Abstract
BackgroundCabbage (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.ResultsIn 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.ConclusionsComprehensive 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.
Highlights
Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide
Identification of the AP2/ETHYLENE RESPONSE FACTOR (ERF) family Transcription factors (TFs) in B. oleracea The availability of complete B. oleracea genome sequences has made it possible to identify all of the AP2/ERF family members in cabbage for the first time
To identify the four family genes, we conducted extensive BLASTN searches based on B. rapa and A. thaliana nomenclature suggestions [23,7]
Summary
Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. 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. Sakuma et al [6] divided the Arabidopsis ERF family into two subfamilies based on the amino acid sequence of the DNA binding domain, the CBF/DREB subfamily (group A) and ERF subfamily (group B). These two families were further subdivided into six groups [7]. 10 groups were identified in the grape and cucumber ERF family [3]
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