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A comprehensive analysis of the Cupin gene family in soybean (Glycine max).

Wang X, Zhang H, Gao Y, Sun G, Zhang W, Qiu L - PLoS ONE (2014)

Bottom Line: The distributions of GmCupin genes implied that long segmental duplications contributed significantly to the expansion of the GmCupin gene family.Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen Gmcupins had selected site(s), with all SNPs in Gmcupin10.3 and Gmcupin07.2 genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication.Taken together, our results contribute to the functional characterization of Gmcupin genes in soybean.

View Article: PubMed Central - PubMed

Affiliation: School of Agronomy, Anhui Agricultural University, Hefei, China.

ABSTRACT
Cupin superfamily of proteins, including germin and germin-like proteins (GLPs) from higher plants, is known to play crucial roles in plant development and defense. To date, no systematic analysis has been conducted in soybean (Glycine max) incorporating genome organization, gene structure, expression compendium. In this study, 69 putative Cupin genes were identified from the whole-genome of soybean, which were non-randomly distributed on 17 of the 20 chromosomes. These Gmcupin proteins were phylogenetically clustered into ten distinct subgroups among which the gene structures were highly conserved. Eighteen pairs (52.2%) of duplicate paralogous genes were preferentially retained in duplicated regions of the soybean genome. The distributions of GmCupin genes implied that long segmental duplications contributed significantly to the expansion of the GmCupin gene family. According to the RNA-seq data analysis, most of the Gmcupins were differentially expressed in tissue-specific expression pattern and the expression of some duplicate genes were partially redundant while others showed functional diversity, suggesting the Gmcupins have been retained by substantial subfunctionalization during soybean evolutionary processes. Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen Gmcupins had selected site(s), with all SNPs in Gmcupin10.3 and Gmcupin07.2 genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication. Taken together, our results contribute to the functional characterization of Gmcupin genes in soybean.

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Conserved domains across cupin proteins in soybean.The sequence logos are based on alignments of 69 Gmcupin domains. Multiple alignment analysis of all typical Gmcupin domains (A: Gmcuppin 1; B: Gmcupin 2) were performed with Clustal W. The bit score indicates the information content for each position in the sequence.
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pone-0110092-g001: Conserved domains across cupin proteins in soybean.The sequence logos are based on alignments of 69 Gmcupin domains. Multiple alignment analysis of all typical Gmcupin domains (A: Gmcuppin 1; B: Gmcupin 2) were performed with Clustal W. The bit score indicates the information content for each position in the sequence.

Mentions: Multiple alignment analysis was performed to discover the features of the homologous domain sequence and the frequency of the amino-acids at each position of the Gmcupin domains. Multiple EM for Motif Elicitation was used to identify the putative cupin motif. Two conserved domains, designated as Gmcupin 1 and Gmcupin 2, were found in these Gmcupins, and were formed by 59 amino acids and 52 amino acids, respectively. In Gmcupin 1, seven highly conserved residues were identified, including H-34, H-36, P-37, E-41, Gly-48, Gly-53 and F-54. In Gmcupin 2, four conserved residues were identified such as Gly-8, P-14, H-19 and N-23 (Figure 1). In the previous reports, the histidines and glutamic acid(s) have been reported to act as ligands for the active-site metal [18], [19], [41]. Additionally, studies showed that a set of conserved histidine residues employed in sugar-binding in the ancestral non-enzymatic domain evolved into the metal-coordinating histidine residues in oxalate oxidase [42] and oxalate decarboxylase [43].


A comprehensive analysis of the Cupin gene family in soybean (Glycine max).

Wang X, Zhang H, Gao Y, Sun G, Zhang W, Qiu L - PLoS ONE (2014)

Conserved domains across cupin proteins in soybean.The sequence logos are based on alignments of 69 Gmcupin domains. Multiple alignment analysis of all typical Gmcupin domains (A: Gmcuppin 1; B: Gmcupin 2) were performed with Clustal W. The bit score indicates the information content for each position in the sequence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4215997&req=5

pone-0110092-g001: Conserved domains across cupin proteins in soybean.The sequence logos are based on alignments of 69 Gmcupin domains. Multiple alignment analysis of all typical Gmcupin domains (A: Gmcuppin 1; B: Gmcupin 2) were performed with Clustal W. The bit score indicates the information content for each position in the sequence.
Mentions: Multiple alignment analysis was performed to discover the features of the homologous domain sequence and the frequency of the amino-acids at each position of the Gmcupin domains. Multiple EM for Motif Elicitation was used to identify the putative cupin motif. Two conserved domains, designated as Gmcupin 1 and Gmcupin 2, were found in these Gmcupins, and were formed by 59 amino acids and 52 amino acids, respectively. In Gmcupin 1, seven highly conserved residues were identified, including H-34, H-36, P-37, E-41, Gly-48, Gly-53 and F-54. In Gmcupin 2, four conserved residues were identified such as Gly-8, P-14, H-19 and N-23 (Figure 1). In the previous reports, the histidines and glutamic acid(s) have been reported to act as ligands for the active-site metal [18], [19], [41]. Additionally, studies showed that a set of conserved histidine residues employed in sugar-binding in the ancestral non-enzymatic domain evolved into the metal-coordinating histidine residues in oxalate oxidase [42] and oxalate decarboxylase [43].

Bottom Line: The distributions of GmCupin genes implied that long segmental duplications contributed significantly to the expansion of the GmCupin gene family.Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen Gmcupins had selected site(s), with all SNPs in Gmcupin10.3 and Gmcupin07.2 genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication.Taken together, our results contribute to the functional characterization of Gmcupin genes in soybean.

View Article: PubMed Central - PubMed

Affiliation: School of Agronomy, Anhui Agricultural University, Hefei, China.

ABSTRACT
Cupin superfamily of proteins, including germin and germin-like proteins (GLPs) from higher plants, is known to play crucial roles in plant development and defense. To date, no systematic analysis has been conducted in soybean (Glycine max) incorporating genome organization, gene structure, expression compendium. In this study, 69 putative Cupin genes were identified from the whole-genome of soybean, which were non-randomly distributed on 17 of the 20 chromosomes. These Gmcupin proteins were phylogenetically clustered into ten distinct subgroups among which the gene structures were highly conserved. Eighteen pairs (52.2%) of duplicate paralogous genes were preferentially retained in duplicated regions of the soybean genome. The distributions of GmCupin genes implied that long segmental duplications contributed significantly to the expansion of the GmCupin gene family. According to the RNA-seq data analysis, most of the Gmcupins were differentially expressed in tissue-specific expression pattern and the expression of some duplicate genes were partially redundant while others showed functional diversity, suggesting the Gmcupins have been retained by substantial subfunctionalization during soybean evolutionary processes. Selective analysis based on single nucleotide polymorphisms (SNPs) in cultivated and wild soybeans revealed sixteen Gmcupins had selected site(s), with all SNPs in Gmcupin10.3 and Gmcupin07.2 genes were selected sites, which implied these genes may have undergone strong selection effects during soybean domestication. Taken together, our results contribute to the functional characterization of Gmcupin genes in soybean.

Show MeSH