Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea

BMC Genomics

Ill-Sup Nou¹  Hee-Jeong Jung¹  Jong-In Park¹  Senthil Kumar Thamilarasan¹ 

[1] Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea

关键词: BoCBF genes;    Abiotic stresses;    Gene expression;    Classification;    Brassica oleracea AP2/ERF;   

Others  :  1216729
DOI  :  10.1186/1471-2164-15-422

 received in 2014-01-09, accepted in 2014-05-20,  发布年份 2014

【 摘 要 】

Background

Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. The entire cabbage genome sequence and more than fifty thousand proteins have been obtained to date. However a high degree of sequence similarity and conserved genome structure remain between cabbage and Arabidopsis; therefore, Arabidopsis is a viable reference species for comparative genomics studies. Transcription factors (TFs) are important regulators involved in plant development and physiological processes and the AP2/ERF protein family contains transcriptional factors that play a crucial role in plant growth and development, as well as response to biotic and abiotic stress conditions in plants. However, no detailed expression profile of AP2/ERF-like genes is available for B. oleracea.

Results

In the present study, 226 AP2/ERF TFs were identified from B. oleracea based on the available genome sequence. Based on sequence similarity, the AP2/ERF superfamily was classified into five groups (DREB, ERF, AP2, RAV and Soloist) and 15 subgroups. The identification, classification, phylogenetic construction, conserved motifs, chromosome distribution, functional annotation, expression patterns and interaction network were then predicted and analyzed. AP2/ERF transcription factor expression levels exhibited differences in response to varying abiotic stresses based on expressed sequence tags (ESTs). BoCBF1a, 1b, 2, 3 and 4, which were highly conserved in Arabidopsis and B. rapa CBF/DREB genes families were well characterized. Expression analysis enabled elucidation of the molecular and genetic level expression patterns of cold tolerance (CT) and susceptible lines (CS) of cabbage and indicated that all BoCBF genes responded to abiotic stresses.

Conclusions

Comprehensive analysis of the physiological functions and biological roles of AP2/ERF superfamily genes and BoCBF family genes in B. oleracea is required to fully elucidate AP2/ERF, which will provide rich resources and opportunities to understand abiotic stress tolerance in crops.

【 授权许可】

   
2014 Thamilarasan et al.; licensee BioMed Central Ltd.

【 图 表 】

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