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Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.).

Zhang L, Zhao HK, Dong QL, Zhang YY, Wang YM, Li HY, Xing GJ, Li QY, Dong YS - Front Plant Sci (2015)

Bottom Line: Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity.The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress.These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

View Article: PubMed Central - PubMed

Affiliation: Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences Changchun, China.

ABSTRACT
Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic relationships and gene structure of soybean HSP70 genes. (A) The unrooted tree was generated with the MEGA5.0 program using the full-length amino acid sequences of the 61 soybean HSP70 proteins by the Neighbor-Joining (NJ) method, with 1000 bootstrap replicates. Subfamilies of HSP70 genes (I–VIII) are highlighted with different colored backgrounds and vertical bars next to the gene names of the tree. (B) Exon/intron organization of soybean HSP70 genes. Green boxes represent exons and black lines represent introns. The untranslated regions (UTRs) are indicated by blue boxes. The numbers 0, 1, and 2 represents the splicing phases. The sizes of exons and introns can be estimated using the scale at the bottom.
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Figure 1: Phylogenetic relationships and gene structure of soybean HSP70 genes. (A) The unrooted tree was generated with the MEGA5.0 program using the full-length amino acid sequences of the 61 soybean HSP70 proteins by the Neighbor-Joining (NJ) method, with 1000 bootstrap replicates. Subfamilies of HSP70 genes (I–VIII) are highlighted with different colored backgrounds and vertical bars next to the gene names of the tree. (B) Exon/intron organization of soybean HSP70 genes. Green boxes represent exons and black lines represent introns. The untranslated regions (UTRs) are indicated by blue boxes. The numbers 0, 1, and 2 represents the splicing phases. The sizes of exons and introns can be estimated using the scale at the bottom.

Mentions: Based on the unrooted phylogenetic tree of the 61 GmHSP70 protein sequences, the soybean HSP70 gene family was categorized into eight major sub-families (sub-family I, II, III, IV, V, VI, VII, and VIII). Sub-family I (containing 29 members) was the largest group, followed by sub-family VIII (12), sub-family VII (7), sub-family III (6), and sub-family II (4). The sub-families IV, V, VI were the smallest, with only one GmHSP70 gene member each (Figure 1A). Correspondingly, Figure 1B provides a detailed illustration of the relative lengths of the introns, and the conservation of the corresponding exon sequences within each HSP70 gene within the soybean. The number of introns in all of these genes ranged from 0 to 13. However, no intron was found in the Glyma13g19330, Glyma02g36700, Glyma17g08020, Glyma18g52470, Glyma18g52471, Glyma11g31670, Glyma07g32921, or Glyma01g44910, whereas 13 introns were found in the Glyma20g16070, Glyma03g03250, Glyma11g31810, and Glyma18g05480. The MEME of the total 61 GmHSP70 genes were also analyzed (Figure 2). The results revealed the conserved domains or motifs shared among related proteins, and identified 15 conserved motifs (Additional Files 7 and 8). The type, order, and number of motifs were similar in proteins with the same sub-family, but differed from the proteins in other sub-families.


Genome-wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.).

Zhang L, Zhao HK, Dong QL, Zhang YY, Wang YM, Li HY, Xing GJ, Li QY, Dong YS - Front Plant Sci (2015)

Phylogenetic relationships and gene structure of soybean HSP70 genes. (A) The unrooted tree was generated with the MEGA5.0 program using the full-length amino acid sequences of the 61 soybean HSP70 proteins by the Neighbor-Joining (NJ) method, with 1000 bootstrap replicates. Subfamilies of HSP70 genes (I–VIII) are highlighted with different colored backgrounds and vertical bars next to the gene names of the tree. (B) Exon/intron organization of soybean HSP70 genes. Green boxes represent exons and black lines represent introns. The untranslated regions (UTRs) are indicated by blue boxes. The numbers 0, 1, and 2 represents the splicing phases. The sizes of exons and introns can be estimated using the scale at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585176&req=5

Figure 1: Phylogenetic relationships and gene structure of soybean HSP70 genes. (A) The unrooted tree was generated with the MEGA5.0 program using the full-length amino acid sequences of the 61 soybean HSP70 proteins by the Neighbor-Joining (NJ) method, with 1000 bootstrap replicates. Subfamilies of HSP70 genes (I–VIII) are highlighted with different colored backgrounds and vertical bars next to the gene names of the tree. (B) Exon/intron organization of soybean HSP70 genes. Green boxes represent exons and black lines represent introns. The untranslated regions (UTRs) are indicated by blue boxes. The numbers 0, 1, and 2 represents the splicing phases. The sizes of exons and introns can be estimated using the scale at the bottom.
Mentions: Based on the unrooted phylogenetic tree of the 61 GmHSP70 protein sequences, the soybean HSP70 gene family was categorized into eight major sub-families (sub-family I, II, III, IV, V, VI, VII, and VIII). Sub-family I (containing 29 members) was the largest group, followed by sub-family VIII (12), sub-family VII (7), sub-family III (6), and sub-family II (4). The sub-families IV, V, VI were the smallest, with only one GmHSP70 gene member each (Figure 1A). Correspondingly, Figure 1B provides a detailed illustration of the relative lengths of the introns, and the conservation of the corresponding exon sequences within each HSP70 gene within the soybean. The number of introns in all of these genes ranged from 0 to 13. However, no intron was found in the Glyma13g19330, Glyma02g36700, Glyma17g08020, Glyma18g52470, Glyma18g52471, Glyma11g31670, Glyma07g32921, or Glyma01g44910, whereas 13 introns were found in the Glyma20g16070, Glyma03g03250, Glyma11g31810, and Glyma18g05480. The MEME of the total 61 GmHSP70 genes were also analyzed (Figure 2). The results revealed the conserved domains or motifs shared among related proteins, and identified 15 conserved motifs (Additional Files 7 and 8). The type, order, and number of motifs were similar in proteins with the same sub-family, but differed from the proteins in other sub-families.

Bottom Line: Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity.The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress.These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

View Article: PubMed Central - PubMed

Affiliation: Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences Changchun, China.

ABSTRACT
Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development.

No MeSH data available.


Related in: MedlinePlus