ArticleThe Plant journal : for cell and molecular biology2011
Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
Article in The Plant journal : for cell and molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 35 citations in OpenAlex.
- African Cultivated, Wild and Weedy Rice (Biology · 2024Review
- Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication.Rice (New York, N.Y.) · 2021Review
- Genomic approach for conservation and the sustainable management of endangered species of the Amazon.PloS one · 2021Article
- Advances in Molecular Genetics and Genomics of African Rice (Plants (Basel, Switzerland) · 2019Review
- Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions.Rice (New York, N.Y.) · 2018Article
- The Nipponbare genome and the next-generation of rice genomics research in Japan.Rice (New York, N.Y.) · 2016Review
- Breeding for plant heat tolerance at vegetative and reproductive stages.Plant reproduction · 2016Review
- Exploring the rice dispensable genome using a metagenome-like assembly strategy.Genome biology · 2015Article
- Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice.Nature genetics · 2015Article
- Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants.BMC plant biology · 2015Article
- How to Isolate a Plant's Hypomethylome in One Shot.BioMed research international · 2015Article
- Positive Darwinian selection is a driving force for the diversification of terpenoid biosynthesis in the genus Oryza.BMC plant biology · 2014Article
- Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Analyses of hypomethylated oil palm gene space.PloS one · 2014Article
- A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.International journal of molecular sciences · 2013Review
- A daily-updated tree of (sequenced) life as a reference for genome research.Scientific reports · 2013Article
- SNP markers retrieval for a non-model species: a practical approach.BMC research notes · 2012Article
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Authors and funding
16 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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