Enrichment of gene-coding sequences in maize by genome filtration.
Approximately 80% of the maize genome comprises highly repetitive sequences interspersed with single-copy, gene-rich sequences, and standard genome sequencing strategies are not readily adaptable to this type of genome. Methodologies that enrich for genic sequences might more rapidly generate useful results from complex genomes. Equivalent numbers of clones from maize selected by techniques called methylation filtering and High C0t selection were sequenced to generate approximately 200,000 reads (approximately 132 megabases), which were assembled into contigs. Combination of the two techniques resulted in a sixfold reduction in the effective genome size and a fourfold increase in the gene identification rate in comparison to a nonenriched library.
Whitelaw
C A
CA
The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.
Barbazuk
W B
WB
Pertea
G
G
Chan
A P
AP
Cheung
F
F
Lee
Y
Y
Zheng
L
L
van Heeringen
S
S
Karamycheva
S
S
Bennetzen
J L
JL
SanMiguel
P
P
Lakey
N
N
Bedell
J
J
Yuan
Y
Y
Budiman
M A
MA
Resnick
A
A
Van Aken
S
S
Utterback
T
T
Riedmuller
S
S
Williams
M
M
Feldblyum
T
T
Schubert
K
K
Beachy
R
R
Fraser
C M
CM
Quackenbush
J
J
D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D019295:Computational Biology; D020451:Contig Mapping; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D018628:Gene Dosage; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*
D018744:DNA, Plant; D018626:Retroelements