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G-quadruplex is a stable, four-stranded DNA or RNA structure formed from guanine-rich regions and implicated in telomere maintenance, replication, gene regulation at transcription level or translation level, etc. Based on bioinformatics methods, we analyzed different putative G-quadruplex motifs (PGQMs) patterns in various genomic regions of two subspecies (indica and japonica) of Oryza sativa and the whole genomes of other 8 species. In total, in the 10 species we discussed, the PGQMs densities in monocots were higher than dicots. 40,483 and 31,795 PGQMs were identified with a density of 108.46 and 84.89 PGQMs/Mb, respectively, in japonica and indica genomes, 10,655 and 5420 loci were found to contain at least one PGQM in their gene bodies (with a percentage of 19% and 14%) indicating a wide distribution of G-quadruplex motifs in O. sativa genome. They preferred to locate in transcription start sites proximal regions and 5'-UTR with relative high enrichment. This phenomenon supports the hypothesis that PGQMs are involved in gene transcription and translation. In addition, we analyzed the distribution of different loop length in G-quadruplex and found the density of long loop PGQMs was less than short loop in indica's intron but it was similar in japonica. Meanwhile, we focused on the loci with PGQMs and conducted gene ontology (GO) analysis of them. As a result, many GO terms were identified and significantly correlated with the loci containing at least one PGQM. The GO analysis in the two subspecies of rice may be helpful for elucidating the functional roles of G-quadruplexes., (Copyright © 2015 Elsevier Ltd. All rights reserved.)