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Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage

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Abstract

The Hsf gene family, one of the most important transcription factor families, plays crucial roles in regulating heat resistance. However, a systematic and comprehensive analysis of this gene family has not been reported in Chinese cabbage. Therefore, systematic analysis of the Hsf gene family in Chinese cabbage has profound significance. In this study, 35 BrHsf genes were identified from Chinese cabbage, which could be classified into three groups according to their structural characteristics and phylogenetic comparisons with Arabidopsis and rice. Thirty-three BrHsf genes mapped on chromosomes were further assigned to three subgenomes and eight ancestral karyotypes. Distribution mapping showed that BrHsf genes were non-randomly localized on chromosomes. Chinese cabbage and Arabidopsis shared 22 orthologous gene pairs. The expansion of BrHsf genes mainly resulted from genome triplication. Comparative analysis showed that the most Hsf genes were in Chinese cabbage among the five species analyzed. Interestingly, the number of Hsf genes of heat-resistant plants (Theobroma cacao and Musa acuminata) was fewer than that in Chinese cabbage. The expression patterns of BrHsf genes were different in six tissues, based on RNA-seq. Quantitative real-time-PCR analysis showed that the expression level of BrHsf genes varied under various abiotic stresses. In conclusion, this comprehensive analysis of BrHsf genes will provide rich resources, aiding the determination of Hsfs functions in plant heat resistance. Furthermore, the comparative genomics analysis deepened our understanding of Hsf genes’ evolution accompanied by the polyploidy event of Chinese cabbage.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Key Program, No. 31330067), National Program on Key Basic Research Projects (The 973 Program: 2012CB113900), National High Technology Research and Development Program of China (863 Program, No. 2012AA100101), and Shanghai ‘2011’ program (No. ZF12051301).

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Correspondence to Xilin Hou.

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X. Song and G. Liu contributed equally to this work.

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Song, X., Liu, G., Duan, W. et al. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Mol Genet Genomics 289, 541–551 (2014). https://doi.org/10.1007/s00438-014-0833-5

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