Extensive concerted evolution of rice paralogs and the road to regaining independence.

PubWeight™: 1.46‹?› | Rank: Top 5%

🔗 View Article (PMC 2147972)

Published in Genetics on November 01, 2007

Authors

Xiyin Wang1, Haibao Tang, John E Bowers, Frank A Feltus, Andrew H Paterson

Author Affiliations

1: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.

Articles citing this

The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94

Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes. Proc Natl Acad Sci U S A (2010) 1.43

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res (2009) 1.35

Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell (2011) 1.23

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

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evol Biol (2009) 1.19

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

Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics (2009) 1.08

Preservation of a pseudogene by gene conversion and diversifying selection. Genetics (2008) 1.01

Extensive gene amplification and concerted evolution within the CPR family of cuticular proteins in mosquitoes. Insect Biochem Mol Biol (2008) 0.98

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations. BMC Genomics (2011) 0.92

Nonallelic gene conversion in the genus Drosophila. Genetics (2010) 0.90

Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization. Genes (Basel) (2011) 0.89

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

Haploid meiosis in Arabidopsis: double-strand breaks are formed and repaired but without synapsis and crossovers. PLoS One (2013) 0.85

Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics (2014) 0.84

Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci (2014) 0.83

ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs. BMC Plant Biol (2011) 0.83

A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond. BMC Plant Biol (2009) 0.82

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species. PLoS One (2015) 0.82

Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: their duplication and diversity. Mol Genet Genomics (2008) 0.78

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ (2014) 0.77

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes. BMC Genomics (2015) 0.75

OsSIZ2 exerts regulatory influences on the developmental responses and phosphate homeostasis in rice. Sci Rep (2017) 0.75

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06

The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature (2003) 12.44

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32

Statistical tests for detecting gene conversion. Mol Biol Evol (1989) 9.86

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66

Selection in the evolution of gene duplications. Genome Biol (2002) 5.58

Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature (1980) 5.12

Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet (2004) 4.63

The probability of preservation of a newly arisen gene duplicate. Genetics (2001) 4.42

Resistance gene complexes: evolution and utilization. Annu Rev Phytopathol (2001) 3.80

Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol (2005) 3.65

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13

Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol Biol Evol (1993) 3.07

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol (2005) 2.41

Possible significances of duplication in evolution. Adv Genet (1951) 2.34

The early stages of duplicate gene evolution. Proc Natl Acad Sci U S A (2003) 2.34

Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol (2005) 2.25

Very low gene duplication rate in the yeast genome. Science (2004) 2.21

Gene duplication and gene conversion in the Caenorhabditis elegans genome. J Mol Evol (1999) 2.03

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

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics (2006) 1.91

Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A (2006) 1.87

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet (2006) 1.84

Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. J Mol Evol (2000) 1.74

Gene conversion drives GC content evolution in mammalian histones. Trends Genet (2003) 1.71

Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol Biol Evol (2005) 1.64

Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc Natl Acad Sci U S A (2005) 1.59

Duplicated genes evolve independently after polyploid formation in cotton. Proc Natl Acad Sci U S A (1999) 1.57

Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes. J Mol Evol (2002) 1.53

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat. Mol Biol Evol (2006) 1.33

Some models of gene conversion for treating the evolution of multigene families. Genetics (1984) 1.28

Evolution by gene duplication revisited: differentiation of regulatory elements versus proteins. Genetica (2003) 0.99

The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis. Plant J (2006) 0.98

Studies on mitotic gene conversion in Ustilago. Genet Res (1966) 0.90

Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc Natl Acad Sci U S A (2006) 0.88

On the role of RNA in gene amplification. Acta Endocrinol Suppl (Copenh) (1972) 0.81

Gene conversions may obscure actin gene family relationships. J Mol Evol (2000) 0.79

Articles by these authors

The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature (2003) 10.65

The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54

Synteny and collinearity in plant genomes. Science (2008) 5.26

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

Polyploidy and angiosperm diversification. Am J Bot (2009) 4.41

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00

Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet (2007) 3.66

Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet (2008) 3.45

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

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics (2004) 2.84

A primitive Y chromosome in papaya marks incipient sex chromosome evolution. Nature (2004) 2.81

Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol (2003) 2.64

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res (2004) 2.56

A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics (2003) 2.40

A global assembly of cotton ESTs. Genome Res (2006) 2.18

Toward sequencing cotton (Gossypium) genomes. Plant Physiol (2007) 2.16

Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol (2002) 2.13

Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A (2005) 2.01

Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell (2009) 2.01

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94

Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res (2002) 1.94

Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet (2005) 1.93

Structure and evolution of cereal genomes. Curr Opin Genet Dev (2003) 1.91

PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res (2012) 1.90

Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A (2006) 1.87

Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics (2007) 1.84

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet (2006) 1.84

A genome triplication associated with early diversification of the core eudicots. Genome Biol (2012) 1.80

The repetitive landscape of the chicken genome. Genome Res (2004) 1.72

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Res (2009) 1.69

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol (2013) 1.59

Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics (2004) 1.58

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56

SNP discovery and development of a high-density genotyping array for sunflower. PLoS One (2012) 1.54

Insights from the comparison of plant genome sequences. Annu Rev Plant Biol (2010) 1.47

A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant J (2005) 1.45

Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet (2011) 1.45

A distributed feedback silicon evanescent laser. Opt Express (2008) 1.42

Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun (2013) 1.38

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res (2009) 1.35

Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol Genet Genomics (2007) 1.35

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proc Natl Acad Sci U S A (2012) 1.35

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics (2010) 1.32

A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics (2010) 1.32

An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics (2014) 1.32

High-density linkage mapping revealed suppression of recombination at the sex determination locus in papaya. Genetics (2004) 1.31

Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor. Genetics (2005) 1.30

Incongruent patterns of local and global genome size evolution in cotton. Genome Res (2004) 1.30

Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor Appl Genet (2005) 1.29

Low X/Y divergence in four pairs of papaya sex-linked genes. Plant J (2007) 1.28

Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol (2009) 1.27

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol (2013) 1.26

Genome and gene duplications and gene expression divergence: a view from plants. Ann N Y Acad Sci (2012) 1.25

A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics (2004) 1.23

Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell (2011) 1.23

Domestication and plant genomes. Curr Opin Plant Biol (2009) 1.22

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database (Oxford) (2013) 1.21

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

Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol Biol Evol (2009) 1.18

Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics (2006) 1.18

Sex chromosomes in flowering plants. Am J Bot (2007) 1.17