Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

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Author
Kim, HyeRan
Hurwitz, Bonnie
Yu, Yeisoo
Collura, Kristi
Gill, Navdeep
SanMiguel, Phillip
Mullikin, James
Maher, Christopher
Nelson, William
Wissotski, Marina
Affiliation
Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, USA
Genome Technology Branch, NHGRI, National Institutes of Health, Bethesda, Maryland, 20892, USA
Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721, USA
USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA
Issue Date
2008

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Publisher
BioMed Central
Citation
Genome Biology 2008, 9:R45 (doi:10.1186/gb-2008-9-2-r45)
Journal
Genome Biology
Rights
© 2008 Kim et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).
Collection Information
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract
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.
DOI
10.1186/gb-2008-9-2-r45
Version
Final published version
Additional Links
http://genomebiology.com/2008/9/2/R45
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© 2008 Kim et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).
Except where otherwise noted, this item's license is described as © 2008 Kim et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0).