The B73 maize genome: complexity, diversity, and dynamics

Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S. M., Belter, E., Du, F., Kim, K., Abbott, R. M., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S. M., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M. J., McMahan, L., Van Buren, P., Vaughn, M. W. (November 2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956). pp. 1112-5. ISSN 1095-9203 (Electronic)0036-8075 (Linking)

Abstract

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Item Type:	Paper
Uncontrolled Keywords:	Base Sequence Centromere genetics Chromosome Mapping Chromosomes Plant genetics Crops Agricultural genetics DNA Copy Number Variations DNA Methylation DNA Transposable Elements DNA Plant genetics Genes Plant Genetic Variation Genome Plant Inbreeding MicroRNAs genetics Molecular Sequence Data Ploidies RNA Plant genetics Recombination Genetic Retroelements Sequence Analysis DNA Zea mays genetics
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant > maize bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes organism description > plant
CSHL Authors:	Ambroise, Claude Faga, Ben P. Kramer, Melissa R. Kumari, Sunita Levy, Dan Liang, Chengzhi Martienssen, Robert A. McCombie, W. Richard McMahan, Linda Miller, Beth Muller, Stephanie Nascimento, Lidia Pasternak, Shiran Ren, Liya Spiegel, Lori Stein, Joshua C. Van Buren, Peter Vaughn, Matthew W. Ware, Doreen H. Wei, Sharon Zutavern, Theresa L.
Communities:	CSHL labs > Martienssen lab CSHL labs > McCombie lab CSHL labs > Ware lab CSHL Cancer Center Shared Resources > Bioinformatics Service CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User:	Matt Covey
Date:	20 November 2009
Date Deposited:	21 Feb 2013 21:39
Last Modified:	30 Dec 2014 16:36
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/27337

Actions (login required)

Administrator's edit/view item