Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2011
Publication Date: 10/11/2011
Publication URL: http://handle.nal.usda.gov/10113/57018
Citation: Buriev, Z.T., Saha, S., Shermatov, S.E., Jenkins, J.N., Abdukarimov, A., Stelly, D.M., Abdurakhmonov, I.Y. 2011. Molecular evolution of the clustered MIC-3 multigene family of Gossypium species. Theoretical and Applied Genetics. 123:1359-1373. Interpretive Summary: Evolutionary fate of biologically functional copies of duplicate genes after the merger of two related different genomes in allopolyploid cotton is an interesting subject of evolution. Clustered localization in a chromosome, exclusive occurrence in cotton and defense-related features of the root-knot nematode resistance-associated MIC-3 gene family has provided a tool for such molecular evolutionary studies. Here we report the molecular evolution and fate of duplicate copies of nematode resistance associated MIC-3 supergene family in cotton genomes based on genomic and amino acid sequences. Our results collectively suggest that MIC-3 genes are evolving by a birth-and-death evolution under strong purifying selection in conjunction with ‘gene amplification’ as a potential mechanism to maintain duplicate copies and develop new functions in the cotton genome. We estimated an approximate divergence time of MIC-3 gene members between cotton genomes and ages of duplicate gene pairs. Genetic buffering effects to MIC-3 genes by complementary mode of evolution in the two subgenomes and exons provided flexibility and fitness advantages against different selective pressures perhaps as defenses against pests and pathogens in tetraploid genome.
Technical Abstract: Uniqueness, content, localization, and defense-related features of the root-knot nematode resistance-associated MIC-3 supergene cluster in the genus Gossypium are all of interest for molecular evolutionary studies of duplicate supergenes in allopolyploids. Here we report molecular evolutionary rates of the MIC-3 supergene family in 15 tetraploid and diploid genotypes of cotton. We observed independent, equal rate, accelerated, and concerted evolutionary patterns among members of the MIC-3 gene family. However, synonymous (Ks) and anonymous (Ka) nucleotide substitution rates suggest that MIC-3 genes, generally, are evolving by a birth-and-death process under strong purifying selection with positively selected copies suggesting a ‘gene amplification’ mechanism that maintains duplicated copies in the genomes in which they occur. 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 every 1 million years (MY) in allotetraploids, every ~2 MY in A/F-genome, and every ~8 MY in D-genome representatives. This pattern clearly bears on allopolyploidization and the rapid diversification of Gossypium species. Our results should be useful in understanding the role of polyploidy and gene duplication in the evolution and adaptation in plants, providing fitness advantages to combat pests and pathogens through plant defenses.