Enrichment of Gene-Coding Sequences in Maize by Genome Filtration

• DOI: 10.1126/science.1090047
• Publication Date: 2003-12-18T22:57:53Z
• Authors: C. A. Whitelaw; W. B. Barbazuk; G. Pertea; A. P. Chan; F. Cheung; Y. Lee; L. Zheng; S. van Heeringen; S. Karamycheva; J. L. Bennetzen; P. SanMiguel; N. Lakey; J. Bedell; Y. Yuan; M. A. Budiman; A. Resnick; S. Van Aken; T. Utterback; S. Riedmuller; M. Williams; T. Feldblyum; K. Schubert; R. Beachy; C. M. Fraser; J. Quackenbush
• Keywords: Expressed Sequence Tags; 0301 basic medicine; 2. Zero hunger; DNA, Plant; Retroelements; Transcription, Genetic; Molecular Sequence Data; Gene Dosage; Computational Biology; Sequence Analysis, DNA; DNA Methylation; Genes, Plant; Zea mays; Chromosomes, Plant; Contig Mapping; 03 medical and health sciences; Cloning, Molecular; Databases, Nucleic Acid; Sequence Alignment; Genome, Plant; Gene Library; Repetitive Sequences, Nucleic Acid

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 C 0 t 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.