The overall goal of this proof-of-concept project is to develop genomic resources for maize that will link together sequences available from other ongoing projects (DBI-0221536 [PI: Schubert] and DBI-0211851 [PI: Messing]). The maize genome is approximately 3,400 million base pairs (MB) in length, yet the genes only cover about 150-450 MB or 20% of the genome. Preliminary results indicate the remaining 80% of the genome comprises repetitive DNAs, much of which is highly methylated. The genes are thought to be distributed as small islands throughout the sea of repetitive DNA. Methods to isolate and sequence the genes are currently being evaluated since it is not feasible or cost-effective to tackle the whole genome at this time.
The first part of this project will use HypoMethylated Partial Restriction (HMPR) libraries to bridge small methylated regions within genes that are lost in gene enrichment methods that filter out repetitive DNA based on methylation. The HMPR sequences could allow contiguous gene sequences to be assembled by bridging these gaps. The second part of this project is to generate and sequence Methylation Spanning Linker Libraries (MSLLs) that will provide a bridge over the sea of methylated repetitive DNA from one gene island to the next. The HMPR and MSLL library clones will be sequenced from both ends and the sequences assembled with the available maize genomic sequence. The end results should contribute to the development of a scaffold of gene-rich sequences positioned across the maize genome map.
All sequence information will be released immediately to GenBank. A web-based display will be created at www.genome.arizona.edu to provide access to the project results.
