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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. 2014 Jun 03; 15:422.BG

Abstract

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.

Authors+Show Affiliations

No affiliation info availableNo affiliation info availableNo affiliation info availableDepartment of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea. nis@sunchon.ac.kr.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24888752

Citation

Thamilarasan, Senthil Kumar, et al. "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, vol. 15, 2014, p. 422.
Thamilarasan SK, Park JI, Jung HJ, et al. 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. 2014;15:422.
Thamilarasan, S. K., Park, J. I., Jung, H. J., & Nou, I. S. (2014). 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, 15, 422. https://doi.org/10.1186/1471-2164-15-422
Thamilarasan SK, et al. 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. 2014 Jun 3;15:422. PubMed PMID: 24888752.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea. AU - Thamilarasan,Senthil Kumar, AU - Park,Jong-In, AU - Jung,Hee-Jeong, AU - Nou,Ill-Sup, Y1 - 2014/06/03/ PY - 2014/01/09/received PY - 2014/05/20/accepted PY - 2014/6/4/entrez PY - 2014/6/4/pubmed PY - 2015/3/13/medline SP - 422 EP - 422 JF - BMC genomics JO - BMC Genomics VL - 15 N2 - 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. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/24888752/Genome_wide_analysis_of_the_distribution_of_AP2/ERF_transcription_factors_reveals_duplication_and_CBFs_genes_elucidate_their_potential_function_in_Brassica_oleracea_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-422 DB - PRIME DP - Unbound Medicine ER -