Genome-Wide Analysis of the GRAS Gene Family Exhibited Expansion Model and Functional Differentiation in Sea Buckthorn

Abstract

Background: GRAS proteins comprise a large family of transcription factors that experienced extensive replication, and play important roles in many aspects of growth regulatory and environmental signals. However, limited information was available about the GRAS genes in sea buckthorn of Elaeagnaceae. We perform a genome-wide investigation into the expansion model and tissue expression profiling of sea buckthorn GRAS genes based on the comparative genomes methods.Results: In this study, 62 sea buckthorn GRAS (HrGRAS) genes were identified and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were further classified into nine subgroups and three HrGRASs did not belong to any of the subfamilies according to their phylogenetic features. HrGRAS genes tend to have a representative GRAS domain, few introns and unevenly distributed on chromosomes. Collinear homology dotplot and the median synonymous substitution sites of collinearity blocks distinguished gene pairs with different duplication models and found that segmental duplication was the main driver of the GRAS gene family expansion in sea buckthorn, followed by whole genome duplication and tandem duplication. The all gene pairs from the different duplication models may experience strong purifying selection pressure during evolution processes according to the Ka/Ks ratios. Expression profiles derived from transcriptome data exhibited distinct expression patterns of HrGRAS genes in various tissues and fruit developmental stages. The interaction network analysis of HrGRAS protein found that some HrGRAS proteins interacted with more proteins and retained more copies in sea buckthorn, which indicate that the products of these genes play more important roles in the growth and development of sea buckthorn.Conclusions: Sea buckthorn GRAS gene family was first comprehensively analyzed in this study. This systematic analysis provided a foundation to further understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.