Sequencing Genes and Gene Islands by Gene Enrichment
Access to the sequence of any gene in a genome greatly accelerates genetics research. Whole genome sequencing is a way to retrieve such information although, for large genomes such as that of maize, it represents a huge effort. Fortunately, a maize genome sequencing project is currently underway but, before this project started, the maize research community benefited from the development of gene enrichment methods that allow selectively cloning and sequencing genes. The application of these methods to maize generated comprehensive gene sequence collections that were extensively used by the community. Once the maize genome project is completed, combination of gene enrichment methods with next-generation sequencing technologies will greatly facilitate genome-wide comparative analysis of different maize inbred lines for functional, population, and evolutionary studies.
KeywordsBacterial Artificial Chromosome Bacterial Artificial Chromosome Clone Repetitive Element Maize Genome Gene Enrichment
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- Childs, K.L., Hamilton, J.P., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P.D., Town, C.D., Buell,C.R., and Chan, A.P. 2006 The TIGR Plant Transcript Assemblies database. Nucleic Acids Res. Google Scholar
- Gardiner, J.M., Buell, C.R., Elumalai, R., Galbraith, D.W., Henderson, D.A., Iniguez, A.L.,Kaeppler, S.M., Kim, J.J., Liu, J., Smith, A. et al. (2005) Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica 50: 425–435.Google Scholar
- Jeck, W.R., Reinhardt, J.A., Baltrus, D.A., Hickenbotham, M.T., Magrini, V., Mardis, E.R., Dangl,J.L., and Jones, C.D. (2007) Extending assembly of short DNA sequences to handle error.Bioinformatics.Google Scholar
- Kalyanaraman, A., Aluru, S., and Schnable, P.S. (2006) Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons. Comput Syst Bioinformatics Conf: 167–178.Google Scholar
- Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R., Antonescu, V., Chan, A.,Cheung, F., and Quackenbush, J. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33: D71–74.PubMedCrossRefGoogle Scholar
- Luo, M.C., Thomas, C., You, F.M., Hsiao, J., Ouyang, S., Buell, C.R., Malandro, M., McGuire,P.E., Anderson, O.D., and Dvorak, J. (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378–389.PubMedCrossRefGoogle Scholar
- Peterson, D.G., Schulze, S.R., Sciara, E.B., Lee, S.A., Bowers, J.E., Nagel, A., Jiang, N., Tibbitts,D.C., Wessler, S.R., and Paterson, A.H. (2002) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 12: 795–807.PubMedCrossRefGoogle Scholar
- Sutton, G., White, O., Adams, M., and Kerlavage, A.R. (1995) TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Tech. 1: 9–19.Google Scholar
- Wheeler D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M.,Dicuccio, M., Edgar, R., Federhen, S. et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. Google Scholar