Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

Prasad, Vandana; Strömberg, Caroline A.E.; Leaché, Adam D.; Samant, Bandana; Patnaik, Rajeev; Tang, Li‐Ping; Mohabey, D. M.; Ge, Song; Sahni, Ashok

doi:10.1038/ncomms1482

Cited by 198 publications

(178 citation statements)

References 52 publications

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“…1C and SI Appendix, Fig. S8), agreeing both with another deep data analysis of these divergence times (24) and with recent fossil evidence suggesting the origin of the tribe Oryzeae at ∼63 Mya (25).…”

Section: Resultssupporting

confidence: 73%

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

138

149

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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...

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Section: Resultssupporting

confidence: 73%

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

138

149

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“…Compound-type starch granules are the most common type in endosperm of Poaceae species (Tateoka, 1962;Grass Phylogeny Working Group, 2001;Prasad et al, 2011;Matsushima et al, 2013). Simple-type starch granules (one starch granule per amyloplast) are produced in some species of the Bambusoideae, Pooideae, Micrairoideae, Chloridoideae, and Panicoideae subfamilies.…”

mentioning

confidence: 99%

Deficiency of Starch Synthase IIIa and IVb Alters Starch Granule Morphology from Polyhedral to Spherical in Rice Endosperm

Toyosawa

Kawagoe

Matsushima³

et al. 2016

Plant Physiol.

135

108

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Starch granule morphology differs markedly among plant species. However, the mechanisms controlling starch granule morphology have not been elucidated. Rice (Oryza sativa) endosperm produces characteristic compound-type granules containing dozens of polyhedral starch granules within an amyloplast. Some other cereal species produce simple-type granules, in which only one starch granule is present per amyloplast. A double mutant rice deficient in the starch synthase (SS) genes SSIIIa and SSIVb (ss3a ss4b) produced spherical starch granules, whereas the parental single mutants produced polyhedral starch granules similar to the wild type. The ss3a ss4b amyloplasts contained compound-type starch granules during early developmental stages, and spherical granules were separated from each other during subsequent amyloplast development and seed dehydration. Analysis of glucan chain length distribution identified overlapping roles for SSIIIa and SSIVb in amylopectin chain synthesis, with a degree of polymerization of 42 or greater. Confocal fluorescence microscopy and immunoelectron microscopy of wild-type developing rice seeds revealed that the majority of SSIVb was localized between starch granules. Therefore, we propose that SSIIIa and SSIVb have crucial roles in determining starch granule morphology and in maintaining the amyloplast envelope structure. We present a model of spherical starch granule production.

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“…An exemplar lineage in which to study the evolution of vernalization responsiveness is the ecologically diverse grass family (Poaceae), which originated 51 to 82 million years ago, probably in tropical forests (Kellogg, 2001;Prasad et al, 2011;Christin and Osborne, 2013;Christin et al, 2014;Magallón et al, 2015). Despite its tropical origins, a few grass clades have successfully diversified in temperate environments Humphreys and Linder, 2013).…”

mentioning

confidence: 99%

Evidence for an Early Origin of Vernalization Responsiveness in Temperate Pooideae Grasses

et al. 2016

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The ability of plants to match their reproductive output with favorable environmental conditions has major consequences both for lifetime fitness and geographic patterns of diversity. In temperate ecosystems, some plant species have evolved the ability to use winter nonfreezing cold (vernalization) as a cue to ready them for spring flowering. However, it is unknown how important the evolution of vernalization responsiveness has been for the colonization and subsequent diversification of taxa within the northern and southern temperate zones. Grasses of subfamily Pooideae, including several important crops, such as wheat (Triticum aestivum), barley (Hordeum vulgare), and oats (Avena sativa), predominate in the northern temperate zone, and it is hypothesized that their radiation was facilitated by the early evolution of vernalization responsiveness. Predictions of this early origin hypothesis are that a response to vernalization is widespread within the subfamily and that the genetic basis of this trait is conserved. To test these predictions, we determined and reconstructed vernalization responsiveness across Pooideae and compared expression of wheat vernalization gene orthologs VERNALIZATION1 (VRN1) and VRN3 in phylogenetically representative taxa under cold and control conditions. Our results demonstrate that vernalization responsive Pooideae species are widespread, suggesting that this trait evolved early in the lineage and that at least part of the vernalization gene network is conserved throughout the subfamily. These results are consistent with the hypothesis that the evolution of vernalization responsiveness was important for the initial transition of Pooideae out of the tropics and into the temperate zone.

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Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

Cited by 198 publications

References 52 publications

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Deficiency of Starch Synthase IIIa and IVb Alters Starch Granule Morphology from Polyhedral to Spherical in Rice Endosperm

Evidence for an Early Origin of Vernalization Responsiveness in Temperate Pooideae Grasses

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