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

Summary 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. sativ...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2011-06, Vol.66 (5), p.796-805
Main Authors: Sakai, Hiroaki, Ikawa, Hiroshi, Tanaka, Tsuyoshi, Numa, Hisataka, Minami, Hiroshi, Fujisawa, Masaki, Shibata, Michie, Kurita, Kanako, Kikuta, Ari, Hamada, Masao, Kanamori, Hiroyuki, Namiki, Nobukazu, Wu, Jianzhong, Itoh, Takeshi, Matsumoto, Takashi, Sasaki, Takuji
Format: Article
Language:English
Subjects:
African rice
Amino Acid Substitution
Base Sequence
Biological and medical sciences
Comparative analysis
Comparative Genomic Hybridization
Data processing
DNA methylation
DNA, Plant - genetics
Evolution
Evolution, Molecular
Evolutionary biology
Filtration
Fundamental and applied biological sciences. Psychology
Genes, Plant
genome evolution
genome sequencing
Genome, Plant
Genomes
Genomics
INDEL Mutation
Introns
Microsatellite Repeats
Nucleotide sequence
Nucleotides
Original
Oryza - genetics
Oryza glaberrima
Oryza sativa
Plant breeding
Plant physiology and development
Rice
RNA Splice Sites
Selection, Genetic
Sequence Analysis, DNA
Simple sequence repeats
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Summary:Summary 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.
ISSN:0960-7412
1365-313X
DOI:10.1111/j.1365-313X.2011.04539.x