A Comprehensive Analysis of the Cupin Gene Family in Soybean (<i>Glycine max</i>)

<div><p>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 (<i>Glycine max</i>) incorporating genome organization, gene structure, expression compendium. In this study, 69 putative <i>Cupin</i> 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 <i>GmCupin</i> genes implied that long segmental duplications contributed significantly to the expansion of the <i>GmCupin</i> gene family. According to the RNA-seq data analysis, most of the <i>Gmcupins</i> 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 <i>Gmcupins</i> 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 <i>Gmcupins</i> had selected site(s), with all SNPs in <i>Gmcupin10.3</i> and <i>Gmcupin07.2</i> 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 <i>Gmcupin</i> genes in soybean.</p>