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Research article
Deep Evaluation to the Evolution History of Heat Shock Factor (HSF) Gene Family and Its Expansion Pattern in Seed Plants
Tao Wan
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518000, China.
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
HSF (Heat shock factor) genes are essential in the irreplaceable functions in some of the basic developmental pathways in plants. Despite the extensive studies on the structure, function diversification, and evolution of HSF, their divergent history and gene duplication pattern remain unsolved. To further illustrate the probable divergent patterns in these subfamilies, we visited the evolutionary history of the HSF via phylogenetic reconstruction and genomic syntenic analyses by taking advantage of the increased sampling of genomic data for pteridophyta, gymnosperms and basal angiosperms.
Results
We identified a novel clade including HSFA2, HSFA6, HSFA7, HSFA9 with complex relationship, very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We suggested that HSFA9 was derived from HSFA2 through gene duplication in eudicots at ancestral state, and then expanded in a lineage-specific way. Our findings indicated that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in common ancestors of monocots. We also presumed that HSFC2 was derived from HSFC1 in ancestral monocots.
Conclusion
This work proposes that in the era of early differentiation of angiosperms during the radiation of flowering plants, the member size of HSF gene family was also being adjusted, accompanied with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying evolution history of multigene family.
Keywords
Heat shock factor, HSFs, basal angiosperms, eudicots, monocots, gene duplication, diversification
Figure 1
Figure 2
Figure 3
Figure 4
Due to technical limitations, table 1-3 is only available as a download in the Supplemental Files section.
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1S9.xlsx
Additional files 5: Table S1. The species list used for HSF identification and analysis in this study. Additional files 6: Table S2. The species list of HSFs data downloaded from Heatster. Additional files 7: Table S3. Plant genomes used in this synteny analysis. Additional files 8: Table S4. The genes used for phylogenetic tree construction. Additional files 9: Table S5. HSF Gene pairs identified on syntenic blocks within different species. Additional files 10: Table S6. HSF Gene pairs identified on syntenic blocks within different species. Additional files 11: Table S7. Detailed information for the inferred duplication events within different species. Additional files 12: Table S8. HSF Gene pairs identified on syntenic blocks between different species. Additional files 13: Table S9. Detailed list of ortologous gene clusters between different species.
- Additionalfile1.fasta
Additional files 1: List of the accession number of HSF sequences used for the phylogenetic analysis.
- FigS3.pdf
Additional files 4: Figure S3. A Maximum-Likelihood phylogenetic reconstruction for the HSFB group.
- FigS2.pdf
Additional files 3: Figure S2. A Maximum-Likelihood phylogenetic reconstruction for the group HSFA and HSFC.
- FigS1.pdf
Additional files 2: Figure S1. A detailed Maximum-Likelihood tree of HSFs constructed with the program RaxML.
- Figurelegends.docx
- Table13.xlsx
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Research article
Deep Evaluation to the Evolution History of Heat Shock Factor (HSF) Gene Family and Its Expansion Pattern in Seed Plants
Tao Wan
Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518000, China.
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 17 Sep, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
HSF (Heat shock factor) genes are essential in the irreplaceable functions in some of the basic developmental pathways in plants. Despite the extensive studies on the structure, function diversification, and evolution of HSF, their divergent history and gene duplication pattern remain unsolved. To further illustrate the probable divergent patterns in these subfamilies, we visited the evolutionary history of the HSF via phylogenetic reconstruction and genomic syntenic analyses by taking advantage of the increased sampling of genomic data for pteridophyta, gymnosperms and basal angiosperms.
Results
We identified a novel clade including HSFA2, HSFA6, HSFA7, HSFA9 with complex relationship, very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We suggested that HSFA9 was derived from HSFA2 through gene duplication in eudicots at ancestral state, and then expanded in a lineage-specific way. Our findings indicated that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in common ancestors of monocots. We also presumed that HSFC2 was derived from HSFC1 in ancestral monocots.
Conclusion
This work proposes that in the era of early differentiation of angiosperms during the radiation of flowering plants, the member size of HSF gene family was also being adjusted, accompanied with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying evolution history of multigene family.
Figure 1
Figure 2
Figure 3
Figure 4
Due to technical limitations, table 1-3 is only available as a download in the Supplemental Files section.