Root nodule symbiosis (RNS) is one of the most efficient biological systems for nitrogen fixation
and it occurs in 90% of genera in the Papilionoideae, the largest subfamily of legumes. Most
papilionoid species show evidence of a polyploidy event occurred approximately 58 million years
ago. Although polyploidy is considered to be an important evolutionary force in plants, the role of
this papilionoid polyploidy event, especially its association with RNS, is not understood. In this
study, we explored this role using an integrated comparative genomic approach and conducted
gene expression comparisons and gene ontology enrichment analyses. The results show the
following: (1) approximately a quarter of the papilionoid-polyploidy-derived duplicate genes are
retained; (2) there is a striking divergence in the level of expression of gene duplicate pairs derived
from the polyploidy event; and (3) the retained duplicates are frequently involved in the processes
crucial for RNS establishment, such as symbiotic signalling, nodule organogenesis, rhizobial
infection and nutrient exchange and transport. Thus, we conclude that the papilionoid polyploidy
event might have further refined RNS and induced a more robust and enhanced symbiotic system.
This conclusion partly explains the widespread occurrence of the Papilionoideae
