Sorghum genome sequencing by methylation filtration.

PubWeight™: 2.02‹?› | Rank: Top 2%

🔗 View Article (PMC 539327)

Published in PLoS Biol on January 04, 2005

Authors

Joseph A Bedell1, Muhammad A Budiman, Andrew Nunberg, Robert W Citek, Dan Robbins, Joshua Jones, Elizabeth Flick, Theresa Rholfing, Jason Fries, Kourtney Bradford, Jennifer McMenamy, Michael Smith, Heather Holeman, Bruce A Roe, Graham Wiley, Ian F Korf, Pablo D Rabinowicz, Nathan Lakey, W Richard McCombie, Jeffrey A Jeddeloh, Robert A Martienssen

Author Affiliations

1: Bioinformatics, Orion Genomics Saint Louis, Missouri United States of America. jbedell@oriongenomics.com

Articles citing this

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69

Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell (2005) 3.18

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature (2013) 2.58

Structure and architecture of the maize genome. Plant Physiol (2005) 2.52

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

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc Natl Acad Sci U S A (2005) 2.27

Comparative plant genomics resources at PlantGDB. Plant Physiol (2005) 2.19

High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell (2006) 2.08

PMRD: plant microRNA database. Nucleic Acids Res (2009) 1.94

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res (2013) 1.78

Differential methylation of genes and repeats in land plants. Genome Res (2005) 1.77

Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol (2009) 1.49

The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants. BMC Genomics (2006) 1.36

Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics (2008) 1.36

TOBFAC: the database of tobacco transcription factors. BMC Bioinformatics (2008) 1.35

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

Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol (2007) 1.19

Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae. Plant Physiol (2008) 1.16

Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. Ann Bot (2011) 1.13

The TIGR Maize Database. Nucleic Acids Res (2006) 1.12

Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep (2006) 1.11

Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol (2005) 1.09

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

Roles of microRNA in plant defense and virus offense interaction. Plant Cell Rep (2008) 1.05

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

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics (2007) 1.01

Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome. BMC Genomics (2013) 1.00

Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench). DNA Res (2009) 0.99

Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One (2011) 0.98

Expansion mechanisms and functional divergence of the glutathione s-transferase family in sorghum and other higher plants. DNA Res (2010) 0.98

Poaceae genomes: going from unattainable to becoming a model clade for comparative plant genomics. Plant Physiol (2008) 0.97

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

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

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

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. Plant J (2014) 0.87

Genetic variation and expression diversity between grain and sweet sorghum lines. BMC Genomics (2013) 0.86

Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation. BMC Genomics (2007) 0.80

Global Gene Expression of Kosteletzkya virginica Seedlings Responding to Salt Stress. PLoS One (2015) 0.80

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

Analyses of hypomethylated oil palm gene space. PLoS One (2014) 0.79

An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago. BMC Genomics (2013) 0.78

The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii. BMC Genomics (2008) 0.75

Articles cited by this

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

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

The sequence of the human genome. Science (2001) 101.55

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (2000) 70.33

Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51

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

Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics (1988) 27.63

Identification of protein coding regions by database similarity search. Nat Genet (1993) 21.58

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science (2002) 21.26

MicroRNAs in plants. Genes Dev (2002) 20.12

Prediction of plant microRNA targets. Cell (2002) 19.20

Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell (2004) 12.97

Nested retrotransposons in the intergenic regions of the maize genome. Science (1996) 12.95

Gene finding in novel genomes. BMC Bioinformatics (2004) 8.64

The paleontology of intergene retrotransposons of maize. Nat Genet (1998) 8.55

Sequence specificity of methylation in higher plant DNA. Nature (1981) 7.58

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

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res (2002) 6.65

Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet (2002) 5.98

Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol (2003) 5.07

Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res (2001) 4.17

OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J (2003) 4.09

MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics (2000) 3.66

Enrichment of gene-coding sequences in maize by genome filtration. Science (2003) 3.41

Maize genome sequencing by methylation filtration. Science (2003) 3.31

DNA methylation and mutation. Mutat Res (1993) 3.23

TRIPTYCHON and CAPRICE mediate lateral inhibition during trichome and root hair patterning in Arabidopsis. EMBO J (2002) 2.92

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

Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci (2001) 2.74

Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc Natl Acad Sci U S A (2002) 2.69

Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci U S A (1994) 2.62

Gene regulation: ancient microRNA target sequences in plants. Nature (2004) 2.61

Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome (1994) 2.56

Role of a positive regulator of root hair development, CAPRICE, in Arabidopsis root epidermal cell differentiation. Development (2002) 2.22

Eukaryotic DNA methylation as an evolutionary device. Bioessays (1999) 2.20

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

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

Maintenance of heterochromatin by RNA interference of tandem repeats. Nat Genet (2003) 1.86

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res (2003) 1.70

Mapping QTLs associated with drought resistance in sorghum (Sorghum bicolor L. Moench). Plant Mol Biol (2002) 1.61

The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol (2003) 1.42

Transposons, DNA methylation and gene control. Trends Genet (1998) 1.38

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

The distribution of 5-methylcytosine in the nuclear genome of plants. Nucleic Acids Res (1992) 1.14

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

Sequencing the maize genome. Curr Opin Plant Biol (2004) 1.12

Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement. Plant J (2003) 1.10

mCCG methylation in angiosperms. Plant J (1996) 1.06

Serial BLAST searching. Bioinformatics (2003) 1.05

DNA sequence arrangement and preliminary evidence on its evolution. Fed Proc (1976) 1.03

iMap: a database-driven utility to integrate and access the genetic and physical maps of maize. Bioinformatics (2003) 0.91

Variability in CpNpG methylation in higher plant genomes. Gene (1997) 0.87

The evolution of grass genome organisation and function. Symp Soc Exp Biol (1998) 0.85

Articles by these authors

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

A core gut microbiome in obese and lean twins. Nature (2008) 52.30

Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97

Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13

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

Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science (2002) 17.04

Prepublication data sharing. Nature (2009) 12.24

Role of transposable elements in heterochromatin and epigenetic control. Nature (2004) 10.51

Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31

De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69

Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62

Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci U S A (2002) 8.25

Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet (2005) 8.23

Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49

The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol (2003) 6.90

Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell (2009) 6.39

A resource for large-scale RNA-interference-based screens in mammals. Nature (2004) 6.36

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell (2009) 6.05

Noncoding RNAs and gene silencing. Cell (2007) 5.99

Vernalization requires epigenetic silencing of FLC by histone methylation. Nature (2004) 5.77

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods (2008) 5.70

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell (2008) 5.47

A physical map of the mouse genome. Nature (2002) 4.97

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

Understanding mechanisms of novel gene expression in polyploids. Trends Genet (2003) 4.90

Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science (2002) 4.49

The zinc finger transcription factor Th-POK regulates CD4 versus CD8 T-cell lineage commitment. Nature (2005) 4.39

Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27

Whole exome capture in solution with 3 Gbp of data. Genome Biol (2010) 4.23

Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol (2011) 4.18

Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011) 4.16

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11

RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science (2005) 3.94

Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature (2004) 3.92

Arabidopsis MET1 cytosine methyltransferase mutants. Genetics (2003) 3.90

Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet (2009) 3.88

The developmental role of microRNA in plants. Curr Opin Plant Biol (2005) 3.81

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol (2011) 3.51

The genome of Theobroma cacao. Nat Genet (2010) 3.47

RNA interference is required for normal centromere function in fission yeast. Chromosome Res (2003) 3.46

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell (2011) 3.39

Maize genome sequencing by methylation filtration. Science (2003) 3.31

Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (2005) 3.21

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet (2013) 3.17

Three-month-olds, but not newborns, prefer own-race faces. Dev Sci (2005) 3.15

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

Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet (2007) 3.11

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res (2009) 3.08

An integrated physical and genetic map of the rice genome. Plant Cell (2002) 3.07

Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr Biol (2006) 3.04

Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods (2004) 3.01

Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol (2009) 2.91

Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science (2004) 2.88

Hermansky-Pudlak syndrome type 7 (HPS-7) results from mutant dysbindin, a member of the biogenesis of lysosome-related organelles complex 1 (BLOC-1). Nat Genet (2003) 2.78

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell (2011) 2.77

The TIGR Plant Transcript Assemblies database. Nucleic Acids Res (2006) 2.62

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61

Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol (2005) 2.60

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature (2013) 2.58

ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis. Development (2002) 2.55

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus. Nat Genet (2011) 2.54

Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature (2010) 2.53

Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A (2008) 2.53

Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol (2010) 2.52

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics (2008) 2.51

Argonaute slicing is required for heterochromatic silencing and spreading. Science (2006) 2.48

A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics (2004) 2.43

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

Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell (2012) 2.29

Assembling genomic DNA sequences with PHRAP. Curr Protoc Bioinformatics (2007) 2.29

Advising patients who seek complementary and alternative medical therapies for cancer. Ann Intern Med (2002) 2.29

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

Survey of archaeal diversity reveals an abundance of halophilic Archaea in a low-salt, sulfide- and sulfur-rich spring. Appl Environ Microbiol (2004) 2.14

Therapeutic applications of fenugreek. Altern Med Rev (2003) 2.12

Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics (2010) 2.01

Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics (2008) 2.01

Release and activity of matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 by alveolar macrophages from patients with chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol (2002) 2.00

Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol Cell Biol (2005) 1.98

Uneven chromosome contraction and expansion in the maize genome. Genome Res (2006) 1.96

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

Focal and generalized folliculitis following smallpox vaccination among vaccinia-naive recipients. JAMA (2003) 1.91

Novelty and uniqueness patterns of rare members of the soil biosphere. Appl Environ Microbiol (2008) 1.90

S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Mol Cell (2007) 1.84

Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet (2005) 1.83

Introns and splicing elements of five diverse fungi. Eukaryot Cell (2004) 1.83

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genet (2013) 1.81

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol (2011) 1.80

Pain, catastrophizing, and depression in the rheumatic diseases. Nat Rev Rheumatol (2011) 1.80

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature (2011) 1.79