Comparative genomic analysis of the Sm gene family in rice and maize

• Identified Sm genes in rice and maize
• Segmental duplication contributed to the expansion of Sm gene family.
• Conserved gene organization and motif compositions in each group
• Different expression profiles implied functional divergence.
• Identified some interactors by functional network analyses

Sm proteins are a group of ubiquitous ring-shaped oligomers that function in multiple aspects of RNA metabolism. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene organization, adaptive evolution, expression profiling and functional networks has been reported for rice and maize. In this study, twenty-five and thirty-three Sm genes have been identified in rice and maize, respectively. Phylogenetic analyses identified eighteen gene groups. Results by gene locations indicated that segmental duplication contributes to the expansion of this gene family in rice and maize. Gene organization and motif compositions of the Sm members are highly conserved in each group, indicative of their functional conservation. Expression profiles have provided insights into the possible functional divergence among members of the Sm gene family. Adaptive evolution analyses suggested that purifying selection was the main force driving Sm evolution, but some critical sites might be responsible for functional divergence. In addition, four hundred and seventy-nine interactions were identified by functional network analyses, and most of which were associated with binding, cellular macromolecule biosynthesis, pre-mRNA processing and transferase activity. Overall, the data contribute to a better understanding of the complexity of Sm gene family in rice and maize and will provide a solid foundation for future functional studies.