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Article|19 Feb 2022|OPEN
Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants
Tong Yu1 , Yun Bai1 , Zhuo Liu1 , Zhiyuan Wang1 , Qihang Yang1 , Tong Wu1 , Shuyan Feng1 , Yu Zhang1 , Shaoqin Shen1 , Qiang Li2 , Liqiang Gu2 and Xiaoming Song,1,3,4 ,
1School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China
2Faculty of Life Science, Tangshan Normal University, Tangshan 063000, Hebei, China
3School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
4Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
*Corresponding author. E-mail: songxm@ncst.edu.cn

Horticulture Research 9,
Article number: uhac035 (2022)
doi: https://doi.org/10.1093/hr/uhac035
Views: 178

Received: 28 Sep 2021
Accepted: 11 Jan 2022
Published online: 19 Feb 2022

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.