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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 Neighbor-Joining phylogenetic tree of Hsf proteins from potato, Arabidopsis, tomato, cucumber and soybean. The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining option with 1000 bootstrap replicates. Branch lines in different colors represented different subgroups.
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Figure 1: The Neighbor-Joining phylogenetic tree of Hsf proteins from potato, Arabidopsis, tomato, cucumber and soybean. The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining option with 1000 bootstrap replicates. Branch lines in different colors represented different subgroups.

Mentions: The phylogenetic analysis of potato helped to classify these Hsf members into several subclasses in comparison with the classification scheme of other species which have a close phylogenetic relationship with potato (Figure 1). One small branch marked with an asterisk was unique in potato and classified them into StHsfA8* members because they have high similarity with other members of A8 subclass (Figure 1 and Table 1). In potato, class A and B members were further divided into A1–A9 and B1–B5 subgroups, respectively. Among these subgroups, HsfA1, HsfA4, HsfA6, HsfA7, HsfA8, HsfB2, HsfB3, and HsfB4 were each composed of more than two members; while class C and other subclasses each contained only one member (Figure 1 and Table 1).


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 Neighbor-Joining phylogenetic tree of Hsf proteins from potato, Arabidopsis, tomato, cucumber and soybean. The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining option with 1000 bootstrap replicates. Branch lines in different colors represented different subgroups.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: The Neighbor-Joining phylogenetic tree of Hsf proteins from potato, Arabidopsis, tomato, cucumber and soybean. The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining option with 1000 bootstrap replicates. Branch lines in different colors represented different subgroups.
Mentions: The phylogenetic analysis of potato helped to classify these Hsf members into several subclasses in comparison with the classification scheme of other species which have a close phylogenetic relationship with potato (Figure 1). One small branch marked with an asterisk was unique in potato and classified them into StHsfA8* members because they have high similarity with other members of A8 subclass (Figure 1 and Table 1). In potato, class A and B members were further divided into A1–A9 and B1–B5 subgroups, respectively. Among these subgroups, HsfA1, HsfA4, HsfA6, HsfA7, HsfA8, HsfB2, HsfB3, and HsfB4 were each composed of more than two members; while class C and other subclasses each contained only one member (Figure 1 and Table 1).

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