title: Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis.
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.
authors.affiliation: Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ikawa
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Hisataka
authors.initials: H
authors.lastname: Numa
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Minami
authors.forename: Masaki
authors.initials: M
authors.lastname: Fujisawa
authors.forename: Michie
authors.initials: M
authors.lastname: Shibata
authors.forename: Kanako
authors.initials: K
authors.lastname: Kurita
authors.forename: Ari
authors.initials: A
authors.lastname: Kikuta
authors.forename: Masao
authors.initials: M
authors.lastname: Hamada
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Jianzhong
authors.initials: J
authors.lastname: Wu
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D019943:Amino Acid Substitution; D001483:Base Sequence; D055028:Comparative Genomic Hybridization; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D054643:INDEL Mutation; D007438:Introns; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D022821:RNA Splice Sites; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D022821:RNA Splice Sites