Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
The Plant Journal (Impact Factor: 5.97). 02/2011; 66(5):796-805. DOI: 10.1111/j.1365-313X.2011.04539.x
Source: PubMed


Here we present the genomic sequence of the African cultivated rice, Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice, Oryza sativa. We obtained gene-enriched sequences of O. glaberrima that correspond to about 25% of the gene regions of the O. sativa (japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes of O. glaberrima generally showed a larger synonymous-nonsynonymous substitution ratio, suggesting that O. glaberrima has undergone a genome-wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes of O. sativa experienced changes at splice sites after the divergence from O. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes of O. glaberrima and O. sativa. Although tri-nucleotide repeats were most common among the SSRs and were overrepresented in the protein-coding sequences, we found that selection against indels of tri-nucleotide repeats was relatively weak in both African and Asian rice. Our genome-wide sequencing of O. glaberrima and in-depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species.

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Available from: Masaki Fujisawa, Mar 10, 2014
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    • "Os08g04500 and Os08g07100 make two completely different sets of terpene products [26]. Analysis of the whole genome sequence available for another Oryza species O. glaberrima [34] also supported that OryzaTPS1 (gene ID ORGLA08G0019200 in this species) has not been duplicated in rice after the divergence of rice from the common ancestor of maize and sorghum as its closest paralog in this species (gene ID ORGLA08G0035300 in this species) also only possessed 48% similarity at the amino acid level to OryzaTPS1. Analysis of the genome sequences of other Oryza species analyzed in this study will be needed to provide undisputable evidence that the positive selection-driven functional divergence of OryzaTPS1 occurred without the direct involvement of gene duplication. "
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    ABSTRACT: Background Terpenoids constitute the largest class of secondary metabolites made by plants and display vast chemical diversity among and within species. Terpene synthases (TPSs) are the pivotal enzymes for terpenoid biosynthesis that create the basic carbon skeletons of this class. Functional divergence of paralogous and orthologous TPS genes is a major mechanism for the diversification of terpenoid biosynthesis. However, little is known about the evolutionary forces that have shaped the evolution of plant TPS genes leading to terpenoid diversity.ResultsThe orthologs of Oryza Terpene Synthase 1 (OryzaTPS1), a rice terpene synthase gene involved in indirect defense against insects in Oryza sativa, were cloned from six additional Oryza species. In vitro biochemical analysis showed that the enzymes encoded by these OryzaTPS1 genes functioned either as (E)-ß-caryophyllene synthases (ECS), or (E)-ß-caryophyllene & germacrene A synthases (EGS), or germacrene D & germacrene A synthases (DAS). Because the orthologs of OryzaTPS1 in maize and sorghum function as ECS, the ECS activity was inferred to be ancestral. Molecular evolutionary detected the signature of positive Darwinian selection in five codon substitutions in the evolution from ECS to DAS. Homology-based structure modeling and the biochemical analysis of laboratory-generated protein variants validated the contribution of the five positively selected sites to functional divergence of OryzaTPS1. The changes in the in vitro product spectra of OryzaTPS1 proteins also correlated closely to the changes in in vivo blends of volatile terpenes released from insect-damaged rice plants.Conclusions In this study, we found that positive Darwinian selection is a driving force for the functional divergence of OryzaTPS1. This finding suggests that the diverged sesquiterpene blend produced by the Oryza species containing DAS may be adaptive, likely in the attraction of the natural enemies of insect herbivores.
    BMC Plant Biology 09/2014; 14(1):239. DOI:10.1186/s12870-014-0239-x · 3.81 Impact Factor
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    • "Unexpectedly, Porteresia transcripts exhibited low similarity with rice proteins, suggesting significant differences between Porteresia and rice genomes. The similarity of Porteresia genes with rice was lower than that of other sequenced wild rice species.45,46 A substantial number of genes appeared specific to Porteresia because they do not have an ortholog in rice and other organisms as predicted based on the sequence similarity. "
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    ABSTRACT: Porteresia coarctata is a wild relative of rice with capability of high salinity and submergence tolerance. The transcriptome analyses of Porteresia can lead to the identification of candidate genes involved in salinity and submergence tolerance. We sequenced the transcriptome of Porteresia under different conditions using Illumina platform and generated about 375 million high-quality reads. After optimized assembly, a total of 152 367 unique transcript sequences with average length of 794 bp were obtained. Many of these sequences might represent fragmented transcripts. Functional annotation revealed the presence of genes involved in diverse cellular processes and 2749 transcription factor (TF)-encoding genes in Porteresia. The differential gene expression analyses identified a total of 15 158 genes involved in salinity and/or submergence response(s). The stress-responsive members of different TF families, including MYB, bHLH, AP2-EREBP, WRKY, bZIP and NAC, were identified. We also revealed key metabolic pathways, including amino acid biosynthesis, hormone biosynthesis, secondary metabolite biosynthesis, carbohydrate metabolism and cell wall structures, involved in stress tolerance in Porteresia. The transcriptome analyses of Porteresia are expected to highlight genes/pathways involved in salinity and submergence tolerance of this halophyte species. The data can serve as a resource for unravelling the underlying mechanism and devising strategies to engineer salinity and submergence tolerance in rice.
    DNA Research 08/2013; DOI:10.1093/dnares/dst042 · 5.48 Impact Factor
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    • "Despite global awareness about the value of genetic variation and efforts to preserve genetic resources in the world's gene banks, only a small fraction of the naturally occurring wild and cultivated variation in rice has been explored to date. This is changing as genomics and sequencingbased activities begin to provide descriptions of germplasm resources at the molecular level (Sakai et al., 2011). Since the mid-1990s, "
    Realizing Africa's Rice Promise, 01/2013: chapter Making rice genomics work for Africa; CABI., ISBN: 978-1845938123
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