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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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Chromosomal locations and predicted clusters for Gmcupin genes.The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). The chromosomal positions of all Gmcupin genes were mapped on each chromosome. Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale. The locations of centromeric repeats are shown as black rectangles over the chromosomes.
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pone-0110092-g003: Chromosomal locations and predicted clusters for Gmcupin genes.The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). The chromosomal positions of all Gmcupin genes were mapped on each chromosome. Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale. The locations of centromeric repeats are shown as black rectangles over the chromosomes.

Mentions: As revealed in Figure 3, Gmcupin genes were non-randomly distributed on 17 of the 20 chromosomes. Fifteen Cupin genes were localized on chromosome 19, while eleveen genes were localized on chromosome 16. In contrast, no more than two Gmcupins genes were localized on eleven chromsomes. What's more, no Cupin genes were distributed on chromosome 11, 14 and 18, respectively. Most Gmcupins presented substantial clustering on several chromosomes especially on those with high densities of the genes. To be exact, 10 Gmcupin genes on chromosome 16 were arranged in four clusters, with each in less than 9-kb (Gmcupin16.1, Gmcupin16.2, and Gmcupin16.3 located within 8.5-kb; Gmcupin16.4, Gmcupin16.5 and Gmcupin16.6 located within 8.8-kb; Gmcupin16.7 and Gmcupin16.8 located within 5.3-kb; Gmcupin16.9 and Gmcupin16.10 located within 5-kb), the other Gmcupin gene Gmcupin16.11 is also close to its neighbor Gmcupin16.10 within a 1.7-kb segment. Similarly, Gmcupin19.7 and Gmcupin19.8 located within a 4.5-kb segment, while Gmcupin19.10 and Gmcupin19.11 located within a 19-kb segment on the same chromosome.


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)

Chromosomal locations and predicted clusters for Gmcupin genes.The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). The chromosomal positions of all Gmcupin genes were mapped on each chromosome. Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale. The locations of centromeric repeats are shown as black rectangles over the chromosomes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110092-g003: Chromosomal locations and predicted clusters for Gmcupin genes.The schematic diagram of genome-wide chromosome organization and segmental duplication arising from the genome duplication event in soybean was derived from the CViT genome search and synteny viewer at the Legume Information System (http://comparative-legumes.org). The chromosomal positions of all Gmcupin genes were mapped on each chromosome. Colored blocks to the left of each chromosome show duplications with chromosomes of the same color. The chromosome numbers are indicated at the top of each bar and sizes of chromosomes are represented by the vertical scale. The locations of centromeric repeats are shown as black rectangles over the chromosomes.
Mentions: As revealed in Figure 3, Gmcupin genes were non-randomly distributed on 17 of the 20 chromosomes. Fifteen Cupin genes were localized on chromosome 19, while eleveen genes were localized on chromosome 16. In contrast, no more than two Gmcupins genes were localized on eleven chromsomes. What's more, no Cupin genes were distributed on chromosome 11, 14 and 18, respectively. Most Gmcupins presented substantial clustering on several chromosomes especially on those with high densities of the genes. To be exact, 10 Gmcupin genes on chromosome 16 were arranged in four clusters, with each in less than 9-kb (Gmcupin16.1, Gmcupin16.2, and Gmcupin16.3 located within 8.5-kb; Gmcupin16.4, Gmcupin16.5 and Gmcupin16.6 located within 8.8-kb; Gmcupin16.7 and Gmcupin16.8 located within 5.3-kb; Gmcupin16.9 and Gmcupin16.10 located within 5-kb), the other Gmcupin gene Gmcupin16.11 is also close to its neighbor Gmcupin16.10 within a 1.7-kb segment. Similarly, Gmcupin19.7 and Gmcupin19.8 located within a 4.5-kb segment, while Gmcupin19.10 and Gmcupin19.11 located within a 19-kb segment on the same chromosome.

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