Genome-wide identification, phylogenetic and expression analysis of the heat shock transcription factor family in bread wheat (Triticum aestivum L.)

Abstract

Background Environmental toxicity from non-essential heavy metals such as cadmium (Cd), which is released from human activities and other environmental causes, is rapidly increasing. Wheat can accumulate high levels of Cd in edible tissues, which poses a major hazard to human health. It has been reported that heat shock transcription factor A 4a ( HsfA4a ) of wheat and rice conferred Cd tolerance by upregulating metallothionein gene expression. However, genome-wide identification, classification, and comparative analysis of the Hsf family in wheat is lacking. Further, because of the promising role of Hsf genes in Cd tolerance, there is need for an understanding of the expression of this family and their functions on wheat under Cd stress. Therefore, here we identify the wheat TaHsf family and to begin to understand the molecular mechanisms mediated by the Hsf family under Cd stress. Results We first identified 78 putative Hsf homologs using the latest available wheat genome information, of which 38 belonged to class A, 16 to class B and 24 to class C subfamily. Then, we determined chromosome localizations, gene structures, conserved protein motifs, and phylogenetic relationships of these TaHsfs . Using RNA sequencing data over the course of development, we surveyed expression profiles of these TaHsfs during development and under different abiotic stresses to characterise the regulatory network of this family. Finally, we selected 13 TaHsf genes for expression level verification under Cd stress using qRT-PCR. Conclusions To our knowledge, this is the first report of the genome organization, evolutionary features and expression profiles of the wheat Hsf gene family. This work therefore lays the foundation for targeted functional analysis of wheat Hsf genes, and contributes to a better understanding of the roles and regulatory mechanism of wheat Hsfs under Cd stress. Electronic supplementary material The online version of this article (10.1186/s12864-019-5876-x) contains supplementary material, which is available to authorized users.

Genome-wide characterization of tea plant (Camellia sinensis) Hsf transcription factor family and role of CsHsfA2 in heat tolerance

“…Phylogenetic analysis showed that the CsHsfs could be divided into three main classes corresponding with those in A. thaliana and P. trichocarpa (Fig. 2), which was consistent with those reported previously [9,61,70]. The length of intron exhibited certain degrees of variation (Fig.…”

“…Interestingly, the qRT-PCR results of CsHsfA2 and CsHsfC1 expression showed the opposite trends with RNA-seq results (Fig. 8), which was a normal phenomenon in other studies [46,61,64] and might be due to the different normalized method between FPKM and qRT-PCR.…”

“…The numbers of Hsf family are diverse in different plant species, and there are 25 Hsfs in pepper, 29 in Chinese white pear, 30 in sesame, 26 in soybean and 78 in bread wheat [12,[61][62][63][64], respectively. In this study, we identified 25 CsHsfs from tea plant genome and classified them into A, B, and C subfamily on the basis of their structures and phylogenetic relationships among C. sinensis, A. thaliana, P. trichocarpa.…”

Genome-Wide Analysis of the Heat Shock Transcription Factor Gene Family in Brassica juncea: Structure, Evolution, and Expression Profiles

“…1B). This indicates that gene loss and replication occur at different stages of evolution, leading to the diversity of HSF (Zhou et al, 2019). Previous studies revealed that members of gene families can spread out into clusters on chromosomes by tandem repeats, or can spread out across different chromosomes by repetition (Steven et al, 2005;Zhu et al, 2017a).…”

“…HSF is found in various plants, and it has diverse family members. Previous studies revealed 78 HSFs in wheat (Zhou et al, 2019), 35 in carrot (Huang et al, 2015), and 25 in tea (Zhang et al, 2020c). Based on the relationship between protein sequence, structure, and evolution, there are three types of members in the HSF family in plants: A, B, and C. All types of HSFs in various plants have great similarity (Zhu et al, 2017b;Chen et al, 2018).…”