Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants

Authors

Tong Yu, North China University of Science and Technology
Yun Bai, North China University of Science and Technology
Zhuo Liu, North China University of Science and Technology
Zhiyuan Wang, North China University of Science and Technology
Qihang Yang, North China University of Science and Technology
Tong Wu, North China University of Science and Technology
Shuyan Feng, North China University of Science and Technology
Yu Zhang, North China University of Science and Technology
Shaoqin Shen, North China University of Science and Technology
Quang Li, Tangshan Normal University
Liqiang Gu, Tangshan Normal University
Xiaoming Song, North China University of Science and Technology; University of Nebraska-Lincoln; University of Electronic Science and Technology of ChinaFollow

Document Type

Article

Date of this Version

2022

Citation

Horticulture Research, 2022, 9: uhac035

https://doi.org/10.1093/hr/uhac035

Comments

©The Author(s) 2022. Published by Oxford University Press on behalf of Nanjing Agricultural University. This is an Open Access article distributed under the terms of the Creative Commons Attribution License

Abstract

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plants, indicating that Hsf genes have undergone sequence variation during their evolution. The number of Hsf genes lost was greater than the number of genes that were duplicated after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes and 2421 downstream and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other in the response to heat stress. Global expression maps were illustrated for Hsf genes under various abiotic and biotic stresses and several developmental stages in Arabidopsis. Syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and the pan-genome of 18 Brassica rapa accessions. We also performed expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between the Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed an Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the study of the evolution and function of Hsf genes.