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

Abstract

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. BackgroundRice (Oryza sativa) provides 20% of the world's dietary energy supply and is the predominant staple food for 17 countries in Asia, 9 countries in North and South America and 8 countries in Africa. Within O. sativa, there are two major varietal groups, Indica and Japonica, that can be further subdivided into five major subpopulations: indica and aus share ancestry within the Indica varietal group, and tropical japonica, temperate japonica and aromatic (Group V) share ancestry within the Japonica varietal group (Figure 1 The time since divergence of the ancestral Indica and Japonica gene pools is estimated at 0.44 million years, based on sequence comparisons between cv Nipponbare (Japonica) and cv . This time estimate pre-dates the domestication of O. sativa by several hundred thousand years, suggesting that rice cultivation proceeded from multiple, pre-differentiated ancestral pools [1,[9][10][11][12][13]. This is consistent with genome-wide estimates of divergence based on gene content [14], transcript levels [15], single nucleotide polymorphisms (SNPs) [3,16], and

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…Most plant disease resistance genes encode intracellular nucleotide-binding, leucinerich repeat (NLR) receptors that directly or indirectly recognize pathogen effector proteins. NLR content is highly variable among rice populations, accounting for the majority of copy number and presence/absence polymorphisms affecting genes [74][75][76] , explained by rapid evolution and balancing selection 77 Fig. 24).…”

Pathways of Rice Diversification across Asia

“…Study of genetics has made it clear that the two traditional subspecies of japonica and indica are quite distant, and there is a third lineage of ricethe aus rices -that today are at their most diverse in northeastern India and Bangladesh (Schatz et al 2014;Travis et al 2015;Civáň et al 2015). Modern genetics also indicates that despite the deep divergence between indica and japonica these subspecies share several mutations that have been selected for during domestication, which in turn implies early hybridization between these two cultivated lines; it is generally inferred that many domestication traits evolved first in japonica, then were transferred to a protoindica through hybridization under cultivation Gross and Zhao 2014).…”

Construction and analysis of the Brassica oleracea pangenome

“…PAVs are sequences that are present in one genome and absent in another and can therefore be considered to be extreme form CNVs, where the sequence is completely missing from one or more individuals (Saxena et al, 2014). The existence of CNVs and PAVs, even between individuals belonging the same species, has been extensively documented in plants Gore et al, 2009;Han and Xue, 2003;Hirsch et al, 2014;Lai et al, 2010;Lam et al, 2010;Li et al, 2014;Ossowski et al, 2008;Schatz et al, 2014;Springer et al, 2009;Swanson-Wagner et al, 2010;Tan et al, 2012;. In order to capture the entire genomic sequence present within the species, including the complete gene set, the pangenome needs to be sequenced.…”

“…Known biological processes influenced by CNVs/PAVs are metabolite production, flowering time, submergence tolerance, phosphorus uptake and biotic stress response (Bakker et al, 2006;Cook et al, 2012;Díaz et al, 2012;Schatz et al, 2014;Shen et al, 2006;Winzer et al, 2012;Xu et al, 2012). Opium poppy contains a 10 gene cluster which displays PAV, being only present in plants producing noscapine, an antitumor alkaloid (Winzer et al, 2012).…”