Title

The Oryza Bacterial Artificial Chromosome Library Resource: Construction and Analysis of 12 Deep-coverage Large-insert Bac Libraries That Represent the 10 Genome Types of the Genus Oryza

Authors

Jetty S.S. Ammiraju, University of Arizona
Meizhong Luo, University of Arizona
José L. Goicoechea, University of Arizona
Wenming Wang, University of Arizona
Dave Kudrna, University of Arizona
Christopher Mueller, University of Arizona
Jayson Talag, University of Arizona
HyeRan Kim, University of Arizona
Nicholas B. Sisneros, University of Arizona
Barbara Blackmon, Clemson University
Eric Fang, Clemson University
Jeffery B. Tomkins, Clemson University
Darshan Brar, International Rice Research Institute (IRRI)
David MacKill, International Rice Research Institute (IRRI)
Susan McCouch, Cornell University
Nori Kurata, National Institute of Genetics (NIG)
Georgina Lambert, University of Arizona
David W. Galbraith, University of Arizona
K. Arumuganathan, Benaroya Research Institute at Virginia Mason
Kiran Rao, University of Arizona
Jason G. Walling, Purdue University
Navdeep Gill, Purdue UniversityFollow
Yeisoo Yu, University of Arizona
Phillip SanMiguel, Purdue University
Carol Soderlund, University of Arizona
Scott Jackson, Purdue University
Rod A. Wing, University of Arizona

Document Type

Article

Publication Date

12-12-2005

Publication Title

Genome Research

ISSN

1549-5469

Volume

16

First Page

140

Last Page

147

Abstract

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%–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.

Comments

©2006 by Cold Spring Harbor Laboratory Press

NSUWorks Citation

Ammiraju, Jetty S.S.; Meizhong Luo; José L. Goicoechea; Wenming Wang; Dave Kudrna; Christopher Mueller; Jayson Talag; HyeRan Kim; Nicholas B. Sisneros; Barbara Blackmon; Eric Fang; Jeffery B. Tomkins; Darshan Brar; David MacKill; Susan McCouch; Nori Kurata; Georgina Lambert; David W. Galbraith; K. Arumuganathan; Kiran Rao; Jason G. Walling; Navdeep Gill; Yeisoo Yu; Phillip SanMiguel; Carol Soderlund; Scott Jackson; and Rod A. Wing. 2005. "The Oryza Bacterial Artificial Chromosome Library Resource: Construction and Analysis of 12 Deep-coverage Large-insert Bac Libraries That Represent the 10 Genome Types of the Genus Oryza." Genome Research 16, (): 140-147. doi:http://www.genome.org/cgi/doi/10.1101/gr.3766306.

ORCID ID

http://orcid.org/0000-0003-3746-1866

DOI

http://www.genome.org/cgi/doi/10.1101/gr.3766306