ARS | Publication request: Molecular Evolution of Clustered MIC-3 (Meloidogyne Induced Cotton -3) Multigene Family of Gossypium Species

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: September 20, 2010
Publication Date: N/A

Technical Abstract: Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 multigene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate genes in allopolyploids. Here we report molecular evolutionary rates of the MIC-3 gene family in 15 tetraploid and diploid cotton genotypes. We observed independent, equal rate, accelerated, and concerted evolutionary patterns among members of the MIC-3 gene family. However, synonymous (Ks) and nonsynonymous (Ka) nucleotide substitution rates suggest that MIC-3 genes are generally evolving by a birth-and-death process under strong purifying selection with positively selected copies. Our results suggest that a ‘gene amplification’ mechanism has maintained duplicated copies in the genomes, which best fits with the “bait and switch” model of R-gene evolution. Comparative analysis showed that the second of the two exons of MIC-3 genes is under strong positive selection pressure, while the first exon is under strong purifying selection to conserve function. Using silent nucleotide substitution rates, we estimated divergence time among allotetraploid genomes and their closest diploid progenitors. We find a MIC-3 gene duplication pattern in which duplication events occur once in every 1 million years (MY) in allotetraploids, once in every ~2 MY in A/F-genome, and once in every ~8 MY in D-genome representatives. This duplication pattern might also be due to pathogen-mediated selection process of cotton genomes. Our results indicated the increased functional stability of MIC-3 gene family, and a capacity to develop novel “switch” pockets for detecting diverse pest and pathogen genotypes. Such evolutionary roles are congruent with the hypothesis that this unique gene family provides fitness advantages in Gossypium as it combats certain pests and pathogens.