編者按：今天出版的Science報(bào)道了玉米基因組被測(cè)序完畢，此次玉米基因組測(cè)序由美國(guó)冷泉港實(shí)驗(yàn)室完成，采用的方法與以往有些區(qū)別，是Genome Filtration方法，可以值得參考,。同期Science還發(fā)表了一篇關(guān)于基因組中基因分析，認(rèn)為玉米中含有大量基因,，出乎意料之外,。當(dāng)然，Science也預(yù)測(cè)明年將有大量特種基因組被測(cè)序,，但我們也應(yīng)注意到大量測(cè)序結(jié)果面對(duì)我們,，我們?cè)撊绾芜M(jìn)行分析，生物信息學(xué)分析相對(duì)滯后,，導(dǎo)致大量數(shù)據(jù)被堆積,。
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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