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Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
Abstract
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 â¼200,000 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.
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
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Lai, J., Li, R., Xu, X., Jin, W., Xu, M., Zhao, H., Xiang, Z., Song, W., Ying, K., Zhang, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.684 · Cited by 470
SNP discovery via 454 transcriptome sequencing
Barbazuk, W. B., Emrich, S. J., Chen, H. D., Li, L., & Schnable, P. S. (2007) · The Plant Journal · doi:10.1111/j.1365-313x.2007.03193.x · Cited by 405
Self-citationSequence and Comparative Analysis of the Maize NB Mitochondrial Genome
Clifton, S. W., Minx, P., Fauron, C. M.-R., Gibson, M., Allen, J. O., Sun, H., Thompson, M., Barbazuk, W. B., Kanuganti, S., Tayloe, C., et al. (2004) · Plant Physiology · doi:10.1104/pp.104.044602 · Cited by 353
Self-citationTrick, M., Long, Y., Meng, J., & Bancroft, I. (2009) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2008.00396.x · Cited by 338
Metadata
- Authors
- Whitelaw, C. A., Barbazuk, W. B., Pertea, G., Chan, A. P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J. L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M. A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy, R., Fraser, C. M., & Quackenbush, J.
- Venue
- Science
- Published
- 2003-12-19
- Volume
- 302
- Issue
- 5653
- Pages
- 2118-2120
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2162252960
- Cited by
- 208
- References
- 1
- FWCI
- 30.59
- Type
- journal article
- Language
- en
- Open access
- closed
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- The paper
- Whitelaw, C. A., Barbazuk, W. B., Pertea, G., Chan, A. P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J. L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M. A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., . . . Quackenbush, J. (2003). Enrichment of Gene-Coding Sequences in Maize by Genome Filtration. Science. https://doi.org/10.1126/science.1090047
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