Lineage-Specific Gene Family Expansions of Legume Signaling Peptides

During nodulation, peptides are known to play crucial roles in the interaction between the plant hosts and their symbiotic rhizobial partners. Nodulation-related signaling peptides share common characteristics, such as their small size and the presence of a signal peptide and often-repetitive motifs. The rapid evolution of these small peptide families among legume lineages, including expansion or contraction, can lead to novel functional traits. The primary goal of this study was to identify lineage-specific expansions (LSEs) of nodulation-related small secreted peptides in a systematic way. Nodule RNA-seq data was obtained for the IRLC legumes Pisum sativum, Trifolium pratense, Medicago truncatula, and Melilotus alba, as well as for Glycine max. Assembled transcripts were filtered to select for small open reading frames that contained signal peptides, and OrthoMCL was used to assign peptides into orthologous groups. Paralogous groups were selected as potential LSEs, which were verified by running HMM searches of each group against legumes with available genome sequences. LSE groups were annotated via InterProScan, HMM searches against the UniRef90 database, and BLAST searches against the annotated M. truncatula proteome. The LEED..PEED gene family is one LSE unique to the Trigonellinae lineage, which includes Medicago and Melilotus legumes. Interestingly, this gene family is exclusively transcribed in nodules and has undergone independent expansions in Medicago and Melilotus but is absent from all other surveyed legumes, suggesting an interesting novel function in nodulation. This work was supported by NSF Plant Genome grant IOS-1237993.