Genome-Wide Identification, Classification And Comparative Analysis Of Heat Shock Transcription Factor Family In Chinese Cabbage And Cabbage

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetable crops grown worldwide, consisting of various widely selection, propagation and cultivation. The heat shock transcription factors (Hsfs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (Hsps), which are critical in the protection against stress damage and some important biological processes. The entire Chinese cabbage genome sequences have been obtained to date. In the present study, on the one hand, the classification, phylogenetic reconstruction, chromosome distribution, conserved motifs, expression analysis, and interaction networks in Chinese cabbage were predicted and analyzed using bioinformatic methods. On the other hand, comparative analysis of hsfs between Chinese cabbage and cabbage were performed. The results are as follows:1. Chinese cabbage contains at least 30 Hsf genes, the length of protein sequence ranged from 239 to 487 aa, the MW ranged from 27.93 to 54.49 kDa, the PI ranged from 4.66 to 9.16. Except two genes on the scaffold could not be mapped to any specific chromosome, the rest 28 Hsf genes were distributed in every chromosome of the Chinese cabbage genome. Cabbage contains at least 36Hsf genes, the length of protein sequence ranged from 219 to 495 aa, the MW ranged from25.69 to 55.38 kDa, the PI ranged from 4.62 to 10.22. Also except 10 genes on the scaffold could not be mapped to any specific chromosome, the rest 26 Hsf genes were distributed in every chromosome of cabbage genome.2. The multiple sequence alignment showed Hsfs in Chinese cabbage and cabbage have highly conserved domain of DBD and conserved motifs, but two insertions and one deletion occurred in Chinese cabbage and the cabbage contained five deletions without insertions, the insertion and deletion events maybe bring genetic diversity of Chinese cabbage and cabbage.3. Phylogenetic relationship analysis of Arabidopsis, Chinese cabbage and cabbage Hsfs showed that these Hsfs can be divided into three classes (A, B, and C), A and B classes are further divided into eight and four subclasses in these two species, class A has significantly higher conservation than class B and C. Phylogenetic relationship analysis revealed 28 pairs of orthologous genes and 2 pairs of paralogous genes, which suggests that the common ancestor from Hsf genes may exist widely among the genome of Arabidopsis, Chinese cabbage and cabbage. Moreover, diversification of Hsf gene families have existed before the differentiation of Cruciferous crops and duplication of these genes had been occurred in the cabbage genome.4. Expression profile showed Hsfs may play differential roles in five organs in Chinese cabbage, and most likely participate in the development of underground parts and regulation of reproductive growth. Orthologous gene interaction network was constructed, and included MBF1C, ROF1, TBP2, CDC2 and HSP70 five genes,which are closely related to heat stress. And HsfAl interacts with HSP70, TBP2, also with CDC2 was shown in interaction network, maybe due to HsfA1 has a unique role as master regulator in Hsf family. Overall, data obtained from our investigation contributes to a better understanding of the complexity of Hsfs in Chinese cabbage and provides the basis for further function genes research.