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

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...

Full description

Saved in:
Bibliographic Details
Published in:Genome Research 2006-01, Vol.16 (1), p.140-147
Main Authors: Ammiraju, Jetty S S, Luo, Meizhong, Goicoechea, José L, Wang, Wenming, Kudrna, Dave, Mueller, Christopher, Talag, Jayson, Kim, HyeRan, Sisneros, Nicholas B, Blackmon, Barbara, Fang, Eric, Tomkins, Jeffery B, Brar, Darshan, MacKill, David, McCouch, Susan, Kurata, Nori, Lambert, Georgina, Galbraith, David W, Arumuganathan, K, Rao, Kiran, Walling, Jason G, Gill, Navdeep, Yu, Yeisoo, SanMiguel, Phillip, Soderlund, Carol, Jackson, Scott, Wing, Rod A
Format: Article
Language:English
Subjects:
Base Sequence
Chromosomes, Artificial, Bacterial
Genome, Plant - genetics
Genomic Library
Molecular Sequence Data
Oryza
Oryza - genetics
Oryza sativa
Resources
Retroelements - genetics
Sequence Analysis, DNA - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1088-9051
1549-5469
1549-5477
DOI:10.1101/gr.3766306