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The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

https://doi.org/10.1101/044016
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What this work says

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

inferredcites →https://doi.org/10.1002/0471250953.bi1110s43openalex-snapshot
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
inferredcites →https://doi.org/10.1007/bf00987954openalex-snapshot
Evolutionary processes in the genusCapsella (Brassicaceae)
inferredcites →https://doi.org/10.1016/0031-9422(80)85004-7openalex-snapshot
Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate
inferredcites →https://doi.org/10.1016/j.pbi.2012.01.015openalex-snapshot
Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
inferredcites →https://doi.org/10.1016/j.pbi.2016.02.006openalex-snapshot
Genomic legacies of the progenitors and the evolutionary consequences of allopolyploidy
inferredcites →https://doi.org/10.1038/nature02651openalex-snapshot
Role of transposable elements in heterochromatin and epigenetic control
inferredcites →https://doi.org/10.1038/ng.2669openalex-snapshot
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nrg3683openalex-snapshot
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
inferredcites →https://doi.org/10.1073/pnas.0811575106openalex-snapshot
The frequency of polyploid speciation in vascular plants
inferredcites →https://doi.org/10.1073/pnas.0907003106openalex-snapshot
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
inferredcites →https://doi.org/10.1073/pnas.1018222108openalex-snapshot
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
inferredcites →https://doi.org/10.1073/pnas.1101368108openalex-snapshot
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
inferredcites →https://doi.org/10.1073/pnas.1402475111openalex-snapshot
Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids
inferredcites →https://doi.org/10.1073/pnas.1412277112openalex-snapshot
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
inferredcites →https://doi.org/10.1073/pnas.1612561114openalex-snapshot
Genomic analysis reveals major determinants of cis- regulatory variation in Capsella grandiflora
inferredcites →https://doi.org/10.1093/bioinformatics/btl140openalex-snapshot
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/genetics/166.2.935openalex-snapshot
Genomic Duplication, Fractionation and the Origin of Regulatory Novelty
inferredcites →https://doi.org/10.1093/molbev/msr281openalex-snapshot
Widespread Interspecific Divergence in Cis-Regulation of Transposable Elements in the Arabidopsis Genus
inferredcites →https://doi.org/10.1093/molbev/msv001openalex-snapshot
Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution
inferredcites →https://doi.org/10.1093/molbev/msv169openalex-snapshot
Cis- Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella
inferredcites →https://doi.org/10.1101/042325openalex-snapshot
Transposable Element Evolution in the Allotetraploid Capsella bursa-pastoris
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.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.119784.110openalex-snapshot
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
inferredcites →https://doi.org/10.1105/tpc.114.124388openalex-snapshot
mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05460.xopenalex-snapshot
‘Missing link’ speciesCapsella orientalisandCapsella thracicaelucidate evolution of model plant genusCapsella(Brassicaceae)
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03107.xopenalex-snapshot
Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1111/mec.13491openalex-snapshot
Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse ( Capsella bursa‐pastoris )
inferredcites →https://doi.org/10.1111/nph.13698openalex-snapshot
On the relative abundance of autopolyploids and allopolyploids
inferredcites →https://doi.org/10.1146/annurev.ecolsys.29.1.467openalex-snapshot
PATHWAYS, MECHANISMS, AND RATES OF POLYPLOID FORMATION IN FLOWERING PLANTS
inferredcites →https://doi.org/10.1186/1471-2164-15-602openalex-snapshot
Mating system shifts and transposable element evolution in the plant genus Capsella
inferredcites →https://doi.org/10.1186/s12870-014-0272-9openalex-snapshot
The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra
inferredcites →https://doi.org/10.1371/journal.pgen.1002487openalex-snapshot
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1003255openalex-snapshot
Transposon Variants and Their Effects on Gene Expression in Arabidopsis
inferredcites →https://doi.org/10.1371/journal.pgen.1004622openalex-snapshot
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/genetics.109.103705openalex-snapshot
Splicing Variation at a FLOWERING LOCUS C Homeolog Is Associated With Flowering Time Variation in the Tetraploid Capsella bursa-pastoris
inferredcites →https://doi.org/10.1534/genetics.111.128348openalex-snapshot
Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs
inferredcites →https://doi.org/10.2307/2807123openalex-snapshot
Atlas Florae Europaeae. Distribution of Vascular Plants in Europe. Volume 10-Cruciferae (Sisymbrium to Aubrieta).
inferredcites →https://doi.org/10.3732/ajb.0800079openalex-snapshot
Polyploidy and angiosperm diversification
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41437-021-00434-9openalex-snapshot
On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)
inferred← citeshttps://doi.org/10.1101/234096openalex-snapshot
Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007949openalex-snapshot
Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
inferred← citeshttps://doi.org/10.1640/0002-8444-109.3.224openalex-snapshot
Expression Level Dominance and Homeolog Expression Bias in Recurrent Origins of the Allopolyploid Fern Polypodium hesperium
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