Method
Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
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* Corresponding author: Rod A Wing rwing@ag.arizona.edu
1 Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
3 Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
4 Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, USA
5 Genome Technology Branch, NHGRI, National Institutes of Health, Bethesda, Maryland, 20892, USA
6 Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
7 Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721, USA
8 USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA
Genome Biology 2008, 9:R45 doi:10.1186/gb-2008-9-2-r45
Published: 28 February 2008Abstract
We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.