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

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.

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

“…The development of next-generation sequencing technologies (NGS) has surpassed traditional Sanger-based sequencing and offers now improved throughput and affordable costs facilitating the generation and mining of genomic diversity of natural variants. Clearly, de novo sequencing (which is based on the assembly of sequence reads without a reference genome [36]) of different accessions/species represents the gold standard for mapping of structural genetic variations, as it allows a complete representation of all presence/absence variants especially when the genomes under investigation are characterized by large structural differences, as was recently carried out for divergent strains of rice [37]. Given that high-quality reference genomes are now available for several species spanning all major crop families [9], also "resequencing" approaches (the alignment of novel reads onto a pre-assembled reference genome) represent a more rapid strategy for the characterization of genome-wide variation in a set of related species.…”

SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?

“…This has led to a series of similar studies in other micro-organisms [4,5,6,7] as well as higher organisms including maize [8,9], soybean [10,11], rice [12,13], and Brassicas [14,15]. The pangenome can be thought of as the full complement of genes in a given species.…”

“…A number of examples are available in a range of species such as maize [8,9], soybean [10,11], Brassica rapa [15], Brassica oleracea [14], and rice [12,13]. Irrespective of the species under study, the main aims have been to gain a better understanding of the core and variable genomes, and to identify candidate genes, which are associated with phenotypic variation.…”

“…In a more recent study revolving around the B. oleracea pangenome, it was found that almost 20% of the genes were affected by presence/absence variation [14]. In a pangenome study of three divergent rice lines, it was revealed that 92% of the genes were core genes, while the remaining were variable, shorter in length, and had fewer exons [12]. Yet another study involving 1483 cultivated rice accessions showed that protein-coding genes not present in the Nipponbare reference genome had been successfully assembled [13].…”

“…Since the starting point of the assembly is a single reference, and new contigs are generated at each step of the iterative assembly process, it is very useful to know the positions and orientations of the contigs relative to the pangenome reference, especially if they harbour genic sequences. In studies involving association mapping or QTL analysis, candidate genes are mapped to a narrow genomic region in which the causal genes are selected based on the gene annotation of the reference genome [12]. In the case of pangenomes, if the positions of novel genes are not known, then such attempts would be futile.…”