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: 6.82). 02/2011; 66(5):796-805. DOI: 10.1111/j.1365-313X.2011.04539.x
Source: PubMed

ABSTRACT 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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The amazing ability of epigenetic mechanisms to respond to a wide range of developmental and environmental signals in eukaryotes has earned them a lot of attention. Indeed, epigenetically regulated gene expression (variations in gene expression obtained without permanent alteration of the DNA sequence) is involved in differentiation, organogenesis and acclimation, and, as such, is hypothesized to participate in both phenotypic diversity and the plasticity of living organisms. While the importance of epigenetic mechanisms in the understanding of such vital processes is now widely recognized, many questions remain to be elucidated. Foremost is the point of transmission of epigenetic marks on (methylated cytosines) and around (modified histone tails) DNA, since research is still needed to explain the inheritance of an epigenetic character and which mechanisms are involved. The present review is aimed at illustrating key concepts when con-sidering the exploitation of epigenetic changes for plant breeding, through both its environmentally responsive character and its potential heritability. In doing so, we have avoided developments relating to complex molecular pathways so as to give a glimpse to the interested but non-expert reader on the current debates and on the experimental challenges still ahead. Review Methodology: We searched mainly through the Google Scholar website, using the following search terms: epigenetic, plant breeding, epiallele, inheritance. For review articles exploring the phenomenon of transgenerational epigenetic inheritance and its implications for plant breeding, the large number of papers that emerged (almost 400) led us to consider mostly results published within the last couple of years. We also tried to avoid any useless redundancy with other exhaustive reviews on the subject published earlier. In addition, we recurrently used references from the articles and reviews obtained by this method to check for recent and additional relevant information.
    CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources 01/2011; 6:048. DOI:10.1079/PAVSNNR20116048
  • Source
    [Show abstract] [Hide abstract]
    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 · 3.94 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored.ResultsWe performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary analysis reveals that the novel exons, comparing with their flanking annotated ones, are generally under weaker selection pressure at the protein level, but under stronger pressure at the RNA level, suggesting that most of the novel exons also represent novel alternatively spliced variants (ASVs). However, we also observed the consistency of evolutionary rates between certain novel exons and their flanking exons, which provided further evidence of their co-occurrence in the transcripts, suggesting that previously-annotated isoforms might be subject to erroneous predictions. Our validation showed that 54% of the tested genes expressed the newly-identified isoforms that contained the novel exons, rather than the previously-annotated isoforms that excluded them. The consistent results were steadily observed across cultivated (Oryza sativa and O. glaberrima) and wild (O. rufipogon and O. nivara) rice species, asserting the necessity of our curation of the crop genome annotations. Our comparative analyses also inferred the common ancestral transcriptome of grass plants and gain- and loss-of-ASV events.Conclusions We have reannotated the rice, maize, and sorghum genomes, and showed that evolutionary rates might serve as an indicator for determining whether the identified exons were alternatively spliced. This study not only presents an effective in silico strategy for the improvement of plant annotations, but also provides further insights into the role of AS events in the evolution and domestication of crop plants. ExonFinder and the novel exons/ASVs identified are publicly accessible at
    BMC Plant Biology 02/2015; 15(1):39. DOI:10.1186/s12870-015-0431-7 · 3.94 Impact Factor

Full-text (2 Sources)

Available from
May 16, 2014