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The Genomics of Selfing in Maize ( Zea mays ssp. mays ): Catching Purging in the Act

https://doi.org/10.1101/594812
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What this work says

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

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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
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Breeding systems and genome evolution
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The effect of linkage on limits to artificial selection
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Associative overdominance caused by linked detrimental mutations
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Genetic loads and estimates of mutation rates in highly inbred plant populations
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Purging inbreeding depression and the probability of extinction: full-sib mating
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Mutation load and rapid adaptation favour outcrossing over self-fertilization
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Improved maize reference genome with single-molecule technologies
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Maize HapMap2 identifies extant variation from a genome in flux
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Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
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Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
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SIFT missense predictions for genomes
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The genetics of inbreeding depression
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The maize W22 genome provides a foundation for functional genomics and transposon biology
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Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes
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Maize (Zea mays L.) genome size indicated by 180-bp knob abundance is associated with flowering time
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Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice
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Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution
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Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
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Genome evolution of wild barley ( Hordeum spontaneum ) by BARE -1 retrotransposon dynamics in response to sharp microclimatic divergence
inferredcites →https://doi.org/10.1073/pnas.1413864112openalex-snapshot
Recombination in diverse maize is stable, predictable, and associated with genetic load
inferredcites →https://doi.org/10.1086/523366openalex-snapshot
Genomic Consequences of Outcrossing and Selfing in Plants
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The Large Genome Constraint Hypothesis: Evolution, Ecology and Phenotype
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Mechanisms and Control of Rapid Genomic Changes in Flax
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The Sequence Alignment/Map format and SAMtools
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MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences
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CrossMap: a versatile tool for coordinate conversion between genome assemblies
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Toward better understanding of artifacts in variant calling from high-coverage samples
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians
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The effect of deleterious mutations on neutral molecular variation.
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Individual variation in inbreeding depression: the roles of inbreeding history and mutation.
inferredcites →https://doi.org/10.1093/genetics/26.6.608openalex-snapshot
GENETIC CHARACTERISTICS OF THE B CHROMOSOMES IN MAIZE
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SELECTION FOR RECOMBINATION IN PARTIALLY SELF-FERTILIZING POPULATIONS
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Deleterious variants in Asian rice and the potential cost of domestication
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SIFT: predicting amino acid changes that affect protein function
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The evolutionary genetics of sexual systems in flowering plants
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Evolutionary consequences of self-fertilization in plants
inferredcites →https://doi.org/10.1101/gr.081851.108openalex-snapshot
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
inferredcites →https://doi.org/10.1101/gr.091678.109openalex-snapshot
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
inferredcites →https://doi.org/10.1101/gr.132102openalex-snapshot
Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis
inferredcites →https://doi.org/10.1101/gr.5347007openalex-snapshot
Allelic variation and heterosis in maize: How do two halves make more than a whole?
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Genomics advances the study of inbreeding depression in the wild
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PERSPECTIVE: PURGING THE GENETIC LOAD: A REVIEW OF THE EXPERIMENTAL EVIDENCE
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The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story
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Inbreeding depression and heterosis in populations of Schiedea viscosa, a highly selfing species
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Selection for Early Flowering Results in Simultaneous Selection for Reduced Nuclear DNA Content in Maize
inferredcites →https://doi.org/10.1111/j.1469-1809.1941.tb02272.xopenalex-snapshot
AVERAGE EXCESS AND AVERAGE EFFECT OF A GENE SUBSTITUTION
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Genome size is a strong predictor of cell size and stomatal density in angiosperms
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Stabilizing selection on genome size in a population of Festuca pallens under conditions of intensive intraspecific competition
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THE EVOLUTION OF SELF‐FERTILIZATION AND INBREEDING DEPRESSION IN PLANTS. I. GENETIC MODELS
inferredcites →https://doi.org/10.1111/nph.12247openalex-snapshot
Genome size variation in wild and cultivated maize along altitudinal gradients
inferredcites →https://doi.org/10.1111/nph.13639openalex-snapshot
Examining the cause of high inbreeding depression: analysis of whole‐genome sequence data in 28 selfed progeny of Eucalyptus grandis
inferredcites →https://doi.org/10.1111/nph.14784openalex-snapshot
Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes
inferredcites →https://doi.org/10.1126/science.1174320openalex-snapshot
Genetic Properties of the Maize Nested Association Mapping Population
inferredcites →https://doi.org/10.1126/science.1177837openalex-snapshot
A First-Generation Haplotype Map of Maize
inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot
The B73 Maize Genome: Complexity, Diversity, and Dynamics
inferredcites →https://doi.org/10.1126/science.aao0827openalex-snapshot
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins
inferredcites →https://doi.org/10.1126/science.aar3684openalex-snapshot
Natural selection interacts with recombination to shape the evolution of hybrid genomes
inferredcites →https://doi.org/10.1146/annurev-arplant-042110-103827openalex-snapshot
Progress Toward Understanding Heterosis in Crop Plants
inferredcites →https://doi.org/10.1146/annurev.ecolsys.30.1.479openalex-snapshot
Do Plant Populations Purge Their Genetic Load? Effects of Population Size and Mating History on Inbreeding Depression
inferredcites →https://doi.org/10.1146/annurev.genet.42.110807.091612openalex-snapshot
Mid-Century Controversies in Population Genetics
inferredcites →https://doi.org/10.1371/journal.pgen.1003258openalex-snapshot
Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect
inferredcites →https://doi.org/10.1371/journal.pgen.1003604openalex-snapshot
From Many, One: Genetic Control of Prolificacy during Maize Domestication
inferredcites →https://doi.org/10.1371/journal.pgen.1004298openalex-snapshot
Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1005323openalex-snapshot
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
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Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts
inferredcites →https://doi.org/10.1371/journal.pgen.1007162openalex-snapshot
Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays
inferredcites →https://doi.org/10.1371/journal.pone.0014473openalex-snapshot
Purging Deleterious Mutations under Self Fertilization: Paradoxical Recovery in Fitness with Increasing Mutation Rate in Caenorhabditis elegans
inferredcites →https://doi.org/10.1534/g3.113.008870openalex-snapshot
The Pattern and Distribution of Deleterious Mutations in Maize
inferredcites →https://doi.org/10.1534/g3.115.023184openalex-snapshot
On the Consequences of Purging and Linkage on Fitness and Genetic Diversity
inferredcites →https://doi.org/10.1534/genetics.104.036384openalex-snapshot
Self-Fertilization and the Evolution of Recombination
inferredcites →https://doi.org/10.1534/genetics.105.048322openalex-snapshot
The Maize Ab10 Meiotic Drive System Maps to Supernumerary Sequences in a Large Complex Haplotype
inferredcites →https://doi.org/10.1534/genetics.108.097238openalex-snapshot
Historical Divergence and Gene Flow in the Genus Zea
inferredcites →https://doi.org/10.1534/genetics.114.172809openalex-snapshot
The Evolution of Selfing Is Accompanied by Reduced Efficacy of Selection and Purging of Deleterious Mutations
inferredcites →https://doi.org/10.2307/3558325openalex-snapshot
Is self‐fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach
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mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models
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The effects of cross and self fertilisation in the vegetable kingdom /
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The Arabidopsis thaliana mobilome and its impact at the species level
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Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
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Testing the link between genome size and growth rate in maize

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

inferred← citeshttps://doi.org/10.1016/j.sajb.2020.04.012openalex-snapshot
Lactuca dregeana DC. (Asteraceae: Chicorieae) – A South African crop relative under threat from hybridization and climate change
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The population genetics of structural variants in grapevine domestication
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Population Genomic Approaches for Weed Science
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