Histone deacetylases tuin (HDT) is a plant-specific protein subfamily of histone deacetylation enzymes (HDAC) which has a variety of functions in plant development, hormone signaling and stress response. Although the HDT family’s genes have been studied in many plant species, they have not been characterized in Brassicaceae. In this study, 14, 8 and 10 HDT genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the HDTs were divided into four groups: HDT1(HD2A), HDT2(HD2B), HDT3(HD2C) and HDT4(HD2D). There was an expansion of HDT2 orthologous genes in Brassicaceae. Most of the HDT genes were intron-rich and conserved in gene structure, and they coded for proteins with a nucleoplasmin-like (NPL) domain. Expression analysis showed that B. napus, B. rapa, and B. oleracea HDT genes were expressed in different organs at different developmental stages, while different HDT subgroups were specifically expressed in specific organs and tissues. Interestingly, most of the Bna/Br/BoHDT2 members were expressed in flowers, buds and siliques, suggesting they have an important role in the development of reproductive organs in Brassicaceae. Expression of BnaHDT was induced by various hormones, such as ABA and ethylene treatment, and some subgroups of genes were responsive to heat treatment. The expression of most HDT members was strongly induced by cold stress and freezing stress after non-cold acclimation, while it was slightly induced after cold acclimation. In this study, the HDT gene family of Brassicaceae was analyzed for the first time, which helps in understanding the function of BnaHDT in regulating plant responses to abiotic stresses, especially freezing stresses.

Low temperature is an important environmental stress factor affecting plant growth and development. The ICE1-CBF-COR [inducer of CBF expression1-c-repeat (CRT)-binding factors-cold responsive] plays an important role in the signaling pathway in response to low temperature stress in plants. To explore the evolution of CBF gene in Brassica napus L. and its function in response to low temperature stress, 11, 6, and 6 CBF genes were detected from Brassica napus, Brassica rapa, and Brassica oleracea, respectively. In addition, the molecular characteristics, protein conserved domains, phylogenetic tree, gene structure, and chromosome distribution were systematically investigated. The results showed that 11 BnaCBF genes could be divided into two subgroups including Subgroup I (CBF1/2/3) and Subgroup II (CBF4). Transcriptome sequencing revealed that all the CBF genes of Brassica napus were induced by low temperature, among which four genes in subgroup Ib responded rapidly and durably to cold stress, and two genes in Subgroup II responded weakly to cold stress, however, the relative expression level of CBF genes in roots was significantly higher than that in leaves, which were involved in salt stress and osmotic stress responses. Further analysis demonstrated that the CBF gene family in Brassica napus responded more strongly to freezing stress, especially BnaA08G30930D, BnaCnng49280D, BnaAnng34260D, BnaC07g39680D in Subsection I, and BnaA10g07630D, BnaC09G28190D in Subsection II. This study lays a foundation for further understanding the biological function of the CBF family gene and its response to low temperature, especially freezing stress in Brassica napus., and provides a reference for bioinformation research of CBF family genes in other species.