Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species.

Xin Qiao,Shaoling Zhang,Meng Li,Hao Yin,Leiting Li,Juyou Wu

doi:10.1186/s12870-014-0401-5

Abstract

BackgroundHeat shock transcription factors (Hsfs), which act as important transcriptional regulatory proteins in eukaryotes, play a central role in controlling the expression of heat-responsive genes. At present, the genomes of Chinese white pear (‘Dangshansuli’) and five other Rosaceae fruit crops have been fully sequenced. However, information about the Hsfs gene family in these Rosaceae species is limited, and the evolutionary history of the Hsfs gene family also remains unresolved.ResultsIn this study, 137 Hsf genes were identified from six Rosaceae species (Pyrus bretschneideri, Malus × domestica, Prunus persica, Fragaria vesca, Prunus mume, and Pyrus communis), 29 of which came from Chinese white pear, designated as PbHsf. Based on the structural characteristics and phylogenetic analysis of these sequences, the Hsf family genes could be classified into three main groups (classes A, B, and C). Segmental and dispersed duplications were the primary forces underlying Hsf gene family expansion in the Rosaceae. Most of the PbHsf duplicated gene pairs were dated back to the recent whole-genome duplication (WGD, 30–45 million years ago (MYA)). Purifying selection also played a critical role in the evolution of Hsf genes. Transcriptome data demonstrated that the expression levels of the PbHsf genes were widely different. Six PbHsf genes were upregulated in fruit under naturally increased temperature.ConclusionA comprehensive analysis of Hsf genes was performed in six Rosaceae species, and 137 full length Hsf genes were identified. The results presented here will undoubtedly be useful for better understanding the complexity of the Hsf gene family and will facilitate functional characterization in future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0401-5) contains supplementary material, which is available to authorized users.

Highlights

Heat shock transcription factors (Hsfs), which act as important transcriptional regulatory proteins in eukaryotes, play a central role in controlling the expression of heat-responsive genes
Identification and classification of Hsf genes in the Rosaceae Two strategies were used to search for members of the Hsfs family in Pyrus bretschneideri and five other Rosaceae species: Hidden Markov Model search (HMMsearch) with the Hsf domain HMM profile (PF00447) and BLASTP using Hsf protein sequences from Arabidopsis thaliana and Populus trichocarpa as queries
A total of 137 full-length Hsf genes were identified in the six Rosaceae genomes, and the Chinese white pear genome contained 29 Hsf genes

Summary

Introduction

Heat shock transcription factors (Hsfs), which act as important transcriptional regulatory proteins in eukaryotes, play a central role in controlling the expression of heat-responsive genes. Qiao et al BMC Plant Biology (2015) 15:12 studies have shown that Hsfs are involved in plant growth and development, as well as in responses to other abiotic stresses such as cold, salt, and drought [12,13,14,15,16,17,18,19,20,21]. Hsfs share a common core structure composed of an N-terminal DNA binding domain (DBD) and an adjacent bipartite oligomerization domain (HR-A/B) [24,25]. The HR-A/B domain is characterized by hydrophobic heptad repeats that form a helical coiledcoil structure, which is a prerequisite for high affinity DNA binding and, subsequently, for transcriptional activity. A flexible linker exists between the DBD domain and HR-A/B domain [28]

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Conclusion