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

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• 作者：Xiaoqing Liu (23) (24)
  Xiaojin Zhou (23) (24)
  Ye Li (23) (25)
  Jian Tian (23) (24)
  Qiuxue Zhang (23) (24)
  Suzhen Li (23) (26)
  Lei Wang (23) (24)
  Jun Zhao (23) (24)
  Rumei Chen (23) (24)
  Yunliu Fan (23) (24)
  
  23. Department of crop genomics and genetic improvement ; Biotechnology Research Institute ; Chinese Academy of Agricultural Sciences ; Beijing ; 100081 ; China
  24. National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) ; Beijing ; 100081 ; China
  25. School of life Science and Engineering ; Southwest Technology University ; Mianyang ; 621000 ; China
  26. Department of Agronomy ; Agricultural University of Hebei ; Baoding ; 071000 ; China
  
• 关键词：Genome ; wide ; Bidirectional gene pair ; Bidirectional promoter ; Maize
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：566 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background 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. Results 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. Conclusions 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.