Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication.

It is well known that nucleotide binding site (NBS)-encoding genes are duplicate-rich and fast-evolving genes. However, there is little information on the relative importance of tandem and segmental NBS duplicates and their exact evolutionary rates. The two rounds of large-scale duplication that have occurred in soybean provide a unique opportunity to investigate these issues. Comparison of NBS and non-NBS genes on segments of syntenic homoeologs shows that NBS-encoding genes evolve at least 1.5-fold faster (~1.5-fold higher synonymous and approximately 2.3-fold higher nonsynonymous substitution rates) and lose their genes approximately twofold faster than the flanking non-NBS genes. Compared with segmental duplicates, tandem NBS duplicates are more abundant in soybean, suggesting that tandem duplication is the major driving force in the expansion of NBS genes. Notably, significant sequence exchanges along with significantly positive selection were detected in most tandem-duplicated NBS gene families. The results suggest that the rapid evolution of NBS genes may be due to the combined effects of diversifying selection and frequent sequence exchanges. Interestingly, TIR-NBS-LRR genes (TNLs) have a higher nucleotide substitution rate than non-TNLs, indicating that these types of NBS genes may have a rather different evolutionary pattern. It is important to determine the exact relative evolutionary rates of TNL, non-TNL, and non-NBS genes in order to understand how fast the host plant can adjust its response to rapidly evolving pathogens in a coevolutionary context.