Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
C. A. Whitelaw,1
W. B. Barbazuk,2*
G. Pertea,1
A. P. Chan,1
F. Cheung,1
Y. Lee,1
L. Zheng,1
S. van Heeringen,1
S. Karamycheva,1
J. L. Bennetzen,3
P. SanMiguel,4
N. Lakey,5
J. Bedell,5
Y. Yuan,3
M. A. Budiman,5
A. Resnick,1
S. Van Aken,1
T. Utterback,6
S. Riedmuller,6
M. Williams,6
T. Feldblyum,6
K. Schubert,2
R. Beachy,2
C. M. Fraser,1
J. Quackenbush1*
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 
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.
1 The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.
2 Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA.
3 Department of Genetics, University of Georgia, Athens, GA 30602, USA.
4 Purdue Genomics Core Facility, Purdue University, West Lafayette, IN 47907, USA.
5 Orion Genomics, 4041 Forest Park Avenue, St. Louis, MO 63108, USA.
6 J. Craig Venter Science Foundation Joint Technology Center (JTC), 5 Research Place, Rockville, MD 20850, USA.
* To whom correspondence should be addressed. E-mail: BBarbazuk{at}danforthcenter.org (W.B.B.); Johnq{at}tigr.org(JQ)
