Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat

BMC Genomics

Ji-Rui Wang³  Yu-Ming Wei³  Ya-Xi Liu³  You-Liang Zheng²  Deng-Cai Liu³  Wei-Ying Chen¹  Zhong-Xu Chen³  Xiao-Jiang Guo³  Zhen-Yong Chen¹ 

[1] College of Life Science, China West Normal University, Nanchong 637009, China;Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Yaan 625014, Sichuan, China;Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China

关键词: Tissue;    Developmental stage;    WheatTFDB;    Triticum aestivum;    Transcription factor;   

Others  :  1131234
DOI  :  10.1186/s12864-015-1313-y

 received in 2014-07-07, accepted in 2015-02-03,  发布年份 2015

【 摘 要 】

Background

Wheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fungal diseases, insects, drought, salinity, and cold. Transcription factors (TFs) regulate gene expression in different tissues and at various developmental stages in plants and animals, and they can be identified and classified into families according to their structural and specialized DNA-binding domains (DBDs). Transcription factors are important regulatory components of the genome, and are the main targets for engineering stress tolerance.

Results

In total, 2407 putative TFs were identified from wheat expressed sequence tags, and then classified into 63 families by using Hmm searches against hidden Markov model (HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes in the wheat genome, a smaller proportion than those reported for other cereals in PlantTFDB V3.0 (3.33%–5.86%) and PlnTFDB (4.30%–6.46%). We assembled information from the various databases for individual TFs, including annotations and details of their developmental stage- and tissue-specific expression patterns. Based on this information, we identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, accounting for 52.22% and 45.87% of the 2407 wheat TFs, respectively. We identified 338, 269, 262, 175, 49, and 18 tissue-specific TFs in the flower, seed, root, leaf, stem, and crown, respectively. There were 100, 6, 342, 141, 390, and 278 TFs specifically expressed at the dormant seed, germinating seed, reproductive, ripening, seedling, and vegetative stages, respectively. We constructed a comprehensive database of wheat TFs, designated as WheatTFDB (http://xms.sicau.edu.cn/wheatTFDB/ webcite).

Conclusions

Approximately 2.22% (2407 genes) of all genes in the wheat genome were identified as TFs, and were clustered into 63 TF families. We identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, based on information about their developmental- and tissue-specific expression patterns obtained from publicly available gene expression databases. The 2407 wheat TFs and their annotations are summarized in our database, WheatTFDB. These data will be useful identifying target TFs involved in the stress response at a particular stage of development.

【 授权许可】

   
2015 Chen et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

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