编者按：今天出版的Science报道了玉米基因组被测序完毕，此次玉米基因组测序由美国冷泉港实验室完成，采用的方法与以往有些区别，是Genome Filtration方法，可以值得参考。同期Science还发表了一篇关于基因组中基因分析，认为玉米中含有大量基因，出乎意料之外。当然，Science也预测明年将有大量特种基因组被测序，但我们也应注意到大量测序结果面对我们，我们该如何进行分析，生物信息学分析相对滞后，导致大量数据被堆积。
Maize Genome Sequencing by Methylation Filtration
Science, Volume 302, Number 5653, Issue of 19 Dec 2003, pp. 2118-2120.
Lance E. Palmer,* Pablo D. Rabinowicz,* Andrew L. O'Shaughnessy, Vivekanand S. Balija, Lidia U. Nascimento, Sujit Dike, Melissa de la Bastide, Robert A. Martienssen, W. Richard McCombie
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.
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
Abstract of this Article
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Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
Science, Volume 302, Number 5653, Issue of 19 Dec 2003, pp. 2118-2120.
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.
Abstract of this Article
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