The Oryza map alignment project (OMAP): a new resource for comparative genomics studies within Oryza
2007
Wing, R.A. | Kim, H.R. | Goicoechea, J.L. | Yu, Y. | Kudrna, D. | Zuccolo, A. | Ammiraju Jetty, S.S. | Luo, M. | Nelson, W. | Soderlund, C. | San Miguel, P. | Gill, N. | Walling, J. | Jackson, S. | Hurwitz, B. | Ware, D. | Stein, L. | Brar, D. | Mackill, D.
With the completion of a finished genome sequence, we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species, in particular, contain an essentially untapped reservoir of agriculturally important gene that must be harnessed to enhance and sustain crop productivity. OMAP was established two years ago to generate a comprehensive set of genomics resources to investigate genome evolution and enhance positional cloning efforts in the genus Oryza. To date, we have generated (1) 12 high-quality BAC libraries that encompass the 10 genome types of Oryza, (2) approximately 1,000 Mb of BAC end sequence from these libraries, and (3) SNaPshot fingerprint databases for 10 of the 12 libraries. All of these resources are publicly available through the AGI BAC/EST Resource Center, GenBank, or at www.OMAP.org. The fingerprints and end sequences have been combined to develop 10 phase I physical maps. Six of these physical maps, O. nivara (AA), O. rufipogon (AA), O. glaberrima (AA), O. punctata (BB), O. officinalis (CC), and O. brachyantha (FF), have been heavily manually edited (HME) and aligned to the reference rice genome sequence. These alignments have revealed a large array of genome rearrangements relative to the japonica (Nipponbare) genome and have allowed us to begin drawing a more complete picture of Oryza genome evolution. We present the current status of OMAP and discuss recent analysis of the HME maps and comparative sequence analysis of select loci across the Oryza AA genome diploids.
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