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Rapid functional divergence of grass duplicate genes

https://doi.org/10.1101/490524
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What this work says

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

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Duplicate Retention After Small‐ and Large‐Scale Duplications
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Polyploidy and the Evolution of Domesticated Plants
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1007/bf00485947openalex-snapshot
Genome size and the proportion of repeated nucleotide sequence DNA in plants
inferredcites →https://doi.org/10.1007/pl00006540openalex-snapshot
On the Possibility of Constructive Neutral Evolution
inferredcites →https://doi.org/10.1007/s001220051371openalex-snapshot
Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers
inferredcites →https://doi.org/10.1007/s00425-014-2190-3openalex-snapshot
Distinct subfunctionalization and neofunctionalization of the B-class MADS-box genes in Physalis floridana
inferredcites →https://doi.org/10.1007/s10709-008-9311-5openalex-snapshot
Preservation of duplicate genes by originalization
inferredcites →https://doi.org/10.1016/0025-5564(87)90074-5openalex-snapshot
Reconstructing ancestral character states under Wagner parsimony
inferredcites →https://doi.org/10.1016/j.pbi.2007.01.010openalex-snapshot
Patterns in grass genome evolution
inferredcites →https://doi.org/10.1016/j.pbi.2013.11.002openalex-snapshot
Gene duplication as a driver of plant morphogenetic evolution
inferredcites →https://doi.org/10.1016/j.tig.2004.07.006openalex-snapshot
How much expression divergence after yeast gene duplication could be explained by regulatory motif evolution?
inferredcites →https://doi.org/10.1016/j.tig.2004.07.008openalex-snapshot
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
inferredcites →https://doi.org/10.1016/j.tig.2004.11.013openalex-snapshot
Plant conserved non-coding sequences and paralogue evolution
inferredcites →https://doi.org/10.1016/j.tig.2005.08.006openalex-snapshot
Expression divergence between duplicate genes
inferredcites →https://doi.org/10.1016/j.tig.2017.04.002openalex-snapshot
The Evolutionary Interplay between Adaptation and Self-Fertilization
inferredcites →https://doi.org/10.1016/j.tpb.2012.02.006openalex-snapshot
Extinction and fixation times with dominance and inbreeding
inferredcites →https://doi.org/10.1016/s0168-9525(02)02837-8openalex-snapshot
Rapid divergence in expression between duplicate genes inferred from microarray data
inferredcites →https://doi.org/10.1016/s0169-5347(03)00033-8openalex-snapshot
Evolution by gene duplication: an update
inferredcites →https://doi.org/10.1017/cbo9780511623486openalex-snapshot
The Neutral Theory of Molecular Evolution
inferredcites →https://doi.org/10.1017/s1479262115000015openalex-snapshot
Assessment of recent bottlenecks and estimation of effective population size in the Ethiopian wild sorghum using simple sequence repeat allele diversity and mutation models
inferredcites →https://doi.org/10.1038/362745a0openalex-snapshot
Male-driven evolution of DNA sequences
inferredcites →https://doi.org/10.1038/hortres.2015.31openalex-snapshot
Subfunctionalization of cation/proton antiporter 1 genes in grapevine in response to salt stress in different organs
inferredcites →https://doi.org/10.1038/nature02424openalex-snapshot
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1038/nature03895openalex-snapshot
The map-based sequence of the rice genome
inferredcites →https://doi.org/10.1038/nature07723openalex-snapshot
The Sorghum bicolor genome and the diversification of grasses
inferredcites →https://doi.org/10.1038/nature08747openalex-snapshot
Genome sequencing and analysis of the model grass Brachypodium distachyon
inferredcites →https://doi.org/10.1038/nature09916openalex-snapshot
Ancestral polyploidy in seed plants and angiosperms
inferredcites →https://doi.org/10.1038/ncomms5438openalex-snapshot
Reduced selection and accumulation of deleterious mutations in genes exclusively expressed in men
inferredcites →https://doi.org/10.1038/ng1355openalex-snapshot
Duplicate genes increase gene expression diversity within and between species
inferredcites →https://doi.org/10.1038/nplants.2016.115openalex-snapshot
Whole-genome duplication as a key factor in crop domestication
inferredcites →https://doi.org/10.1038/nrg2167openalex-snapshot
The evolution of sex-biased genes and sex-biased gene expression
inferredcites →https://doi.org/10.1038/nrg2487openalex-snapshot
RNA-based gene duplication: mechanistic and evolutionary insights
inferredcites →https://doi.org/10.1038/nrg2526openalex-snapshot
Effective population size and patterns of molecular evolution and variation
inferredcites →https://doi.org/10.1038/nrg2600openalex-snapshot
The evolutionary significance of ancient genome duplications
inferredcites →https://doi.org/10.1038/scientificamerican1179-98openalex-snapshot
The Neutral Theory of Molecular Evolution
inferredcites →https://doi.org/10.1073/pnas.0307901101openalex-snapshot
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
inferredcites →https://doi.org/10.1073/pnas.0437015100openalex-snapshot
The Tre2 ( USP6 ) oncogene is a hominoid-specific gene
inferredcites →https://doi.org/10.1073/pnas.0501102102openalex-snapshot
Modeling gene and genome duplications in eukaryotes
inferredcites →https://doi.org/10.1073/pnas.0502365102openalex-snapshot
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses
inferredcites →https://doi.org/10.1073/pnas.0509809103openalex-snapshot
Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression
inferredcites →https://doi.org/10.1073/pnas.0511307103openalex-snapshot
Evolutionary fate of retroposed gene copies in the human genome
inferredcites →https://doi.org/10.1073/pnas.1313759110openalex-snapshot
Neofunctionalization of young duplicate genes in Drosophila
inferredcites →https://doi.org/10.1073/pnas.1501339112openalex-snapshot
Sexual selection drives evolution and rapid turnover of male gene expression
inferredcites →https://doi.org/10.1093/aob/mci008openalex-snapshot
Mechanisms of Recent Genome Size Variation in Flowering Plants
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/bti042openalex-snapshot
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
inferredcites →https://doi.org/10.1093/bioinformatics/btq315openalex-snapshot
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/btr008openalex-snapshot
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/gbe/evs027openalex-snapshot
The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes
inferredcites →https://doi.org/10.1093/gbe/evu206openalex-snapshot
“Out of Pollen” Hypothesis for Origin of New Genes in Flowering Plants: Study from Arabidopsis thaliana
inferredcites →https://doi.org/10.1093/gbe/evx081openalex-snapshot
The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?
inferredcites →https://doi.org/10.1093/gbe/evx276openalex-snapshot
Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon
inferredcites →https://doi.org/10.1093/genetics/146.4.1501openalex-snapshot
Structured Coalescent Processes on Different Time Scales
inferredcites →https://doi.org/10.1093/molbev/msj051openalex-snapshot
Expression Pattern Shifts Following Duplication Indicative of Subfunctionalization and Neofunctionalization in Regulatory Genes of Arabidopsis
inferredcites →https://doi.org/10.1093/molbev/mss162openalex-snapshot
Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications
inferredcites →https://doi.org/10.1093/molbev/msx230openalex-snapshot
Natural Selection Drives Rapid Functional Evolution of Young Drosophila Duplicate Genes
inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot
An efficient algorithm for large-scale detection of protein families
inferredcites →https://doi.org/10.1093/nar/gkn1048openalex-snapshot
Structure and expression analysis of rice paleo duplications
inferredcites →https://doi.org/10.1093/nar/gkt1292openalex-snapshot
Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication
inferredcites →https://doi.org/10.1093/nar/gku986openalex-snapshot
PLAZA 3.0: an access point for plant comparative genomics
inferredcites →https://doi.org/10.1098/rspb.2003.2560openalex-snapshot
Duplicate genes and robustness to transient gene knock-downs inCaenorhabditis elegans
inferredcites →https://doi.org/10.1101/gr.076588.108openalex-snapshot
On the origin of new genes in Drosophila
inferredcites →https://doi.org/10.1101/gr.101386.109openalex-snapshot
Origins, evolution, and phenotypic impact of new genes
inferredcites →https://doi.org/10.1101/gr.1133803openalex-snapshot
Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate Genes
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.1252603openalex-snapshot
Asymmetric Sequence Divergence of Duplicate Genes
inferredcites →https://doi.org/10.1101/gr.4825606openalex-snapshot
Widespread genome duplications throughout the history of flowering plants
inferredcites →https://doi.org/10.1101/gr.6049openalex-snapshot
Retroposed New Genes Out of the X in Drosophila
inferredcites →https://doi.org/10.1104/pp.16.00523openalex-snapshot
Evolution of Gene Duplication in Plants
inferredcites →https://doi.org/10.1105/tpc.021410openalex-snapshot
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution[W]
inferredcites →https://doi.org/10.1105/tpc.110.081281openalex-snapshot
Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints
inferredcites →https://doi.org/10.1105/tpc.5.10.1217openalex-snapshot
Anther Development: Basic Principles and Practical Applications
inferredcites →https://doi.org/10.1111/evo.13356openalex-snapshot
Gene duplication and the evolution of phenotypic diversity in insect societies
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.02923.xopenalex-snapshot
Gene duplication and evolutionary novelty in plants
inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04253.xopenalex-snapshot
Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops
inferredcites →https://doi.org/10.1111/j.1558-5646.2012.01674.xopenalex-snapshot
GENOME SIZE IS NOT CORRELATED WITH EFFECTIVE POPULATION SIZE IN THEORYZASPECIES
inferredcites →https://doi.org/10.1111/tpj.12569openalex-snapshot
Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines
inferredcites →https://doi.org/10.1126/science.1089370openalex-snapshot
The Origins of Genome Complexity
inferredcites →https://doi.org/10.1126/science.1143986openalex-snapshot
Genome Plasticity a Key Factor in the Success of Polyploid Wheat Under Domestication
inferredcites →https://doi.org/10.1142/9789812836939_0012openalex-snapshot
IDENTIFYING PARENT-DAUGHTER RELATIONSHIPS AMONG DUPLICATED GENES
inferredcites →https://doi.org/10.1146/annurev.arplant.043008.092122openalex-snapshot
Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition
inferredcites →https://doi.org/10.1186/1471-2148-10-45openalex-snapshot
Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)
inferredcites →https://doi.org/10.1186/1471-2148-5-28openalex-snapshot
Subfunctionalization of duplicated genes as a transition state to neofunctionalization
inferredcites →https://doi.org/10.1186/gb-2006-7-2-r13openalex-snapshot
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1186/gb-2007-8-10-r209openalex-snapshot
All duplicates are not equal: the difference between small-scale and genome duplication
inferredcites →https://doi.org/10.1186/s12862-015-0426-xopenalex-snapshot
Rapid divergence and diversification of mammalian duplicate gene functions
inferredcites →https://doi.org/10.1186/s12862-016-0644-xopenalex-snapshot
CDROM: Classification of Duplicate gene RetentiOn Mechanisms
inferredcites →https://doi.org/10.1371/journal.pbio.0030357openalex-snapshot
Emergence of Young Human Genes after a Burst of Retroposition in Primates
inferredcites →https://doi.org/10.1371/journal.pone.0022594openalex-snapshot
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
inferredcites →https://doi.org/10.1534/genetics.104.037051openalex-snapshot
Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution
inferredcites →https://doi.org/10.1534/genetics.106.058008openalex-snapshot
Widespread Adaptive Evolution of Drosophila Genes With Sex-Biased Expression
inferredcites →https://doi.org/10.1534/genetics.115.178533openalex-snapshot
Effects of Interference Between Selected Loci on the Mutation Load, Inbreeding Depression, and Heterosis
inferredcites →https://doi.org/10.2134/agronj1938.00021962003000090005xopenalex-snapshot
Extent of Natural Crossing in Rice1
inferredcites →https://doi.org/10.4161/fly.29131openalex-snapshot
Drosophiladuplicate genes evolve new functions on the fly

What points at this work

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

inferred← citeshttps://doi.org/10.1093/gbe/evab149openalex-snapshot
BLAST from the Past: Impacts of Evolving Approaches on Studies of Evolution by Gene Duplication
inferred← citeshttps://doi.org/10.1093/molbev/msaa267openalex-snapshot
Learning Retention Mechanisms and Evolutionary Parameters of Duplicate Genes from Their Expression Data
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