Old School/New School Genome Sequencing: One Step Backward - a Quantum Leap Forward

As the costs for genome sequencing have decreased the number of “genome” sequences have increased at a rapid pace. Unfortunately, the quality and completeness of these so–called “genome” sequences have suffered enormously. We prefer to call such genome assemblies as “gene assembly space” (GAS). We believe it is important to distinguish GAS assemblies from reference genome assemblies (RGAs) as all subsequent research that depends on accurate genome assemblies can be highly compromised If the only assembly available is a GAS assembly.

To date, the highest quality genomes available (e.g. human, Arabidopsis, and rice) have relied on BAC-based physical maps, shotgun sequencing of individual BACs, finishing and assembly. Our lab has been experimenting with a modification of this Old School approach by first: a) generating whole genome profiling sequence-based physical maps of BACs; 2) sequencing pools of BACs (i.e. 24, 32, or 48) with PacBio long read chemistry; and 3) assembling all reads into reference quality genomes.

Data will be presented for a rice genome recently sequenced using this approach.