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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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Expression profiles of 35 expressed Gmcupin genes in different tissues.a. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes among various tissues analyzed. b. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes during the development of soybean seeds.
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pone-0110092-g005: Expression profiles of 35 expressed Gmcupin genes in different tissues.a. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes among various tissues analyzed. b. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes during the development of soybean seeds.

Mentions: To highlight the expression profiles of Gmcupin genes, we then analyzed the previously publicly-available RNA-Seq data regarding seven soybean tissues, three pod development stages and seven seed developmental stages. Thirty-five Gmcupin genes had sequence reads in at least one tissue, and most of them showed a distinct tissue-specific expression pattern (Figure 4). For example, two genes (Gmcupin17.1 and Gmcupin15.3) had a significantly higher transcript accumulation in the young leaf of soybean. Gmcupin16.8 was mainly expressed during pod development, while Gmcupin16.5, Gmcupin03.2 and Gmcupin20.4 were specifically expressed in soybean root. Besides, three genes (Gmcupin03.1, Gmcupin13.2 and Gmcupin19.13) of subfamily X were highly expressed at the later stage of seed development. Most Gmcupin genes showed a relative low expression level in soybean nodule (Figure 4). These genes were clustered into five groups (A–E) and four groups (I–IV) based on their expression patterns in soybean tissues (excet seeds) and the expression profiles during seven soybean seed development stages (Figure 5). The genes in clusters A–E were mainly expressed in flower/root, root, pod/root, young leaf and pod, respectively. Six genes in cluster I mainly expressed during the early stage of soybean seed development, while seven genes in cluster II and III mainly expressed during the later stage of soybean seed development. In addition, three genes in cluster III having a much higher and specific expression level during soybean seed development from 25 days after flower (DAF) to 42DAF. Further, genes of cluster IV were expressed in most stages of soybean seed development.


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)

Expression profiles of 35 expressed Gmcupin genes in different tissues.a. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes among various tissues analyzed. b. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes during the development of soybean seeds.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110092-g005: Expression profiles of 35 expressed Gmcupin genes in different tissues.a. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes among various tissues analyzed. b. Heatmap showing hierarchical clustering of 35 expressed Gmcupin genes during the development of soybean seeds.
Mentions: To highlight the expression profiles of Gmcupin genes, we then analyzed the previously publicly-available RNA-Seq data regarding seven soybean tissues, three pod development stages and seven seed developmental stages. Thirty-five Gmcupin genes had sequence reads in at least one tissue, and most of them showed a distinct tissue-specific expression pattern (Figure 4). For example, two genes (Gmcupin17.1 and Gmcupin15.3) had a significantly higher transcript accumulation in the young leaf of soybean. Gmcupin16.8 was mainly expressed during pod development, while Gmcupin16.5, Gmcupin03.2 and Gmcupin20.4 were specifically expressed in soybean root. Besides, three genes (Gmcupin03.1, Gmcupin13.2 and Gmcupin19.13) of subfamily X were highly expressed at the later stage of seed development. Most Gmcupin genes showed a relative low expression level in soybean nodule (Figure 4). These genes were clustered into five groups (A–E) and four groups (I–IV) based on their expression patterns in soybean tissues (excet seeds) and the expression profiles during seven soybean seed development stages (Figure 5). The genes in clusters A–E were mainly expressed in flower/root, root, pod/root, young leaf and pod, respectively. Six genes in cluster I mainly expressed during the early stage of soybean seed development, while seven genes in cluster II and III mainly expressed during the later stage of soybean seed development. In addition, three genes in cluster III having a much higher and specific expression level during soybean seed development from 25 days after flower (DAF) to 42DAF. Further, genes of cluster IV were expressed in most stages of soybean seed development.

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