Genome-Wide characterization and expression in analysis of PRR gene family in Glycine max and Glycine soja

Abstract Background The genes in the PRR family are key components of the transcription-translation circadian network in plants, and comprise the core genes in the central oscillator translation feedback loop of Arabidopsis sp. They play important roles in several physiological processes and environmental adaptation. However, there is little information regarding the PRR genes of soybean, which is an important food crop. A genome-wide study of the PRR genes of soybean was performed herein using the available complete genome sequences of Glycine max and Glycine soja. Results In total, 12 PRR genes of G. max (GmPRR) and 14 PRR genes of G. soja (GsPRR) were identified and labelled according to their chromosomal location. The sequence length, relative molecular weight, and subcellular localization of the encoded proteins were predicted, and fundamental information was obtained for the genes. GmPRR and GsPRR were further categorized into three main groups based on their phylogenetic characteristics. The gene structures and characteristics of protein motifs were similar in the same subfamily. Conserved domain analyses of the proteins revealed that the integrity of the conserved domains differed among proteins from different subfamilies. GmPRR genes were absent on chromosomes 11 and 12, contrary to GsPRR genes. The results indicated that fragment replication events played an important role in the amplification of GmPRR and GsPRR genes. Intergenomic collinearity analysis of G. max, G. soja, and A. sp. revealed that the PRR genes of soybean and A. sp. were highly homologous. Analysis of transcriptome data revealed that the expression patterns of GmPRR genes differed at different times. Quantitative polymerase chain reaction (qPCR) analyses determined the relative transcript abundances of the different GmPRR and GsPRR varied across the studied plant materials. Conclusions In this study, 12 PRR genes of G. max (GmPRR) and 14 PRR genes of G. soja (GsPRR) were identified, and the structure, evolution, and expression patterns of the encoded proteins were investigated. The results of systematic analysis provides a basis for the subsequent identification of the functions of PRR genes, and the preliminary data can be used for analyzing the specific functions of the PRR genes of soybean.