Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery.

PubWeight™: 1.94‹?› | Rank: Top 3%

🔗 View Article (PMC 186575)

Published in Genome Res on May 01, 2002

Authors

Daniel G Peterson1, Stefan R Schulze, Erica B Sciara, Scott A Lee, John E Bowers, Alexander Nagel, Ning Jiang, Deanne C Tibbitts, Susan R Wessler, Andrew H Paterson

Author Affiliations

1: Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602, USA. dgp@arches.uga.edu

Articles citing this

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics (2004) 3.37

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev (2008) 3.35

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

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol (2009) 2.17

Sorghum genome sequencing by methylation filtration. PLoS Biol (2005) 2.02

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

A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics (2004) 1.94

Comparative analyses of potato expressed sequence tag libraries. Plant Physiol (2003) 1.84

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci U S A (2004) 1.75

Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics (2004) 1.75

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

Locating sequence on FPC maps and selecting a minimal tiling path. Genome Res (2003) 1.67

The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics (2005) 1.63

Evolution of genome size and complexity in Pinus. PLoS One (2009) 1.52

Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46

Extension of Lander-Waterman theory for sequencing filtered DNA libraries. BMC Bioinformatics (2005) 1.31

Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol (2004) 1.27

Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res (2007) 1.19

Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine. PLoS One (2011) 1.10

FISH mapping and molecular organization of the major repetitive sequences of tomato. Chromosome Res (2008) 1.09

Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics (2005) 1.06

An improved method to identify BAC clones using pooled overgos. Nucleic Acids Res (2006) 1.03

Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosome Res (2007) 1.01

Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol (2005) 0.98

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution. Heredity (Edinb) (2013) 0.98

Genomics of sorghum. Int J Plant Genomics (2008) 0.96

Dental caries pathogenicity: a genomic and metagenomic perspective. Int Dent J (2011) 0.93

Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One (2013) 0.93

Evolutionary dynamics of heterochromatin in the genome of Dichotomius beetles based on chromosomal analysis. Genetica (2011) 0.91

Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res (2007) 0.90

NOR activity and repeat sequences of the paternal sex ratio chromosome of the parasitoid wasp Trichogramma kaykai. Chromosoma (2005) 0.90

Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering. Biomed Res Int (2014) 0.89

Toward sequencing the sorghum genome. A U.S. National Science Foundation-sponsored workshop report. Plant Physiol (2005) 0.87

A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization. BMC Genomics (2009) 0.87

Characterization of the genome of bald cypress. BMC Genomics (2011) 0.86

Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus. BMC Genomics (2010) 0.86

Environmental heterogeneity and phenotypic divergence: can heritable epigenetic variation aid speciation? Genet Res Int (2012) 0.84

Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing. Plant Physiol (2002) 0.83

Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics. PLoS One (2016) 0.83

Isolation and characterization of genomic and transcribed retrotransposon sequences from sorghum. Mol Genet Genomics (2004) 0.81

Maize DNA-sequencing strategies and genome organization. Genome Biol (2004) 0.81

Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L. Mol Genet Genomics (2014) 0.80

Synergy of two reference genomes for the grass family. Plant Physiol (2009) 0.80

Epigenomics and bolting tolerance in sugar beet genotypes. J Exp Bot (2015) 0.79

Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics (2014) 0.79

Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biol (2010) 0.78

A functional approach to transcriptome profiling: linking gene expression patterns to metabolites that matter. Mar Biotechnol (NY) (2007) 0.77

Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome. Mob DNA (2016) 0.75

Primitive Genepools of Asian Pears and Their Complex Hybrid Origins Inferred from Fluorescent Sequence-Specific Amplification Polymorphism (SSAP) Markers Based on LTR Retrotransposons. PLoS One (2016) 0.75

Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.). Int J Mol Sci (2016) 0.75

Satellite DNA: An Evolving Topic. Genes (Basel) (2017) 0.75

Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum. Mol Genet Genomics (2016) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

The complete genome sequence of Escherichia coli K-12. Science (1997) 84.27

Serial analysis of gene expression. Science (1995) 60.15

Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science (1968) 30.37

PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res (1997) 13.48

Role for DNA methylation in genomic imprinting. Nature (1993) 12.65

Analysis of repeating DNA sequences by reassociation. Methods Enzymol (1974) 10.63

High throughput fingerprint analysis of large-insert clones. Genome Res (1997) 6.91

Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet (1999) 3.95

Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci U S A (1994) 3.73

Denaturing high-performance liquid chromatography: A review. Hum Mutat (2001) 3.58

An 'equalized cDNA library' by the reassociation of short double-stranded cDNAs. Nucleic Acids Res (1990) 3.47

A program for least squares analysis of reassociation and hybridization data. Nucleic Acids Res (1977) 3.13

Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet (1999) 2.87

Comparative aspects of DNA organization in Metazoa. Chromosoma (1975) 2.82

Grass genomes. Proc Natl Acad Sci U S A (1998) 2.33

Molecular mapping of rice chromosomes. Theor Appl Genet (1988) 2.33

A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc Natl Acad Sci U S A (1996) 2.32

The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc Natl Acad Sci U S A (1995) 2.29

Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet Test (2000) 2.01

Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics (1998) 1.80

A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J (1998) 1.77

Nonmethylated transposable elements and methylated genes in a chordate genome. Science (1999) 1.75

DNA methylation: a molecular lock. Curr Biol (1997) 1.73

DNA sequence organization in the soybean plant. Biochem Genet (1978) 1.72

A detailed RFLP map of Sorghum bicolor x S. propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes or chromosomal segments. Theor Appl Genet (1994) 1.71

Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell (2000) 1.70

Athila, a new retroelement from Arabidopsis thaliana. Plant Mol Biol (1995) 1.40

Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation. Plant Physiol (2001) 1.34

Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor (Poaceae). Am J Bot (2000) 1.23

Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics (1993) 1.18

Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proc Natl Acad Sci U S A (1999) 1.13

DNA sequence organization in the genomes of five marine invertebrates. Chromosoma (1975) 1.07

Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting. Genomics (1999) 0.99

Maternal-specific methylation of the human IGF2R gene is not accompanied by allele-specific transcription. Genomics (1996) 0.99

Comparative physical mapping of the 18S-5.8S-26S rDNA in three sorghum species. Genome (2000) 0.97

Lack of correlation between DNA methylation and transcriptional inactivation: the chicken lysozyme gene. Proc Natl Acad Sci U S A (1991) 0.96

Minilibraries constructed from cDNA generated by arbitrarily primed RT-PCR: an alternative to normalized libraries for the generation of ESTs from nanogram quantities of mRNA. Gene (1997) 0.96

The rice Rim2 transcript accumulates in response to Magnaporthe grisea and its predicted protein product shares similarity with TNP2-like proteins encoded by CACTA transposons. Mol Gen Genet (2000) 0.93

Characterization of the interaction between the restriction endonuclease McrBC from E. coli and its cofactor GTP. J Mol Biol (1997) 0.92

Active beta-globin gene transcription occurs in methylated, DNase I-resistant chromatin of nonerythroid chicken cells. Mol Cell Biol (1990) 0.90

DNA hybridization analyses of a Gossypium allotetmploid and two closely related diploid species. Theor Appl Genet (1989) 0.89

Rapid purification of fluorescent dye-labeled products in a 96-well format for high-throughput automated DNA sequencing. Nucleic Acids Res (1995) 0.89

Sequence repetition in the DNA of Nassaria (Iiyanassa) obsoleta. Dev Biol (1971) 0.79

News & notes. Efficient library construction with a TA vector and its application to cloning of the phytoene synthase gene from the cyanobacterium Spirulina platensis. Curr Microbiol (1998) 0.79

[Intragenome distribution of 5-methyl cytosine and reassociation kinetics of cow blood lymphocyte DNA under normal conditions and in chronic lymphoid leukemia]. Biokhimiia (1979) 0.78

From cot curves to genomics. How gene cloning established new concepts in plant biology. Plant Physiol (2001) 0.78

Articles by these authors

The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73

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

Plant transposable elements: where genetics meets genomics. Nat Rev Genet (2002) 5.96

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

Pack-MULE transposable elements mediate gene evolution in plants. Nature (2004) 5.13

High-throughput sequencing of the zebrafish antibody repertoire. Science (2009) 4.46

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

An active DNA transposon family in rice. Nature (2003) 3.24

The kinetics of two-dimensional TCR and pMHC interactions determine T-cell responsiveness. Nature (2010) 3.04

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

Prognostic value of a microRNA signature in nasopharyngeal carcinoma: a microRNA expression analysis. Lancet Oncol (2012) 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

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76

A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science (2008) 2.66

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

Evolutionary conservation of the clk-1-dependent mechanism of longevity: loss of mclk1 increases cellular fitness and lifespan in mice. Genes Dev (2005) 2.39

Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature (2009) 2.24

Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science (2009) 2.20

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

sSgo1, a major splice variant of Sgo1, functions in centriole cohesion where it is regulated by Plk1. Dev Cell (2008) 2.12

Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci U S A (2006) 2.07

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

[Dynamic simulation of nitrogen application level effects on rice yield and optimization analysis of fertilizer supply in paddy field]. Ying Yong Sheng Tai Xue Bao (2003) 1.93

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

PIF- and Pong-like transposable elements: distribution, evolution and relationship with Tourist-like miniature inverted-repeat transposable elements. Genetics (2004) 1.79

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci U S A (2004) 1.75

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

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A (2011) 1.65

Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2007) 1.63

Transposing from the laboratory to the classroom to generate authentic research experiences for undergraduates. Genetics (2012) 1.63

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res (2010) 1.62

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

Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs). Curr Opin Plant Biol (2004) 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

Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs). Genetics (2003) 1.56

Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell (2008) 1.55

Optimal schedule of bacillus calmette-guerin for non-muscle-invasive bladder cancer: a meta-analysis of comparative studies. BMC Cancer (2013) 1.54

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

The extraction of neural information from the surface EMG for the control of upper-limb prostheses: emerging avenues and challenges. IEEE Trans Neural Syst Rehabil Eng (2014) 1.52

Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics (2002) 1.51

Extremely rapid extraction of DNA from bacteria and yeasts. Biotechnol Lett (2006) 1.49

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol (2013) 1.48

Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci U S A (2001) 1.46

Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 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

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

Simultaneous and proportional force estimation for multifunction myoelectric prostheses using mirrored bilateral training. IEEE Trans Biomed Eng (2010) 1.44

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

DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs. Nucleic Acids Res (2005) 1.40

Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development. Plant Cell (2010) 1.38

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

Seroepidemiology of human Toxoplasma gondii infection in China. BMC Infect Dis (2010) 1.37

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