Whole genome sequencing: Methodology and progress in cereals

Genome sequencing is an essential means to rapidly obtain comprehensive information for a genome. This information is used to catalogue genes and study gene function on a genome wide scale. Additionally, it supports the understanding of genome organization and evolution in related organisms. With these consequences in mind, sequencing of whole genomes and transcripts has been exponential. Much of the expansion in genome sequencing can be attributed to improvements in DNA sequencing technologies and the availability of genome sequencing frameworks. Although there is an on-going debate, two major approaches, clone-by clone sequencing (CBC) and whole genome shotgun sequencing (WGS), are being applied to sequence many genomes. The clone-by-clone approach provides highly accurate sequence across the genome but generates large redundant sequences and progress is relatively slow. Whole genome shotgun sequencing rapidly generates sequences in a cost-effective manner but sequence coverage is poor in large repeat and high G/C areas. More recently, a hybrid method, an integration of CBC and WGS, was used to sequence the mouse genome and resulted in an efficient generation of very accurate genomic sequence. Despite the highly conserved gene order among major cereals, their genome sizes vary from 750 Mb of sorghum to 16000 Mb of wheat. Therefore it becomes technically and economically more difficult to generate complete genome sequences of the large and complex genomes of maize, barley and wheat. Unlike other cereals, rice has a compact genome (430Mb) and it serves as the principle source of nutrition for over one-third of the worlds population. Thus, it is clear that rice is a very attractive model for studying cereal genomes. IRGSPs ambitious objective is underway to provide a complete and publicly available sequence map of rice genome. This comprehensive genome information will provide an unprecedented opportunity to gain a fundamental and basic understanding of the rice genome that can be used as a foundation to study other cereal genomes and plant biology in general.