Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

BMC Genomics

Wen-Hsiung Li³  Sean Chun-Chang Chen¹  Yao-Ming Chang¹  Chun-Ping Yu²  Jinn-Jy Lin¹ 

[1] Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan;Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan;Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

关键词: Functional annotation;    Comparative genomics;    Coregulators;    Transcription factor annotation;   

Others  :  1139513
DOI  :  10.1186/1471-2164-15-818

 received in 2014-04-19, accepted in 2014-09-23,  发布年份 2014

【 摘 要 】

Background

Transcription factors (TFs) contain DNA-binding domains (DBDs) and regulate gene expression by binding to specific DNA sequences. In addition, there are proteins, called transcription coregulators (TCs), which lack DBDs but can alter gene expression through interaction with TFs or RNA Polymerase II. Therefore, it is interesting to identify and classify the TFs and TCs in a genome. In this study, maize (Zea mays) and foxtail millet (Setaria italica), two important species for the study of C4 photosynthesis and kranz anatomy, were selected.

Result

We conducted a comprehensive genome-wide annotation of TFs and TCs in maize B73 and in two strains of foxtail millet, Zhang gu and Yugu1, and classified them into families. To gain additional support for our predictions, we searched for their homologous genes in Arabidopsis or rice and studied their gene expression level using RNA-seq and microarray data. We identified many new TF and TC families in these two species, and described some evolutionary and functional aspects of the 9 new maize TF families. Moreover, we detected many pseudogenes and transposable elements in current databases. In addition, we examined tissue expression preferences of TF and TC families and identified tissue/condition-specific TFs and TCs in maize and millet. Finally, we identified potential C4-related TF and TC genes in maize and millet.

Conclusions

Our results significantly expand current TF and TC annotations in maize and millet. We provided supporting evidence for our annotation from genomic and gene expression data and identified TF and TC genes with tissue preference in expression. Our study may facilitate the study of regulation of gene expression, tissue morphogenesis, and C4 photosynthesis in maize and millet. The data we generated in this study are available at http://sites.google.com/site/jjlmmtf webcite.

【 授权许可】

   
2014 Lin et al.; licensee BioMed Central Ltd.

【 图 表 】

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