Genome-wide analysis of the GRAS gene family exhibited expansion model and functional differentiation in sea buckthorn (Hippophae rhamnoides L.)

Key message Genome-wide identification of the sea buckthorn GRAS genes and their transcription profiles in different organizations. 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. Sea buckthorn is a unique and valuable plant which has tremendous value for medical researching, ecological protection, and providing daily necessities. We identified, characterized, and distinguished duplication models of GRAS transcription factors in sea buckthorn. A systematic whole-genome analysis was performed to identify and characterize the GRAS gene family of sea buckthorn, especially the comparative genome method was used to demonstrate its different duplication models. We identified 62 sea buckthorn GRAS (HrGRAS) genes and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were 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. Segmental duplication was the main driver of the GRAS gene family expansion, followed by whole-genome duplication (WGD) and tandem duplication, according to the results of comparative genome analysis. GRAS genes involved in duplication experienced strong purifying selection pressure according to the Ka/Ks ratios. The expression profile derived from transcriptome data shows the expression patterns of HrGRAS gene in different tissues and the characterization of differentially expressed genes. This systematic analysis provided a foundation to understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.