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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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Phylogenetic relationships and gene structure of Gmcupin genes.The phylogenetic tree of Gmcupin proteins constructed from a complete alignment of 69 Gmcupin proteins using MEGA 5.0 by the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Percentage bootstrap scores of>50% are indicated on the nodes. Ten major phylogenetic subgroups (designated as I to X) are indicated. Exons of Gmcupin genes are represented by green boxes and introns and untranslated region (UTR) by black and blue lines. The sizes of exons and introns can be estimated using the scale below.
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pone-0110092-g002: Phylogenetic relationships and gene structure of Gmcupin genes.The phylogenetic tree of Gmcupin proteins constructed from a complete alignment of 69 Gmcupin proteins using MEGA 5.0 by the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Percentage bootstrap scores of>50% are indicated on the nodes. Ten major phylogenetic subgroups (designated as I to X) are indicated. Exons of Gmcupin genes are represented by green boxes and introns and untranslated region (UTR) by black and blue lines. The sizes of exons and introns can be estimated using the scale below.

Mentions: The abundance of Gmcupin genes may derive from multiple gene duplication events, which was represented by a whole-genome duplication following multiple segmental and tandem duplications [44]. In this study, an unrooted tree was constructed to examine the phylogenetic relationships among the Cupin domains using alignments of the full-length amino-acid sequences in all Gmcupin proteins (Figure 2). The Gmcupin gene family was classified into ten subgroups (I-X) with 2-22 members in each subgroup. The very high bootstrap value in each subgroup suggested a common origin for the Gmcupin gene in each group except subgroup I. Surprisingly, 12 Gmcupin genes (80%) on chromosome 19 were classified into subgroup I with five genes (Gmcupin19.2, Gmcupin19.3, Gmcupin19.4, Gmcupin19.5 and Gmcupin19.6) showed the same base composition. Phylogenetic tree topology revealed that 22 Gmcupin pairs located at the terminal nodes shared high similarities. Thus, they were assigned as paralogous pairs (homologous genes that diverged by gene duplication, Figure 2). These paralogous pairs of Gmcupin genes, accounted for more than 63% of the entire Gmcupin family, and showed a sequence similarity of 77.2%∼100% (Table S1). This implied that these genes may evolve from a recent soybean genome duplication event [45].


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)

Phylogenetic relationships and gene structure of Gmcupin genes.The phylogenetic tree of Gmcupin proteins constructed from a complete alignment of 69 Gmcupin proteins using MEGA 5.0 by the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Percentage bootstrap scores of>50% are indicated on the nodes. Ten major phylogenetic subgroups (designated as I to X) are indicated. Exons of Gmcupin genes are represented by green boxes and introns and untranslated region (UTR) by black and blue lines. The sizes of exons and introns can be estimated using the scale below.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110092-g002: Phylogenetic relationships and gene structure of Gmcupin genes.The phylogenetic tree of Gmcupin proteins constructed from a complete alignment of 69 Gmcupin proteins using MEGA 5.0 by the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the taxa analyzed. Percentage bootstrap scores of>50% are indicated on the nodes. Ten major phylogenetic subgroups (designated as I to X) are indicated. Exons of Gmcupin genes are represented by green boxes and introns and untranslated region (UTR) by black and blue lines. The sizes of exons and introns can be estimated using the scale below.
Mentions: The abundance of Gmcupin genes may derive from multiple gene duplication events, which was represented by a whole-genome duplication following multiple segmental and tandem duplications [44]. In this study, an unrooted tree was constructed to examine the phylogenetic relationships among the Cupin domains using alignments of the full-length amino-acid sequences in all Gmcupin proteins (Figure 2). The Gmcupin gene family was classified into ten subgroups (I-X) with 2-22 members in each subgroup. The very high bootstrap value in each subgroup suggested a common origin for the Gmcupin gene in each group except subgroup I. Surprisingly, 12 Gmcupin genes (80%) on chromosome 19 were classified into subgroup I with five genes (Gmcupin19.2, Gmcupin19.3, Gmcupin19.4, Gmcupin19.5 and Gmcupin19.6) showed the same base composition. Phylogenetic tree topology revealed that 22 Gmcupin pairs located at the terminal nodes shared high similarities. Thus, they were assigned as paralogous pairs (homologous genes that diverged by gene duplication, Figure 2). These paralogous pairs of Gmcupin genes, accounted for more than 63% of the entire Gmcupin family, and showed a sequence similarity of 77.2%∼100% (Table S1). This implied that these genes may evolve from a recent soybean genome duplication event [45].

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
Related in: MedlinePlus