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. 2021 Jun 8:12:658847.
doi: 10.3389/fgene.2021.658847. eCollection 2021.

Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes

Yajun Liang  1   2 , Junduo Wang  1 , Juyun Zheng  1 , Zhaolong Gong  1 , Zhiqiang Li  3 , Xiantao Ai  2 , Xueyuan Li  1 , Quanjia Chen  2
Affiliations

Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes

Yajun Liang et al. Front Genet. .

Abstract

Heat shock transcription factors (HSFs) are involved in environmental stress response and plant development, such as heat stress and flowering development. According to the structural characteristics of the HSF gene family, HSF genes were classified into three major types (HSFA, HSFB, and HSFC) in plants. Using conserved domains of HSF genes, we identified 621 HSF genes among 13 cotton genomes, consisting of eight diploid and five tetraploid genomes. Phylogenetic analysis indicated that HSF genes among 13 cotton genomes were grouped into two different clusters: one cluster contained all HSF genes of HSFA and HSFC, and the other cluster contained all HSF genes of HSFB. Comparative analysis of HSF genes in Arabidopsis thaliana, Gossypium herbaceum (A1), Gossypium arboreum (A2), Gossypium raimondii (D5), and Gossypium hirsutum (AD1) genomes demonstrated that four HSF genes were inherited from a common ancestor, A0, of all existing cotton A genomes. Members of the HSF gene family in G. herbaceum (A1) genome indicated a significant loss compared with those in G. arboretum (A2) and G. hirsutum (AD1) A genomes. However, HSF genes in G. raimondii (D5) showed relative loss compared with those in G. hirsutum (AD1) D genome. Analysis of tandem duplication (TD) events of HSF genes revealed that protein-coding genes among different cotton genomes have experienced TD events, but only the two-gene tandem array was detected in Gossypium thurberi (D1) genome. The expression analysis of HSF genes in G. hirsutum (AD1) and Gossypium barbadense (AD2) genomes indicated that the expressed HSF genes were divided into two different groups, respectively, and the expressed HSF orthologous genes between the two genomes showed totally different expression patterns despite the implementation of the same abiotic stresses. This work will provide novel insights for the study of evolutionary history and expression characterization of HSF genes in different cotton genomes and a widespread application model for the study of HSF gene families in plants.

Keywords: Gossypium lineage; expression divergence; genome-wide; heat shock transcription factor; tandem duplication.

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Conflict of interest statement

ZL was employed by company Adsen Biotechnology Corporation. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic relationship of HSF genes in 13 cotton genomes. The phylogenetic tree with maximum likelihood was constructed by MEGA software with 1,000 replications. I and II represent different groups that the HSF gene clustered. A, B, and C represent different types (HSFA, HSFB, and HSFC) of HSF genes in 13 cotton genomes.
FIGURE 2
FIGURE 2
Phylogenetic analysis of HSF genes among A. thaliana, G. herbaceum (A1), G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1) genomes. The phylogenetic tree with maximum likelihood was constructed by MEGA software with 1,000 replications. I and II represent different groups of HSF genes among the five plant species. Different types of HSF genes are shown by different colors. Blue, red, and green colors represent the HSFA, HSFB, and HSFC types of HSF genes, respectively.
FIGURE 3
FIGURE 3
Subgroups of HSF genes in A. thaliana, G. herbaceum (A1), G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1) genomes. (A–D) represent the subgroups of HSF orthologous genes in A. thaliana, G. herbaceum (A1), G. arboreum (A2), G. raimondii (D5), and G. hirsutum (AD1) genomes, respectively.
FIGURE 4
FIGURE 4
Expression profile of HSF orthologous genes between G. hirsutum (AD1) and G. barbadense (AD2) genomes. The black line represents the collinear relationships of HSF orthologous genes between G. hirsutum (AD1) and G. barbadense (AD2) genomes.
FIGURE 5
FIGURE 5
Expression difference of three HSF orthologous genes in G. hirsutum (AD1) and G. barbadense (AD2) genomes compared with G. herbaceum (A1) genome. The black line represents the collinear relationships of HSF orthologous genes among G. herbaceum (A1), G. hirsutum (AD1), and G. barbadense (AD2) genomes.
FIGURE 6
FIGURE 6
The evolution of the cotton genomes.
See this image and copyright information in PMC

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