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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

The number of StHsf-co-expressed genes in each co-expression module. The modules are numbered according to the gene numbers. StHsf genes involved in the corresponding module are placed at the top of each column.
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Figure 7: The number of StHsf-co-expressed genes in each co-expression module. The modules are numbered according to the gene numbers. StHsf genes involved in the corresponding module are placed at the top of each column.

Mentions: In order to delve into the potential regulatory relationship between StHsfs and their related genes, a co-expression network was constructed using WGCNA according to the RNAseq data. As shown in Figure 7, 15 modules containing different StHsfs and their co-expressed genes were formed based on the correlation of biological function among genes. Some StHsfs (StHsf002, StHsf003, StHsf006, StHsf014, StHsf015, StHsf016, StHsf017, StHsf018, and StHsf025) were not shown in Figure 7 because of their low expression levels in RNAseq data. Module 1, which contained StHsf005 and other 642 related gene members, was the largest module among the 15 modules; while module 15, containing only 10 genes, was the smallest module (Figure 7). Because module 1 contained more genes than other modules, we hypothesize that module 1 is involved in more biological functions than other modules.


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)

The number of StHsf-co-expressed genes in each co-expression module. The modules are numbered according to the gene numbers. StHsf genes involved in the corresponding module are placed at the top of each column.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: The number of StHsf-co-expressed genes in each co-expression module. The modules are numbered according to the gene numbers. StHsf genes involved in the corresponding module are placed at the top of each column.
Mentions: In order to delve into the potential regulatory relationship between StHsfs and their related genes, a co-expression network was constructed using WGCNA according to the RNAseq data. As shown in Figure 7, 15 modules containing different StHsfs and their co-expressed genes were formed based on the correlation of biological function among genes. Some StHsfs (StHsf002, StHsf003, StHsf006, StHsf014, StHsf015, StHsf016, StHsf017, StHsf018, and StHsf025) were not shown in Figure 7 because of their low expression levels in RNAseq data. Module 1, which contained StHsf005 and other 642 related gene members, was the largest module among the 15 modules; while module 15, containing only 10 genes, was the smallest module (Figure 7). Because module 1 contained more genes than other modules, we hypothesize that module 1 is involved in more biological functions than other modules.

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