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Genome-Wide Identification and Function Analyses of Heat Shock Transcription Factors in Potato.

Tang R, Zhu W, Song X, Lin X, Cai J, Wang M, Yang Q - Front Plant Sci (2016)

Bottom Line: Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development.StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions.A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Heat shock transcription factors (Hsfs) play vital roles in the regulation of tolerance to various stresses in living organisms. To dissect the mechanisms of the Hsfs in potato adaptation to abiotic stresses, genome and transcriptome analyses of Hsf gene family were investigated in Solanum tuberosum L. Twenty-seven StHsf members were identified by bioinformatics and phylogenetic analyses and were classified into A, B, and C groups according to their structural and phylogenetic features. StHsfs in the same class shared similar gene structures and conserved motifs. The chromosomal location analysis showed that 27 Hsfs were located in 10 of 12 chromosomes (except chromosome 1 and chromosome 5) and that 18 of these genes formed 9 paralogous pairs. Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development. Promoter and quantitative real-time polymerase chain reaction (qRT-PCR) detections of StHsfs were conducted and demonstrated that these genes were all responsive to various stresses. StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions. A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.

No MeSH data available.


Related in: MedlinePlus

Co-expression network of Hsfs and their co-expressed genes in potato. TOM (Topological overlap matrix) value is 0.07. Nodes represent StHsf and co-expressed genes in potato, edges indicate pairwise correlation constructed by WGCNA. Red circles indicate Hsfs, blue circles represent Hsps. The network was created using Cytoscape (see Materials and Methods). The length of the line segment doesn't stand for the closeness of the relationship between StHsf and each gene; it is simply for distinguishing different genes.
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Figure 8: Co-expression network of Hsfs and their co-expressed genes in potato. TOM (Topological overlap matrix) value is 0.07. Nodes represent StHsf and co-expressed genes in potato, edges indicate pairwise correlation constructed by WGCNA. Red circles indicate Hsfs, blue circles represent Hsps. The network was created using Cytoscape (see Materials and Methods). The length of the line segment doesn't stand for the closeness of the relationship between StHsf and each gene; it is simply for distinguishing different genes.

Mentions: The co-expression network of Hsfs and their related genes in potato was created by Cytoscape with TOM (Topological overlap matrix) value 0.07 (Figure 8). The genes in a module were formed into a circle with StHsf as a center (red points) and other related genes around (blue points). The sequence numbers and potential functions of these genes related to StHsfs in Spud DB Potato Genomics Resources were provided in Supplementary Table S3. Proteins, encoded by these genes, are not only StHsps like Heat shock cognate 70 kDa protein (PGSC0003DMT400001180) and 10 kDa chaperonin (PGSC0003DMT400060280), but also other genes with a variety of functions, such as DELLA protein (PGSC0003DMT400049445), MAPK (PGSC0003DMT400077272) and MAPKKK (PGSC0003DMT400057171) in the module 3 which contained StHsf007. Except the relationship between StHsfs and their correlated genes, there also existed direct or indirect interactions between StHsfs, such as StHsf001, StHsf005, StHsf008, StHsf009, StHsf020, and StHsf027 (Figure 8). These results provide some basis for further study of function mechanism of StHsfs.


Genome-Wide Identification and Function Analyses of Heat Shock Transcription Factors in Potato.

Tang R, Zhu W, Song X, Lin X, Cai J, Wang M, Yang Q - Front Plant Sci (2016)

Co-expression network of Hsfs and their co-expressed genes in potato. TOM (Topological overlap matrix) value is 0.07. Nodes represent StHsf and co-expressed genes in potato, edges indicate pairwise correlation constructed by WGCNA. Red circles indicate Hsfs, blue circles represent Hsps. The network was created using Cytoscape (see Materials and Methods). The length of the line segment doesn't stand for the closeness of the relationship between StHsf and each gene; it is simply for distinguishing different genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836240&req=5

Figure 8: Co-expression network of Hsfs and their co-expressed genes in potato. TOM (Topological overlap matrix) value is 0.07. Nodes represent StHsf and co-expressed genes in potato, edges indicate pairwise correlation constructed by WGCNA. Red circles indicate Hsfs, blue circles represent Hsps. The network was created using Cytoscape (see Materials and Methods). The length of the line segment doesn't stand for the closeness of the relationship between StHsf and each gene; it is simply for distinguishing different genes.
Mentions: The co-expression network of Hsfs and their related genes in potato was created by Cytoscape with TOM (Topological overlap matrix) value 0.07 (Figure 8). The genes in a module were formed into a circle with StHsf as a center (red points) and other related genes around (blue points). The sequence numbers and potential functions of these genes related to StHsfs in Spud DB Potato Genomics Resources were provided in Supplementary Table S3. Proteins, encoded by these genes, are not only StHsps like Heat shock cognate 70 kDa protein (PGSC0003DMT400001180) and 10 kDa chaperonin (PGSC0003DMT400060280), but also other genes with a variety of functions, such as DELLA protein (PGSC0003DMT400049445), MAPK (PGSC0003DMT400077272) and MAPKKK (PGSC0003DMT400057171) in the module 3 which contained StHsf007. Except the relationship between StHsfs and their correlated genes, there also existed direct or indirect interactions between StHsfs, such as StHsf001, StHsf005, StHsf008, StHsf009, StHsf020, and StHsf027 (Figure 8). These results provide some basis for further study of function mechanism of StHsfs.

Bottom Line: Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development.StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions.A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Heat shock transcription factors (Hsfs) play vital roles in the regulation of tolerance to various stresses in living organisms. To dissect the mechanisms of the Hsfs in potato adaptation to abiotic stresses, genome and transcriptome analyses of Hsf gene family were investigated in Solanum tuberosum L. Twenty-seven StHsf members were identified by bioinformatics and phylogenetic analyses and were classified into A, B, and C groups according to their structural and phylogenetic features. StHsfs in the same class shared similar gene structures and conserved motifs. The chromosomal location analysis showed that 27 Hsfs were located in 10 of 12 chromosomes (except chromosome 1 and chromosome 5) and that 18 of these genes formed 9 paralogous pairs. Expression profiles of StHsfs in 12 different organs and tissues uncovered distinct spatial expression patterns of these genes and their potential roles in the process of growth and development. Promoter and quantitative real-time polymerase chain reaction (qRT-PCR) detections of StHsfs were conducted and demonstrated that these genes were all responsive to various stresses. StHsf004, StHsf007, StHsf009, StHsf014, and StHsf019 were constitutively expressed under non-stress conditions, and some specific Hsfs became the predominant Hsfs in response to different abiotic stresses, indicating their important and diverse regulatory roles in adverse conditions. A co-expression network between StHsfs and StHsf -co-expressed genes was generated based on the publicly-available potato transcriptomic databases and identified key candidate StHsfs for further functional studies.

No MeSH data available.


Related in: MedlinePlus