Maize genome sequencing by methylation filtration.
Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.
Palmer
Lance E
LE
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
Rabinowicz
Pablo D
PD
O'Shaughnessy
Andrew L
AL
Balija
Vivekanand S
VS
Nascimento
Lidia U
LU
Dike
Sujit
S
de la Bastide
Melissa
M
Martienssen
Robert A
RA
McCombie
W Richard
WR
D000465:Algorithms; D022202:Chromosomes, Artificial, Bacterial; D003001:Cloning, Molecular; D019295:Computational Biology; D017124:Conserved Sequence; D020451:Contig Mapping; D018899:CpG Islands; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018742:DNA, Chloroplast / Q000235:genetics; D018076:DNA, Complementary; D004272:DNA, Mitochondrial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D004926:Escherichia coli / Q000235:genetics; D005091:Exons; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D015698:Genomic Library; D012275:Oryza / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements; D018742:DNA, Chloroplast; D018076:DNA, Complementary; D004272:DNA, Mitochondrial; D018744:DNA, Plant; D018626:Retroelements