Distinct evolutionary patterns of Oryza glaberrima deciphered by genome sequencing and comparative analysis
Journal
Plant Journal
Journal Volume
66
Journal Issue
5
Date Issued
2011-06-01
Author(s)
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
Matsumoto, Takashi
Sasaki, Takuji
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. © 2011 Blackwell Publishing Ltd.
Subjects
African rice | genome evolution | genome sequencing | Oryza glaberrima
Type
journal article