Open Access Research article

Identification and functional characterization of bidirectional gene pairs and their intergenic regions in maize

Xiaoqing Liu12, Xiaojin Zhou12, Ye Li13, Jian Tian12, Qiuxue Zhang12, Suzhen Li14, Lei Wang12, Jun Zhao12, Rumei Chen12* and Yunliu Fan12*

Author Affiliations

1 Department of crop genomics and genetic improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China

2 National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing 100081, China

3 School of life Science and Engineering, Southwest Technology University, Mianyang 621000, China

4 Department of Agronomy, Agricultural University of Hebei, Baoding 071000, China

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BMC Genomics 2014, 15:338  doi:10.1186/1471-2164-15-338

Published: 5 May 2014



Bidirectional gene pairs exist as a specific form of gene organization in microorganisms and mammals as well as in model plant species, such as Arabidopsis and rice. Little is known about bidirectional gene pairs in maize, which has a large genome and is one of the most important grain crops.


We conducted a genome-wide search in maize using genome sequencing results from the inbred line B73. In total, 1696 bidirectional transcript pairs were identified using a modified search model. We functionally characterized the promoter activity of the intergenic regions of most of the bidirectional transcript pairs that were expressed in embryos using a maize embryo transient expression system. A comparative study of bidirectional gene pairs performed for three monocot (Zea mays, Sorghum bicolor and Oryza sativa) and two dicot (Arabidopsis thaliana and Glycine max) plant genomes showed that bidirectional gene pairs were abundant in the five plant species. Orthologous bidirectional gene pairs were clearly distinguishable between the monocot and dicot species although the total numbers of orthologous bidirectional genes were similar. Analysis of the gene pairs using the Blast2GO software suite showed that the molecular functions (MF), cellular components (CC), and biological processes (BP) associated with the bidirectional transcripts were similar among the five plant species.


The evolutionary analysis of the function and structure of orthologous bidirectional gene pairs in various plant species revealed a potential pathway of their origin, which may be required for the evolution of a new species.

Genome-wide; Bidirectional gene pair; Bidirectional promoter; Maize