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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

Evolutionary relationships (A), gene structures (B) and functional motifs (C) of StHsfs. (A) The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining method with 1000 bootstrap replicates. Subtrees branch lines in different colors represent different Hsf classes. (B) The exon/intron distribution of corresponding StHsf genes was detected by comparing these predicted coding sequences (CDS) with their corresponding genomic sequences using GSDS online (http://gsds.cbi.pku.edu.cn). The green boxes represent CDS; the blue boxes indicate upstream or downstream; the discontinuous lines refer to introns of these genes. (C) The motif composition related to each StHsf protein is displayed on the right-hand side. The motifs, numbered 1–20, are displayed in different colored boxes. The sequence information for each motif is presented in Table 3.
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Figure 3: Evolutionary relationships (A), gene structures (B) and functional motifs (C) of StHsfs. (A) The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining method with 1000 bootstrap replicates. Subtrees branch lines in different colors represent different Hsf classes. (B) The exon/intron distribution of corresponding StHsf genes was detected by comparing these predicted coding sequences (CDS) with their corresponding genomic sequences using GSDS online (http://gsds.cbi.pku.edu.cn). The green boxes represent CDS; the blue boxes indicate upstream or downstream; the discontinuous lines refer to introns of these genes. (C) The motif composition related to each StHsf protein is displayed on the right-hand side. The motifs, numbered 1–20, are displayed in different colored boxes. The sequence information for each motif is presented in Table 3.

Mentions: All of the 27 StHsfs were single copy genes. According to the phylogenetic tree of deduced StHsf sequences (Figure 3A), we linked the paralogous pairs of StHsfs, and found a total of 9 pairs of paralogous StHsfs: StHsf001/StHsf003, StHsf006/StHsf008, StHsf004/StHsf018, StHsf010/StHsf011, StHsf012/StHsf013, StHsf015/StHsf016, StHsf020/StHsf021, StHsf022/StHsf023, and StHsf024/StHsf025 (Figure 2). Tandem duplications of paralogous genes, defined as two paralogs separated by less than five average-gene-length in the same chromosome, have been suggested to be the main cause for gene family expansion in plants (Yuan et al., 2015). With that definition, StHsf012 and StHsf013 on chromosome 9 (location: 48.449647Mb/48.466395Mb) was found to be a pair of tandem duplications. A chromosome region containing two or more genes within 200 kb can be defined as a gene cluster (Holub, 2001; Zhang et al., 2015). Therefore, StHsf012 and StHsf013 also belong to a gene cluster.


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)

Evolutionary relationships (A), gene structures (B) and functional motifs (C) of StHsfs. (A) The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining method with 1000 bootstrap replicates. Subtrees branch lines in different colors represent different Hsf classes. (B) The exon/intron distribution of corresponding StHsf genes was detected by comparing these predicted coding sequences (CDS) with their corresponding genomic sequences using GSDS online (http://gsds.cbi.pku.edu.cn). The green boxes represent CDS; the blue boxes indicate upstream or downstream; the discontinuous lines refer to introns of these genes. (C) The motif composition related to each StHsf protein is displayed on the right-hand side. The motifs, numbered 1–20, are displayed in different colored boxes. The sequence information for each motif is presented in Table 3.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Evolutionary relationships (A), gene structures (B) and functional motifs (C) of StHsfs. (A) The phylogenetic tree was constructed by Clustal X 2.1 and MEGA 4.0 software using the neighbour-joining method with 1000 bootstrap replicates. Subtrees branch lines in different colors represent different Hsf classes. (B) The exon/intron distribution of corresponding StHsf genes was detected by comparing these predicted coding sequences (CDS) with their corresponding genomic sequences using GSDS online (http://gsds.cbi.pku.edu.cn). The green boxes represent CDS; the blue boxes indicate upstream or downstream; the discontinuous lines refer to introns of these genes. (C) The motif composition related to each StHsf protein is displayed on the right-hand side. The motifs, numbered 1–20, are displayed in different colored boxes. The sequence information for each motif is presented in Table 3.
Mentions: All of the 27 StHsfs were single copy genes. According to the phylogenetic tree of deduced StHsf sequences (Figure 3A), we linked the paralogous pairs of StHsfs, and found a total of 9 pairs of paralogous StHsfs: StHsf001/StHsf003, StHsf006/StHsf008, StHsf004/StHsf018, StHsf010/StHsf011, StHsf012/StHsf013, StHsf015/StHsf016, StHsf020/StHsf021, StHsf022/StHsf023, and StHsf024/StHsf025 (Figure 2). Tandem duplications of paralogous genes, defined as two paralogs separated by less than five average-gene-length in the same chromosome, have been suggested to be the main cause for gene family expansion in plants (Yuan et al., 2015). With that definition, StHsf012 and StHsf013 on chromosome 9 (location: 48.449647Mb/48.466395Mb) was found to be a pair of tandem duplications. A chromosome region containing two or more genes within 200 kb can be defined as a gene cluster (Holub, 2001; Zhang et al., 2015). Therefore, StHsf012 and StHsf013 also belong to a gene cluster.

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