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, 9 (2), e27848

Substantial Expression of Novel Small Open Reading Frames in Oryza Sativa

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Substantial Expression of Novel Small Open Reading Frames in Oryza Sativa

Masanori Okamoto et al. Plant Signal Behav.

Abstract

In our previous integrated study combining informatics and molecular biology analyses, we revealed that Arabidopsis small open reading frames (sORFs) predicted by computational analysis have biological functions in morphogenesis. Here, we report that sequences homologous to Arabidopsis sORFs are abundant in intergenic regions of the rice genome. These sequences represent a subset of non-protein-coding DNA, and some are transcribed into mRNA. These results indicate that many sORFs associated with morphogenesis are hidden in the genomes of crop species.

Keywords: Arabidopsis; comparative genomics; rice; small open reading frame; small peptide.

Figures

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Figure 1. Molecular features of rice homologs of functional Arabidopsis sORFs. (A) Comparison of amino acid sequences encoded by sORFs between rice and Arabidopsis. Homologous sequences to Arabidopsis sORFs in rice were identified by BLAST searches. Sequences were aligned using CLUSTALW. Asterisk (*) indicates positions with a single fully conserved residue. Colon (:) indicates conservation between groups with strongly similar properties (scoring > 0.5 in Gonnet PAM 250 matrix). Period (.) indicates conservation between groups with weakly similar properties (scoring = < 0.5 in Gonnet PAM 250 matrix). (B) Physical map of rice sORFs on rice genome. DNA sequences for rice sORFs were input into RiceGE database (http://signal.salk.edu/cgi-bin/RiceGE), and physical locations of rice sORFs were identified by BLAST searches. (C) Detection of transcribed rice sORFs. A mixture of cDNAs was synthesized from mRNAs from 40 different samples (22 different organs, and shoots and roots of plants in nine different environmental conditions). Asterisk (*) represents expected PCR product size.

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