The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza

Authors: KIM, HYE RAN - ARIZONA GENOMICS INST; HURWITZ, BONNIE - COLD SPRING HARBOR LAB; YU, YEISOO - ARIZONA GENOMICS INST; COLLURA, KRISTI - ARIZONA GENOMICS INST; GILL, NAVDEEP - PURDUE UNIVERSITY; MIGUEL, PHILLIP - PURDUE UNIVERSITY; MULLIKIN, JAMES - NHGRI, NATL INST OF HEALT; NELSON, WILLIAM - ARIZONA GENOMICS COMP LAB; WISSOTSKI, MARINA - ARIZONA GENOMICS INST; BRAIDOTTI, MICHELE - ARIZONA GENOMICS INST; KUDRNA, DAVE - ARIZONA GENOMICS INST; GOICOECHEA, JOSE - ARIZONA GENOMICS INST; STEIN, LINCOLN - COLD SPRING HARBOR LAB; Ware, Doreen; JACKSON, SCOTT - PURDUE UNIVERSITY; SODERLUND, CAROL - ARIZONA GENOMICS COMP LAB; WING, ROD - ARIZONA GENOMICS INST

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/13/2008
Publication Date: 2/14/2008
Citation: Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., Miguel, P.S., Mullikin, J., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.L., Stein, L., Ware, D., Jackson, S., Soderlund, C., Wing, R. 2008. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza. Genome Research. 9:R45.1-R45.15.

Interpretive Summary: The Oryza Map Alignment Project (OMAP) provides the first set of experimental data for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. The wild rice species of the genus Oryza offer a largely untapped resource of agriculturally-important genes that have the potential to solve many of the problems in rice production that we face today, such as yield, drought and salt tolerance as well as disease and insect resistance. To this end, we have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid genomes from twelve different species of Oryza. These libraries were end sequenced and assembled into phase I physical maps using fluorescence-based DNA fingerprinting technology and FPC program. Over 1.4 million BAC end sequences (BESs) from the twelve OMAP species genomes have been positioned on the finished sequence of the O. sativa genome. The total amount of sequence from the OMAP BESs samples 8-16% of each species’ genome, corresponding to one high quality BES tag of approximately 650 bp per 4-8 Kb of the rice genome. Fingerprints from BAC clones representing 8-18 fold coverage of the twelve OMAP species were assembled into phase I physical maps consisting 422-3,962 contigs with an average of 2-11% singletons. Using the OMAP phase I physical maps in conjunction with the O. sativa genome sequence, we were able to map 8-60% of the BESs and 81-99% of the clones based on conserved sequence and collinear segments with the O. sativa genome, which is thought to have diverged 10 million years ago. Moreover, we gained insight into the genome size, repeat content, and repeat characteristics of the genus Oryza providing a first glimpse at the resources and comparative analysis generated from the OMAP project.

Technical Abstract: The Oryza Map Alignment Project (OMAP) provides the first comprehensive experimental system for understanding the evolution, physiology and biochemistry of a full genus in plants or animals. We have constructed twelve deep-coverage BAC libraries that are representative of both diploid and tetraploid genomes from twelve different species of Oryza. These libraries were end sequenced and assembled into phase I physical maps using fluorescence-based DNA fingerprinting technology and FPC program. Over 1.4 million BAC end sequences (BESs) from the twelve OMAP species genomes have been aligned to the finished sequence of the O. sativa genome. The total amount of sequence from the OMAP BESs samples 8-16% of each species’ genome, corresponding to one high quality BES tag of approximately 650 bp per 4-8 Kb of the OMAP rice genome. Fingerprints from BAC clones representing 8-18 fold coverage of the twelve OMAP species were assembled into phase I physical maps consisting 422-3,962 contigs with an average of 2-11% singletons. Using the OMAP phase I physical maps in conjunction with the O. sativa genome sequence, we were able to map 8-60% of the BESs and 81-99% of the clones based on conserved sequence and collinear segments with the O. sativa genome, which is thought to have diverged 10 million years ago. Moreover, we gained insight into the genome size, repeat content, and repeat characteristics of the genus Oryza providing a first glimpse at the resources and comparative analysis generated from the OMAP project.