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Comparative Study
. 2008;9(2):R45.
doi: 10.1186/gb-2008-9-2-r45. Epub 2008 Feb 28.

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

HyeRan Kim  1 , Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Luis Goicoechea, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund, Rod A Wing
Affiliations
Comparative Study

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

HyeRan Kim et al. Genome Biol. 2008.

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.

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Figures

Figure 1
Figure 1
SyMAP view of unedited physical maps of chromosome 1 from eight diploid Oryza species aligned to the O. sativa ssp. japonica chromosome 1 RefSeq. The numbers in the small rectangles on the left are contig numbers of OMAP phase I physical maps. Beige bars on the right represent the O. sativa RefSeq (IRGSP V.4 assembly) and the red crosses on the beige bars represent the CentO position of O. sativa [18]. Purple lines represent BESs aligned to the O. sativa RefSeq. The order of the species from the left to right is; O. nivara [AA], O. rufipogon [AA], O. glaberrima [AA], O. punctata [BB]; O. officinalis [CC], O. australiensis [EE]; O. brachyantha [FF], O. granulata [GG].
Figure 2
Figure 2
Comparison of classified repeat composition in the genomes of 12 Oryza species and the O. sativa RefSeq.
Figure 3
Figure 3
Comparison of the ten most frequent SSR motif compositions in 14 Oryza species (japonica, O. sativa ssp. japonica; indica, O. sativa ssp. indica; OMAP, average of 12 OMAP species).
See this image and copyright information in PMC

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