Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions

Zhu, Ting; Xu, Peng; Liu, Jiang-Peng; Peng, Sheng; Mo, Xinchun; Gao, Li‐Zhi

doi:10.1016/j.ympev.2013.10.008

Cited by 38 publications

(59 citation statements)

References 89 publications

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“…S8 and S9). This robust phylogeny provides solid grounds for performing evolutionary and comparative analyses, and is consistent with the calculated phylogeny of all eight AA-genome Oryza species in an earlier study (12). With the same large gene set, we dated the speciation events leading to these major extant AA lineages to be within 4.8 million years (Myr) and 35.3 Myr between AA and FF genomes ( Fig.…”

Section: Resultssupporting

confidence: 83%

“…Many genes involved in rice improvement are derived from wild AA-genome species, and broadening the gene pool of cultivated rice through introgression from other wild relatives of Oryza has attracted increasing attention (11). Phylogenetic analysis of the diploid AA-genome species indicated a closely spaced series of recent speciation events in this genus (12). These species span a wide range of global pantropical regions and are disjunctively distributed in Asia, Africa, Australia, and South America (13).…”

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confidence: 99%

“…These species span a wide range of global pantropical regions and are disjunctively distributed in Asia, Africa, Australia, and South America (13). Having diverged less than 3 Mya from a common AA-genome ancestor (12), these eight species have generated extensive adaptive and breeding traits (14,15).…”

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confidence: 99%

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Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

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

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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: 83%

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Rapid diversification of five Oryza AA genomes associated with rice adaptation

Zhang

Zhu

Xia

et al. 2014

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

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149

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“…meridionalis population is more extreme than previously reported. Most likely this extreme distortion is due to O. meridionalis being the most divergent of the AAgenome Oryza species from O. sativa (Zhu and Ge 2005;Zhang et al 2014;Zhu et al 2014). Segregation distortion was reported in two Bengal/O.…”

Section: Segregation Distortionmentioning

confidence: 98%

Exploring sheath blight quantitative trait loci in a Lemont/O. meridionalis advanced backcross population

et al. 2015

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“…Many genes that have led to rice improvement are derived from wild rice AA-genome species, and much attention has been directed on broadening the gene pool of cultivated rice through introgression of other wild relatives of Oryza [18]. Phylogenetic analysis of the diploid AA-genome species, i.e., O. sativa Japonica, O. sativa Indica, O. nivara , O. rufipogon , O. glaberrima , O. barthii , O. glumaepatula and O. meridionalis , indicated that a closely spaced series of recent speciation events in this genus has occurred [19]. These species span a wide range of global pantropical geographical regions and are disjunctively distributed in Asia, Africa, Australia, and South America [20].…”

Section: Introductionmentioning

confidence: 99%

Domestication of rice has reduced the occurrence of transposable elements within gene coding regions

Guo

Zhu

et al. 2017

BMC Genomics

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BackgroundTransposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production.ResultsWe analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations.ConclusionsThis study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3454-z) contains supplementary material, which is available to authorized users.

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Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions

Cited by 38 publications

References 89 publications

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Rapid diversification of five Oryza AA genomes associated with rice adaptation

Exploring sheath blight quantitative trait loci in a Lemont/O. meridionalis advanced backcross population

Domestication of rice has reduced the occurrence of transposable elements within gene coding regions

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