis for a Postmeiotic X Versus Y Chromosome Intragenomic Conflict in the Mouse

inferredcites →https://doi.org/10.1371/journal.pgen.1004362openalex-snapshot

Meiotic Drive Impacts Expression and Evolution of X-Linked Genes in Stalk-Eyed Flies

inferredcites →https://doi.org/10.1371/journal.pgen.1005269openalex-snapshot

The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster

inferredcites →https://doi.org/10.1371/journal.pone.0015925openalex-snapshot

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

inferredcites →https://doi.org/10.1371/journal.pone.0027254openalex-snapshot

Reduced Polymorphism Associated with X Chromosome Meiotic Drive in the Stalk-Eyed Fly Teleopsis dalmanni

inferredcites →https://doi.org/10.1371/journal.pone.0059262openalex-snapshot

Characterization of an Ancient Lepidopteran Lateral Gene Transfer

inferredcites →https://doi.org/10.1534/genetics.105.051755openalex-snapshot

Organization of the sex-ratio Meiotic Drive Region in Drosophila simulans

inferredcites →https://doi.org/10.1534/genetics.106.064758openalex-snapshot

Evaluation of the Genomic Extent of Effects of Fixed Inversion Differences on Intraspecific Variation and Interspecific Gene Flow in Drosophila pseudoobscura and D. persimilis

inferredcites →https://doi.org/10.1534/genetics.110.123059openalex-snapshot

Genomic Differentiation Between Temperate and Tropical Australian Populations ofDrosophila melanogaster

inferredcites →https://doi.org/10.1534/genetics.112.145714openalex-snapshot

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

inferredcites →https://doi.org/10.1534/genetics.112.147561openalex-snapshot

Mutations to the piRNA Pathway ComponentAubergineEnhance Meiotic Drive of Segregation Distorter inDrosophila melanogaster

inferredcites →https://doi.org/10.1534/genetics.114.167536openalex-snapshot

Haldane’s Rule Is Linked to Extraordinary Sex Ratios and Sperm Length in Stalk-Eyed Flies

inferredcites →https://doi.org/10.1534/genetics.117.300567openalex-snapshot

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

inferredcites →https://doi.org/10.1534/genetics.120.303460openalex-snapshot

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura

inferredcites →https://doi.org/10.1554/04-291openalex-snapshot

RAPID EVOLUTION OF POSTZYGOTIC REPRODUCTIVE ISOLATION IN STALK-EYED FLIES

inferredcites →https://doi.org/10.4159/9780674029118openalex-snapshot

Genes in Conflict

inferredcites →https://doi.org/10.5860/choice.43-5875openalex-snapshot

Genes in conflict: the biology of selfish genetic elements

inferredcites →https://doi.org/10.7554/elife.25762openalex-snapshot

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

inferredcites →https://doi.org/10.7554/elife.35468openalex-snapshot

Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

What points at this work

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

inferred← citeshttps://doi.org/10.1098/rsbl.2022.0352openalex-snapshot

Meiotic drive adaptive testes enlargement during early development in the stalk-eyed fly

inferred← citeshttps://doi.org/10.3390/biology10090896openalex-snapshot

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

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