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

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

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion.

In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question.

The wild relatives of rice contain a virtually untapped reservoir of traits that can be used help drive the 21st century green revolution aimed at solving world food security issues by 2050. To better understand and exploit the 23 species of the Oryza genus the rice research community is developing foundational resources composed of: 1) reference genomes and transcriptomes for all 23 species; 2) advanced mapping populations for functional and breeding studies; and 3) in situ conservation sites for ecological, evolutionary and population genomics. To this end, 16 genome sequencing projects are currently underway, and all completed assemblies have been annotated; and several advanced mapping populations have been developed, and more will be generated, mapped, and phenotyped, to uncover useful alleles. As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus.

A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond.

BACKGROUND: The role of gene duplication in the structural and functional evolution of genomes has been well documented. Analysis of complete rice (Oryza sativa) genome sequences suggested an ancient whole genome duplication, common to all the grasses, some 50-70 million years ago and a more conserved segmental duplication between the distal regions of the short arms of chromosomes 11 and 12, whose evolutionary history is controversial. RESULTS: We have carried out a comparative analysis of this duplication within the wild species of the genus Oryza, using a phylogenetic approach to specify its origin and evolutionary dynamics. Paralogous pairs were isolated for nine genes selected throughout the region in all Oryza genome types, as well as in two outgroup species, Leersia perrieri and Potamophila parviflora. All Oryza species display the same global evolutionary dynamics but some lineage-specific features appear towards the proximal end of the duplicated region. The same level of conservation is observed between the redundant copies of the tetraploid species Oryza minuta. The presence of orthologous duplicated blocks in the genome of the more distantly-related species, Brachypodium distachyon, strongly suggests that this duplication between chromosomes 11 and 12 was formed as part of the whole genome duplication common to all Poaceae. CONCLUSION: Our observations suggest that recurrent but heterogeneous concerted evolution throughout the Oryza genus and in related species has led specifically to the extremely high sequence conservation occurring in this region of more than 2 Mbp.