OMAP - The Oryza Map Alignment Project
(OMAP)
provides the first ever closed experimental system for understanding the
evolution, physiology and biochemistry of a single genus in plants or animals.
In this project, twelve deep coverage BAC libraries have been constructed and
are representative of both diploid and tetraploid genomes from wild species of
Oryza. These libraries were end sequenced and assembled into physical maps
using DNA fingerprinting (FPC). Presently, three FPC maps have been manually
edited (O. rufipogon, O. nivara, O. glaberrima) and are available in Gramene
along with phase 1 maps from the other species. Additionally, over 1.4 million
BAC end sequences (BES) from the twelve wild rice genomes have been aligned to
the finished sequence of the rice genome and can be viewed through the Gramene Genome Browser.
Unordered FPC Maps |
Species | Map Set Name | |
---|
Oryza alta | FPC OA_BB Jul 2006 | View |
Oryza australiensis | FPC OA_CB Dec 2006 | View |
Oryza brachyantha | FPC OB__B Jun 2007 | View |
Oryza coarctata | FPC OC__B Dec 2006 | View |
Oryza granulata | FPC OG_AB Apr 2006 | View |
Oryza glaberrima | Curated FPC OG_BB Feb 2006 | View |
Oryza minuta | FPC OM__B Sep 2006 | View |
Oryza officinalis | FPC OO__B Jun 2007 | View |
Oryza punctata | FPC OP__B May 2007 | View |
Oryza ridleyi | FPC OR_AB May 2007 | View |
Oryza nivara | Curated FPC OR_BB Feb 2006 | View |
Oryza rufipogon | Curated FPC OR_CB Feb 2006 | View |
OMAP Ordered Maps
Using these data we can begin to address important biological
questions on a whole-genome scale including elucidating patterns of
conservation and divergence, genome rearrangement, evolution,
domestication and gene regulation. To this end, we have constructed a
synteny pipeline to align clones and contigs from the wild species to
rice based on BES alignments to rice in conjunction with the assembly
of wild rice clones in fingerprint contigs. Detailed maps showing
correspondences between the wild rice chromosomes and rice by the
clones and contigs, clones alone, or contigs alone ordered along
chromosomes are listed below. The methods for determining the clone
and contig positions in the ordered maps are listed here. These methods have been
applied to Gramene's annotated version of the O. sativa assembly from
TIGR.
O. sativa (TIGR) Ordered Maps
Clone and Contig View |
|
rufipogon |
nivara |
glaberrima |
punctata |
minuta |
officinalis |
alta |
australiensis |
coarctata |
brachyantha |
ridleyi |
granulata |
Chr. 1 |
2,309 |
3,320 |
1,923 |
750 |
1,073 |
617 |
118 |
401 |
1,571 |
472 |
137 |
215 |
Chr. 2 |
2,102 |
3,104 |
1,659 |
607 |
1,026 |
535 |
89 |
283 |
1,243 |
439 |
396 |
191 |
Chr. 3 |
1,998 |
3,086 |
1,796 |
773 |
1,202 |
554 |
111 |
361 |
1,655 |
593 |
439 |
352 |
Chr. 4 |
1,444 |
2,271 |
1,291 |
461 |
766 |
374 |
139 |
275 |
993 |
302 |
317 |
166 |
Chr. 5 |
1,396 |
1,992 |
1,199 |
388 |
573 |
362 |
29 |
180 |
724 |
249 |
245 |
114 |
Chr. 6 |
1,474 |
1,963 |
1,071 |
376 |
559 |
324 |
14 |
142 |
797 |
200 |
178 |
106 |
Chr. 7 |
1,300 |
1,890 |
1,017 |
348 |
482 |
255 |
53 |
129 |
613 |
172 |
215 |
81 |
Chr. 8 |
1,238 |
1,754 |
969 |
290 |
334 |
201 |
38 |
114 |
569 |
123 |
148 |
99 |
Chr. 9 |
909 |
1,334 |
862 |
296 |
376 |
222 |
48 |
129 |
474 |
159 |
107 |
54 |
Chr. 10 |
902 |
1,138 |
744 |
226 |
314 |
213 |
69 |
106 |
464 |
136 |
122 |
75 |
Chr. 11 |
1,054 |
1,404 |
799 |
208 |
505 |
904 |
12 |
35 |
218 |
34 |
34 |
16 |
Chr. 12 |
978 |
1,334 |
717 |
205 |
384 |
154 |
22 |
80 |
327 |
64 |
106 |
33 |
Unordered FPC Maps |
Species | Map Set Name | |
---|
Oryza rufipogon | Curated FPC OR_CB Feb 2006 | View |
Oryza nivara | Curated FPC OR_BB Feb 2006 | View |
Oryza glaberrima | Curated FPC OG_BB Feb 2006 | View |
Oryza alta | FPC OA_BB Jul 2006 | View |
Oryza granulata | FPC OG_AB Apr 2006 | View |