Divergence in expression between duplicated genes in Arabidopsis.

PubWeight™: 1.83‹?› | Rank: Top 3%

🔗 View Article (PMID 17670808)

Published in Mol Biol Evol on August 01, 2007

Authors

Eric W Ganko1, Blake C Meyers, Todd J Vision

Author Affiliations

1: Department of Biology, University of North Carolina at Chapel Hill, USA.

Articles citing this

The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) 5.75

Evidence for network evolution in an Arabidopsis interactome map. Science (2011) 5.57

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res (2012) 3.02

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population. Genome Res (2013) 1.72

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science (2016) 1.48

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. BMC Genomics (2016) 1.43

Extensive functional diversification of the Populus glutathione S-transferase supergene family. Plant Cell (2009) 1.29

Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol (2010) 1.29

The evolution of nuclear auxin signalling. BMC Evol Biol (2009) 1.27

A role for gene duplication and natural variation of gene expression in the evolution of metabolism. PLoS One (2008) 1.23

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One (2011) 1.20

Neofunctionalization of young duplicate genes in Drosophila. Proc Natl Acad Sci U S A (2013) 1.14

Structure and expression analysis of rice paleo duplications. Nucleic Acids Res (2009) 1.13

Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family. Plant Cell (2014) 1.10

Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet (2009) 1.09

Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell (2010) 1.09

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol (2011) 1.07

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PLoS One (2012) 1.05

Diverse transcriptional programs associated with environmental stress and hormones in the Arabidopsis receptor-like kinase gene family. Mol Plant (2009) 1.03

Expansion and subfunctionalisation of flavonoid 3',5'-hydroxylases in the grapevine lineage. BMC Genomics (2010) 1.02

Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol Evol (2011) 1.00

Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol (2012) 0.99

Expression pattern divergence of duplicated genes in rice. BMC Bioinformatics (2009) 0.94

Increased expression and protein divergence in duplicate genes is associated with morphological diversification. PLoS Genet (2009) 0.94

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res (2011) 0.93

Dual function of the cytochrome P450 CYP76 family from Arabidopsis thaliana in the metabolism of monoterpenols and phenylurea herbicides. Plant Physiol (2014) 0.92

Different patterns of gene structure divergence following gene duplication in Arabidopsis. BMC Genomics (2013) 0.89

Genome-wide expression analysis of soybean MADS genes showing potential function in the seed development. PLoS One (2013) 0.88

Origin and evolution of genes related to ABA metabolism and its signaling pathways. J Plant Res (2011) 0.88

Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects. Nucleic Acids Res (2010) 0.87

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis. Genome Biol (2012) 0.86

Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol (2015) 0.86

Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PLoS One (2013) 0.85

Expression diversity and evolutionary dynamics of rice duplicate genes. Mol Genet Genomics (2009) 0.85

Rapid divergence and diversification of mammalian duplicate gene functions. BMC Evol Biol (2015) 0.84

Complexity of gene expression evolution after duplication: protein dosage rebalancing. Genet Res Int (2014) 0.84

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean. Front Plant Sci (2015) 0.83

The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis. Plant Physiol (2015) 0.82

Locally duplicated ohnologs evolve faster than nonlocally duplicated ohnologs in Arabidopsis and rice. Genome Biol Evol (2013) 0.82

Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol (2010) 0.81

Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes. Plant Cell (2015) 0.81

Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases. BMC Evol Biol (2012) 0.81

Polyploidy in the Arabidopsis genus. Chromosome Res (2014) 0.80

Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet, and their expression in rice. Sci Rep (2016) 0.79

Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes. Plant Cell (2013) 0.79

Evolution of Gene Duplication in Plants. Plant Physiol (2016) 0.78

Sequence, structural and expression divergence of duplicate genes in the bovine genome. PLoS One (2014) 0.78

Asymmetric functional divergence of young, dispersed gene duplicates in Arabidopsis thaliana. J Mol Evol (2013) 0.78

Comprehensive Evolutionary and Expression Analysis of FCS-Like Zinc finger Gene Family Yields Insights into Their Origin, Expansion and Divergence. PLoS One (2015) 0.77

Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana. Plant Physiol (2015) 0.77

Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. Front Plant Sci (2015) 0.77

Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids. BMC Evol Biol (2008) 0.76

Drosophila duplicate genes evolve new functions on the fly. Fly (Austin) (2014) 0.76

Gene duplication and the environmental regulation of physiology and development. Ecol Evol (2014) 0.76

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias. BMC Genomics (2016) 0.75

Transcriptome Analysis Identifies Candidate Genes Related to Triacylglycerol and Pigment Biosynthesis and Photoperiodic Flowering in the Ornamental and Oil-Producing Plant, Camellia reticulata (Theaceae). Front Plant Sci (2016) 0.75

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes. Plant Physiol (2016) 0.75

Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots. PLoS One (2016) 0.75

Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. BMC Genomics (2016) 0.75

Evolutionary and Functional Analysis of Membrane-Bound NAC Transcription Factor Genes in Soybean. Plant Physiol (2016) 0.75

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns. Sci Rep (2016) 0.75

Genome-wide Analysis and Expression Divergence of the Trihelix family in Brassica Rapa: Insight into the Evolutionary Patterns in Plants. Sci Rep (2017) 0.75

Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens. Genome Biol Evol (2017) 0.75

Expansion and evolutionary patterns of cysteine-rich peptides in plants. BMC Genomics (2017) 0.75

Articles by these authors

(truncated to the top 100)

Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol (2008) 6.18

Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet (2006) 5.81

The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94

The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23

The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci (2011) 4.16

MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08

Data archiving is a good investment. Nature (2011) 3.53

An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol (2007) 3.45

Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res (2006) 2.95

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A (2008) 2.92

Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics (2003) 2.68

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev (2011) 2.66

Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (2010) 2.62

Construction of small RNA cDNA libraries for deep sequencing. Methods (2007) 2.43

Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol (2004) 2.41

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30

Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res (2002) 2.27

Phenex: ontological annotation of phenotypic diversity. PLoS One (2010) 2.13

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc (2009) 2.12

The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol (2010) 2.07

A spatial dissection of the Arabidopsis floral transcriptome by MPSS. BMC Plant Biol (2008) 1.99

Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol (2002) 1.97

Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol (2004) 1.96

Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell (2004) 1.94

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One (2010) 1.93

Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell (2011) 1.93

Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A (2008) 1.92

Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J Virol (2006) 1.91

Data reuse and the open data citation advantage. PeerJ (2013) 1.79

Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell (2013) 1.69

A computational system to select candidate genes for complex human traits. Bioinformatics (2007) 1.60

Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol Biol (2008) 1.59

Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol (2009) 1.55

Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis. BMC Plant Biol (2007) 1.50

Deep sequencing of chicken microRNAs. BMC Genomics (2008) 1.48

Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife (2013) 1.48

Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol (2004) 1.46

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol (2008) 1.45

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytol (2011) 1.44

Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet (2008) 1.43

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J (2011) 1.42

The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol (2012) 1.40

Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics (2010) 1.39

Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta x Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait. Plant Physiol (2003) 1.39

Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A (2012) 1.39

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton. J Appl Ichthyol (2012) 1.38

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol (2010) 1.36

Phytome: a platform for plant comparative genomics. Nucleic Acids Res (2006) 1.35

Sequence conservation and differential expression of Marek's disease virus microRNAs. J Virol (2008) 1.34

RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep (2009) 1.32

Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet (2009) 1.29

Dm3 is one member of a large constitutively expressed family of nucleotide binding site-leucine-rich repeat encoding genes. Mol Plant Microbe Interact (2002) 1.27

Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell (2006) 1.27

The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell (2009) 1.27

RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci U S A (2010) 1.26

Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics (2005) 1.25

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics (2006) 1.24

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics (2012) 1.19

Characterization of paralogous protein families in rice. BMC Plant Biol (2008) 1.19

A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics (2007) 1.17

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res (2011) 1.13

Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol (2010) 1.13

siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res (2010) 1.12

Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA (2009) 1.12

Discovery of ADP-ribosylation and other plant defense pathway elements through expression profiling of four different Arabidopsis-Pseudomonas R-avr interactions. Mol Plant Microbe Interact (2008) 1.11

INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A (2012) 1.11

AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One (2011) 1.09

Bioinformatics analysis of small RNAs in plants using next generation sequencing technologies. Methods Mol Biol (2010) 1.08

Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol (2010) 1.07

MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA Biogenesis in Eudicots. Plant Cell (2013) 1.03

Conservation and divergence in eukaryotic DNA methylation. Proc Natl Acad Sci U S A (2010) 1.02

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. J Biomed Semantics (2013) 1.02

Biogenesis and function of rice small RNAs from non-coding RNA precursors. Curr Opin Plant Biol (2013) 0.99

Plant microRNAs display differential 3' truncation and tailing modifications that are ARGONAUTE1 dependent and conserved across species. Plant Cell (2013) 0.98

MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific. Virology (2009) 0.97

Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol (2013) 0.97

MicroRNAs in the rhizobia legume symbiosis. Plant Physiol (2009) 0.95

Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol (2011) 0.95

Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars. BMC Genomics (2011) 0.94

HDT701, a histone H4 deacetylase, negatively regulates plant innate immunity by modulating histone H4 acetylation of defense-related genes in rice. Plant Cell (2012) 0.94

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A (2014) 0.94

A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One (2012) 0.93

Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol (2004) 0.93

Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Res (2013) 0.93

Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae. BMC Genomics (2013) 0.92

Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity. Plant J (2008) 0.92

The role of TIR-NBS and TIR-X proteins in plant basal defense responses. Plant Physiol (2013) 0.91

Tracking the evolution of alternatively spliced exons within the Dscam family. BMC Evol Biol (2006) 0.90

Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol Evol (2013) 0.89

required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. Plant Cell (2012) 0.89

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc Natl Acad Sci U S A (2011) 0.89

Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol (2013) 0.89

hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures. Plant Mol Biol (2005) 0.87

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol (2012) 0.86

Fine mapping a QTL for carbon isotope composition in tomato. Theor Appl Genet (2008) 0.86

An integrated workflow for DNA methylation analysis. J Genet Genomics (2013) 0.85

Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology. Methods Mol Biol (2011) 0.85

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics (2013) 0.85