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

Michael C Schatz,Eric Antoniou,Jer-Ming Chia,Lyza G Maron,Melissa Kramer,Elena Ghiban,James Gurtowski,Eric Biggers,Mark H Wright,Susan R Mccouch,Doreen Ware,Alejandro Hernandez Wences,Joshua C Stein,W Richard Mccombie,Hayan Lee

doi:10.1186/s13059-014-0506-z

Abstract

BackgroundThe 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.ResultsHere, 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.ConclusionsMany 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 materialThe online version of this article (doi:10.1186/s13059-014-0506-z) contains supplementary material, which is available to authorized users.

Highlights

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
Despite ongoing debate about the precise moment and location of the first domestication 'event' in rice, these studies all demonstrate that natural variation in the rice genome is deeply partitioned and that divergent haplotypes can be readily associated with major varietal groups and subpopulations
All three of our assemblies had excellent results: approximately 90% of each of the genomes were assembled into scaffolds at least 1 kbp long, with scaffold N50 sizes ranging from 213 kbp to 323 kbp, and contig N50 sizes ranging from 21.9 kbp to 25.5 kbp (Table 1)

Summary

Introduction

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. The course of domestication, as rice transitioned from its ancestral state as a tropical, outcrossing, aquatic, perennial species to a predominantly inbreeding, annual species adapted to a wide range of ecologies, was punctuated by persistent episodes of intermating among the different subpopulations This resulted in both natural and human-directed gene flow between the different gene pools, but the essential differentiation that distinguishes the Indica and Japonica genomes was maintained and reinforced over time as a result of numerous partial sterility barriers scattered throughout the genome [22,23,24,25]

Methods

Results

Conclusion