Sequencing and Comparative Analysis of Tiled BACs from Different Rice Strains using the GS FLX+ System

Roche Applied Science and the Arizona Genome Institute (University of Arizona in Tucson) have collaborated to sequence selected BAC clones of the Chromosome 3 region of different rice strains, Oryza meridionalis and Oryza glumaepatula, using GS FLX+ System long-read technology. The assembled results were compared with the previously sequenced data from O. sativa, an Asian cultivated rice and O. glaberrima, an African cultivated rice.  Rice chromosomes share large blocks of synteny with maize and sorghum, thus suggesting a high level of conservation among cereals and therefore among Poaceae family, the origin of which can be traced over 50 million years. In this experiment, BACs spanning 3 Mb of the chromosome 3 short arm of O. meridionalis and O. glumaepatula were divided into 6 and 7 pools, respectively. Minimum-tiling-path BACs spanning 18 Mb in length were selected from each strain based on physical maps. We selected 181 O. meridionalis BACs orthologous to 3 Mb of O. sativa as well as O. glaberrima chromosome 3 sequence. We also selected 199 O. glumaepatula BACs using the same approach. Each pool of BACs was transformed into a library, tagged with molecular barcodes (MID), and sequenced with a full GS FLX+ System run for each arm. Modal read lengths of 760 bp and 775 bp, respectively, were generated for each run.  The raw data was assembled using the GS de novo Assembler and compared with the publicly available sequence of O. sativa and O. glaberrima.  Detailed analysis of the assembled data demonstrates the utility of long reads for investigating complex plant genomes. Sequencing and comparative analysis will lead to a better understanding of the molecular dynamics within related strains of important crops over short evolutionary time.

For life science research only. Not for use in diagnostic procedures.

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