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Background  The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate.    Results  Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive  de novo  assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two.    Conclusions  Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the  S5  hybrid sterility locus, the  Sub1  submergence tolerance locus, the  LRK  gene cluster associated with improved yield, and the  Pup1  cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-014-0506-z) contains supplementary material, which is available to authorized users.

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica