Jetty S.S. Ammiraju,1,3,12 Meizhong Luo,1,3,12 JosÃ© L. Goicoechea,1,3,12 Wenming Wang,1,3 Dave Kudrna,1,3 Christopher Mueller,1,3 Jayson Talag,1,3,6 HyeRan Kim,1,3 Nicholas B. Sisneros,1,3 Barbara Blackmon,5 Eric Fang,5 Jeffery B. Tomkins,5 Darshan Brar,6 David MacKill,6 Susan McCouch,7 Nori Kurata,8 Georgina Lambert,2,3 David W. Galbraith,2,3 K. Arumuganathan,9 Kiran Rao,1,3,4 Jason G. Walling,10 Navdeep Gill,10 Yeisoo Yu,1,3 Phillip SanMiguel,11 Carol Soderlund,3,4 Scott Jackson,10 and Rod A. Wing1
Genome Res. 2006 January; 16(1): 140â€“147.
1 Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 USA
2 Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA
3 BIO5 Institute, University of Arizona, Tucson, Arizona 85721 USA
4 Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721 USA
5 Clemson University Genomics Institute, Clemson University, Clemson, South Carolina 29634, USA
6 Department of Plant Breeding and Genetics, International Rice Research Institute (IRRI), Los BaÃ±os, 4031 The Philippines
7 Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA
8 National Institute of Genetics (NIG), Shizuoka 411-8540, Japan
9 Flow Cytometry and Imaging Core Laboratory, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
10 Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
11 Genomics Core Facility, Purdue University, West Lafayette, Indiana 47907, USA
12These authors contributed equally to the work.
13Corresponding author. E-mail firstname.lastname@example.org; fax (520) 621-1259.
Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. 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 contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%â€“4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed.