Published in Genetics on September 09, 2008
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell (2010) 2.45
Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol (2011) 1.54
Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics (2011) 1.22
Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol (2012) 1.19
A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. Plant Physiol (2011) 1.10
First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One (2011) 1.09
Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics (2012) 1.06
Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent. PLoS One (2013) 1.03
Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics (2010) 1.01
Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis. Evol Appl (2011) 1.01
Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources. BMC Genomics (2010) 0.94
Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats. Mol Genet Genomics (2010) 0.91
Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics (2009) 0.89
Genome size variation in diploid and tetraploid wild wheats. AoB Plants (2010) 0.88
Methylation, transcription, and rearrangements of transposable elements in synthetic allopolyploids. Int J Plant Genomics (2011) 0.87
Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biol (2014) 0.86
Differential dynamics of transposable elements during long-term diploidization of Nicotiana section Repandae (Solanaceae) allopolyploid genomes. PLoS One (2012) 0.86
Fat element-a new marker for chromosome and genome analysis in the Triticeae. Chromosome Res (2010) 0.85
How does selfing affect the dynamics of selfish transposable elements? Mob DNA (2012) 0.84
Gypsy, RTE and Mariner transposable elements populate Eyprepocnemis plorans genome. Genetica (2012) 0.83
The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats. BMC Plant Biol (2011) 0.82
Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii. Front Plant Sci (2016) 0.81
A wheat ABC transporter contributes to both grain formation and mycotoxin tolerance. J Exp Bot (2015) 0.81
A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC Plant Biol (2010) 0.81
MnTEdb, a collective resource for mulberry transposable elements. Database (Oxford) (2015) 0.78
The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae. PLoS One (2015) 0.77
Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics (2015) 0.77
Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization. Mol Genet Genomics (2010) 0.77
Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization. Plant Cell Rep (2013) 0.77
Quantification and organization of WIS2-1A and BARE-1 retrotransposons in different genomes of Triticum and Aegilops species. Mol Genet Genomics (2009) 0.76
The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements. BMC Genomics (2016) 0.75
Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3 (Bethesda) (2016) 0.75
Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei. PLoS One (2016) 0.75
Intragenomic distribution of RTE retroelements suggests intrachromosomal movement. Chromosome Res (2015) 0.75
Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae. BMC Evol Biol (2017) 0.75
Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage. Funct Integr Genomics (2011) 0.75
The characteristics and functions of a miniature inverted-repeat transposable element TaMITE81 in the 5' UTR of TaCHS7BL from Triticum aestivum. Mol Genet Genomics (2016) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Basic local alignment search tool. J Mol Biol (1990) 659.07
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol (2000) 128.08
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol (1980) 113.75
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform (2004) 72.40
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04
Nested retrotransposons in the intergenic regions of the maize genome. Science (1996) 12.95
A unified classification system for eukaryotic transposable elements. Nat Rev Genet (2007) 11.03
Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci (1976) 10.59
The paleontology of intergene retrotransposons of maize. Nat Genet (1998) 8.55
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66
Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A (2003) 6.34
Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell (2000) 6.16
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A (2004) 5.35
Polyploidy and genome evolution in plants. Curr Opin Plant Biol (2005) 5.30
Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res (2002) 5.15
Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet (2002) 4.67
Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res (2004) 4.43
Evidence for DNA loss as a determinant of genome size. Science (2000) 4.25
Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res (2001) 4.17
Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature (1993) 3.89
Do Plants Have a One-Way Ticket to Genomic Obesity? Plant Cell (1997) 3.86
Mechanisms of recent genome size variation in flowering plants. Ann Bot (2005) 3.86
Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci U S A (2002) 3.51
Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum. Plant Cell (1999) 3.30
Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell (2008) 3.25
Transposable element contributions to plant gene and genome evolution. Plant Mol Biol (2000) 3.24
Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res (2006) 3.02
Transposable elements and the evolution of genome size in eukaryotes. Genetica (2002) 3.00
Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature (2006) 2.97
Comparative sequence analysis of plant nuclear genomes:m microcolinearity and its many exceptions. Plant Cell (2000) 2.82
Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res (2006) 2.69
Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell (2003) 2.58
Structure and architecture of the maize genome. Plant Physiol (2005) 2.52
Mutational equilibrium model of genome size evolution. Theor Popul Biol (2002) 2.42
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40
Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m). Funct Integr Genomics (2002) 2.23
The evolution of polyploid wheats: identification of the A genome donor species. Genome (1993) 2.15
Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica (2002) 2.09
Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci U S A (2006) 2.05
DNA loss and evolution of genome size in Drosophila. Genetica (2002) 2.00
Allopolyploidy--a shaping force in the evolution of wheat genomes. Cytogenet Genome Res (2005) 1.99
Sequence composition, organization, and evolution of the core Triticeae genome. Plant J (2004) 1.79
Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res (2007) 1.78
Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat. Mol Biol Evol (2006) 1.78
Feast and famine in plant genomes. Genetica (2002) 1.78
Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics (2002) 1.76
Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J (2006) 1.70
Plant genome size research: a field in focus. Ann Bot (2005) 1.55
Acc homoeoloci and the evolution of wheat genomes. Proc Natl Acad Sci U S A (2008) 1.53
Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc Natl Acad Sci U S A (2005) 1.50
Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol (2004) 1.50
Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci U S A (2005) 1.48
Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J (1998) 1.46
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
CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol (2003) 1.43
The rice genome. Opening the door to comparative plant biology. Science (2002) 1.33
Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J (2004) 1.31
Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics (2006) 1.31
A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am2 in Triticum monococcum. Mol Genet Genomics (2005) 1.30
Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol (2007) 1.25
A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A (2007) 1.23
TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol (2007) 1.23
Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: the B genome of wheat. Genome (1999) 1.22
Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics (2005) 1.21
Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res (2005) 1.15
Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics (2004) 1.15
Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol (2006) 1.11
Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes. Mol Genet Genomics (2002) 1.06
Flow cytogenetics and plant genome mapping. Chromosome Res (2004) 1.01
Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res (2007) 1.01
Variation in nuclear DNA content in the genus vicia. Genetics (1971) 1.00
Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theor Appl Genet (1990) 0.94
A phylogenetic analysis of indel dynamics in the cotton genus. Mol Biol Evol (2008) 0.92
[Complete rice genome sequence information: the key for elucidation of Rosetta stones of other cereal genome]. Tanpakushitsu Kakusan Koso (2005) 0.76
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
A unified classification system for eukaryotic transposable elements. Nat Rev Genet (2007) 11.03
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J (2014) 4.02
Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One (2008) 3.94
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res (2006) 3.53
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52
The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science (2006) 3.50
Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science (2007) 3.42
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40
A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science (2004) 3.23
A physical map of the 1-gigabase bread wheat chromosome 3B. Science (2008) 3.21
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol (2009) 3.10
Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature (2010) 2.61
Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell (2010) 2.45
The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol (2008) 2.43
Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila. Nat Biotechnol (2006) 2.41
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40
Quantitative resistance increases the durability of qualitative resistance to Leptosphaeria maculans in Brassica napus. New Phytol (2009) 2.23
An extreme case of plant-insect codiversification: figs and fig-pollinating wasps. Syst Biol (2012) 2.20
The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. PLoS Genet (2008) 2.10
Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet (2007) 2.08
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun (2011) 2.03
The DNA sequence and analysis of human chromosome 14. Nature (2003) 2.02
A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94
Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature (2013) 1.76
The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics (2009) 1.71
Molecular characterization and mapping of ALMT1, the aluminium-tolerance gene of bread wheat (Triticum aestivum L.). Genome (2005) 1.68
Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C R Biol (2011) 1.64
Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet (2009) 1.61
A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet (2007) 1.59
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol (2009) 1.48
Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat. BMC Plant Biol (2010) 1.46
RNF213, a new nuclear marker for acanthomorph phylogeny. Mol Phylogenet Evol (2008) 1.45
Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. C R Biol (2008) 1.40
The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes. C R Biol (2006) 1.37
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biol (2011) 1.36
Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol (2008) 1.34
Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J (2004) 1.31
Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics (2006) 1.31
Homeologous recombination plays a major role in chromosome rearrangements that occur during meiosis of Brassica napus haploids. Genetics (2006) 1.31
Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets. BMC Microbiol (2009) 1.30
A randomised control trial of a self-management program for people with a chronic illness from Vietnamese, Chinese, Italian and Greek backgrounds. Patient Educ Couns (2006) 1.29
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One (2010) 1.28
New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics (2008) 1.26
Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol (2007) 1.24
Transcriptome of Aphanomyces euteiches: new oomycete putative pathogenicity factors and metabolic pathways. PLoS One (2008) 1.24
Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics (2005) 1.21
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
High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. New Phytol (2010) 1.17
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics (2010) 1.17
Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome (2006) 1.15
Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels. Genome Res (2005) 1.15
Large intraspecific haplotype variability at the Rph7 locus results from rapid and recent divergence in the barley genome. Plant Cell (2005) 1.14
Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol (2012) 1.10
Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids. Plant Cell (2009) 1.10
Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus. Ann Bot (2011) 1.10
Evolution of the mitochondrial genome in mammals living at high altitude: new insights from a study of the tribe Caprini (Bovidae, Antilopinae). J Mol Evol (2009) 1.09
Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol (2010) 1.09
Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size. Plant Biotechnol J (2004) 1.08
Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog (2010) 1.08
Secondary sympatry caused by range expansion informs on the dynamics of microendemism in a biodiversity hotspot. PLoS One (2012) 1.08
Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes. Syst Biol (2009) 1.07
Integrative biology of Idas iwaotakii (Habe, 1958), a 'model species' associated with sunken organic substrates. PLoS One (2013) 1.07
Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes?--Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity. BMC Evol Biol (2007) 1.06
Genome structure affects the rate of autosyndesis and allosyndesis in AABC, BBAC and CCAB Brassica interspecific hybrids. Chromosome Res (2010) 1.06
Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol (2010) 1.05