Rapid diversification of five Oryza AA genomes associated with rice adaptation

Abstract

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.comparative genomics | full-genome sequencing | genomic variation | positive selection | Oryza D rawing the landscape of genomic divergence among multiple lineages is fundamental to understanding plant gene and genome evolution (1, 2). The comprehensive comparison of closely related genomes in different chronologically ordered stages under a well-resolved phylogenetic framework could dramatically improve the inference precision and sensitivity of gene evolution studies and should allow more robust results for investigating broad-scale patterns of genomic architecture in the course of the speciation process compared with analyses of single genomes (3, 4). For instance, studies of yeast, Drosophila, and human genomes have demonstrated how comparisons of closely related genome sequences can reveal mechanisms of gene and genome evolution in fungi and animals (5-7). In plants, however, we know little about broad-scale patterns of evolutionary dynamics, differentiation, and consequences. Studies are needed of very closely related plant species that span the speciation continuum and have well-characterized biogeographic histories.The genus Oryza, consisting of 24 species, provides a uniquely powerful system for studying comparative genomics and evolutionary biology, and can contribute to the improvement of rice, which is of pivotal significance in worldwide food production and security (8-10). Many genes involved in rice improvement are derived from wild AA-genome species, and broadening the gene pool of cultivated rice through i...

Improvement of Salinity Stress Tolerance in Rice: Challenges and Opportunities

“…The O. meridionalis from northern Australia had great divergence in protein-coding genes, non-coding RNA genes, structural variation and specific functional enrichment of miRNA target genes. It was 2.5-fold more distantly related to the other AA taxa than the genomes of the other species were to each other [165].…”

“…Sequencing of the genomes of the following wild rice species has already been completed: [166] in addition to African and Asian cultivated rice, O. glaberrima [165] and O. sativa. These studies reveal very high levels of genomic structural variation leading to considerable morphological and reproductive diversification [165].…”

“…These studies reveal very high levels of genomic structural variation leading to considerable morphological and reproductive diversification [165]. Lineage-specific, protein-coding genes under positive selection included those involved in flower development, reproduction and biotic and abiotic defences.…”

“…In most areas where wild rices grow, introgression from cultivated paddy fields nearby has occurred [15,165,[170][171][172]. As a result, many accessions of wild rices are not necessarily representative of the wild genome [15,165].…”

“…Most populations of wild Oryza are under threat from habitat destruction and/or introgression from cultigens from paddy fields into nearby wild populations. For example in China, O. rufipogon is currently threatened due to habitat fragmentation and reduction, in addition to introgression from cultivated rice [165,171,173]. Rates of gene flow from cultivated rice to O. rufipogon have been measured as 1.1% to 2.2% [170] and up to 2.94% [173].…”